has_source,help_version_command,help_version_error_type,help_version_flag,help_version_ok,help_version_probed,import_error_type,import_ok,server,source,startup_error_type,startup_ok,syntax_error_type,syntax_ok
True,abnumber,missing_executable_or_file,,False,True,none,True,abnumber,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_abnumber/app/abnumber_shim_server.py,none,True,none,True
True,abricate,missing_executable_or_file,,False,True,none,True,abricate,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_abricate/app/abricate_shim_server.py,none,True,none,True
True,abundancebin,missing_executable_or_file,,False,True,none,True,abundancebin,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_abundancebin/app/abundancebin_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,abyss,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_abyss/app/abyss_shim_server.py,none,True,none,True
True,AdapterRemoval,missing_executable_or_file,,False,True,none,True,adapterremoval,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_adapterremoval/app/adapterremoval_shim_server.py,none,True,none,True
True,alfred,missing_executable_or_file,,False,True,none,True,alfred,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_alfred/app/alfred_shim_server.py,none,True,none,True
True,snakemake,missing_executable_or_file,,False,True,none,True,anansescanpy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_anansescanpy/app/anansescanpy_shim_server.py,none,True,none,True
True,ANARCI,missing_executable_or_file,,False,True,none,True,anarci,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_anarci/app/anarci_shim_server.py,none,True,none,True
True,aragorn,missing_executable_or_file,,False,True,none,True,aragorn,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_aragorn/app/aragorn_shim_server.py,none,True,none,True
True,aria2c,missing_executable_or_file,,False,True,none,True,aria2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_aria2/app/aria2_shim_server.py,none,True,none,True
True,ariba,missing_executable_or_file,,False,True,none,True,ariba,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ariba/app/ariba_shim_server.py,none,True,none,True
True,arriba,missing_executable_or_file,,False,True,none,True,arriba,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_arriba/app/arriba_shim_server.py,none,True,none,True
True,art_454,missing_executable_or_file,,False,True,none,True,art,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_art/app/art_shim_server.py,none,True,none,True
True,arvados-cwl-runner,missing_executable_or_file,,False,True,none,True,arvados-cwl-runner,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_arvados-cwl-runner/app/arvados-cwl-runner_shim_server.py,none,True,none,True
True,arv-copy,missing_executable_or_file,,False,True,none,True,arvados-python-client,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_arvados-python-client/app/arvados-python-client_shim_server.py,none,True,none,True
True,atropos,missing_executable_or_file,,False,True,none,True,atropos,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_atropos/app/atropos_shim_server.py,none,True,none,True
False,,,,,,,,augur,,,,,
True,augustus,missing_executable_or_file,,False,True,none,True,augustus,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_augustus/app/augustus_shim_server.py,none,True,none,True
True,auspice,missing_executable_or_file,,False,True,none,True,auspice,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_auspice/app/auspice_shim_server.py,none,True,none,True
True,bactopia,missing_executable_or_file,,False,True,none,True,bactopia,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bactopia/app/bactopia_shim_server.py,none,True,none,True
True,bamtools,missing_executable_or_file,,False,True,none,True,bamtools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bamtools/app/bamtools_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,barrnap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_barrnap/app/barrnap_shim_server.py,none,True,none,True
True,bbmap.sh,missing_executable_or_file,,False,True,none,True,bbmap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bbmap/app/bbmap_shim_server.py,none,True,none,True
True,gff_filter_by_attribute.py,missing_executable_or_file,,False,True,none,True,bcbio-gff,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bcbio-gff/app/bcbio-gff_shim_server.py,none,True,none,True
True,bcbio_nextgen.py,missing_executable_or_file,,False,True,none,True,bcbio-nextgen,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bcbio-nextgen/app/bcbio-nextgen_shim_server.py,none,True,none,True
True,bcftools,missing_executable_or_file,,False,True,none,True,bcftools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bcftools/app/bcftools_shim_server.py,none,True,none,True
True,bedops,missing_executable_or_file,,False,True,none,True,bedops,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bedops/app/bedops_shim_server.py,none,True,none,True
True,bedtools,missing_executable_or_file,,False,True,none,True,bedtools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bedtools/app/bedtools_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bin2cell,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bin2cell/app/bin2cell_shim_server.py,none,True,none,True
True,bioawk,missing_executable_or_file,,False,True,none,True,bioawk,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioawk/app/bioawk_shim_server.py,none,True,none,True
True,bamadapterclip,missing_executable_or_file,,False,True,none,True,biobambam,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_biobambam/app/biobambam_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-affy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-affy/app/bioconductor-affy_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-affyio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-affyio/app/bioconductor-affyio_shim_server.py,none,True,none,True
False,,,,,,,,bioconductor-affyio copy,,,,,
True,,no_command_literal,,False,False,none,True,bioconductor-alabaster,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-alabaster/app/bioconductor-alabaster_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-alabaster.sfe,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-alabaster.sfe/app/bioconductor-alabaster.sfe_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-alabaster.spatial,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-alabaster.spatial/app/bioconductor-alabaster.spatial_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-ancombc,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-ancombc/app/bioconductor-ancombc_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-annotate,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-annotate/app/bioconductor-annotate_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-annotationdbi,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-annotationdbi/app/bioconductor-annotationdbi_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-annotationfilter,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-annotationfilter/app/bioconductor-annotationfilter_shim_server.py,none,True,none,True
False,,,,,,,,bioconductor-annotationhub,,,,,
True,,no_command_literal,,False,False,none,True,bioconductor-apeglm,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-apeglm/app/bioconductor-apeglm_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-apl,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-apl/app/bioconductor-apl_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-awaggregator,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-awaggregator/app/bioconductor-awaggregator_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-banksy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-banksy/app/bioconductor-banksy_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-beachmat,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-beachmat/app/bioconductor-beachmat_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-benchdamic,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-benchdamic/app/bioconductor-benchdamic_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biobase,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biobase/app/bioconductor-biobase_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biocbaseutils,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biocbaseutils/app/bioconductor-biocbaseutils_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biocfilecache,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biocfilecache/app/bioconductor-biocfilecache_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biocgenerics,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biocgenerics/app/bioconductor-biocgenerics_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biocio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biocio/app/bioconductor-biocio_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biocneighbors,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biocneighbors/app/bioconductor-biocneighbors_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biocparallel,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biocparallel/app/bioconductor-biocparallel_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biocsingular,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biocsingular/app/bioconductor-biocsingular_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biomart,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biomart/app/bioconductor-biomart_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biomformat,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biomformat/app/bioconductor-biomformat_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biostrings,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biostrings/app/bioconductor-biostrings_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-biovizbase,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-biovizbase/app/bioconductor-biovizbase_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-blase,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-blase/app/bioconductor-blase_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-bluster,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-bluster/app/bioconductor-bluster_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-bsgenome,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-bsgenome/app/bioconductor-bsgenome_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-bulksignalr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-bulksignalr/app/bioconductor-bulksignalr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-cardspa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-cardspa/app/bioconductor-cardspa_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-catscradle,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-catscradle/app/bioconductor-catscradle_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-cdi,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-cdi/app/bioconductor-cdi_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-cellhashr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-cellhashr/app/bioconductor-cellhashr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-cellid,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-cellid/app/bioconductor-cellid_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-cellmigration,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-cellmigration/app/bioconductor-cellmigration_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-clusterfoldsimilarity,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-clusterfoldsimilarity/app/bioconductor-clusterfoldsimilarity_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-clusterprofiler,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-clusterprofiler/app/bioconductor-clusterprofiler_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-clustifyr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-clustifyr/app/bioconductor-clustifyr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-clustsignal,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-clustsignal/app/bioconductor-clustsignal_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-complexheatmap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-complexheatmap/app/bioconductor-complexheatmap_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-concordexr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-concordexr/app/bioconductor-concordexr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-cotan,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-cotan/app/bioconductor-cotan_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-csoa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-csoa/app/bioconductor-csoa_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-ctsv,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-ctsv/app/bioconductor-ctsv_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-curatedatlasqueryr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-curatedatlasqueryr/app/bioconductor-curatedatlasqueryr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-cytomapper,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-cytomapper/app/bioconductor-cytomapper_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-dada2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-dada2/app/bioconductor-dada2_shim_server.py,none,True,none,True
True,curl,none,--help,True,True,none,True,bioconductor-data-packages,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-data-packages/app/bioconductor-data-packages_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-decipher,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-decipher/app/bioconductor-decipher_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-decontam,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-decontam/app/bioconductor-decontam_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-decontx,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-decontx/app/bioconductor-decontx_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-deconvobuddies,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-deconvobuddies/app/bioconductor-deconvobuddies_shim_server.py,none,True,none,True
False,,,,,,,,bioconductor-delayedarray,,,,,
True,fastqc,missing_executable_or_file,,False,True,none,True,bioconductor-delayedmatrixstats,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-delayedmatrixstats/app/bioconductor-delayedmatrixstats_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-deseq2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-deseq2/app/bioconductor-deseq2_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-despace,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-despace/app/bioconductor-despace_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-diffbind,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-diffbind/app/bioconductor-diffbind_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-dino,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-dino/app/bioconductor-dino_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-dirichletmultinomial,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-dirichletmultinomial/app/bioconductor-dirichletmultinomial_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-dnacopy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-dnacopy/app/bioconductor-dnacopy_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-dose,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-dose/app/bioconductor-dose_shim_server.py,none,True,none,True
False,,,,,,,,bioconductor-ebseq,,,,,
True,,no_command_literal,,False,False,none,True,bioconductor-edger,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-edger/app/bioconductor-edger_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-ensembldb,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-ensembldb/app/bioconductor-ensembldb_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-erma,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-erma/app/bioconductor-erma_shim_server.py,none,True,none,True
True,escher,missing_executable_or_file,,False,True,none,True,bioconductor-escher,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-escher/app/bioconductor-escher_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,schema_or_argument_error,False,bioconductor-experimentsubset,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-experimentsubset/app/bioconductor-experimentsubset_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-fgsea,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-fgsea/app/bioconductor-fgsea_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-genefilter,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-genefilter/app/bioconductor-genefilter_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-geneplotter,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-geneplotter/app/bioconductor-geneplotter_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-genomeinfodb,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-genomeinfodb/app/bioconductor-genomeinfodb_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-genomeinfodbdata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-genomeinfodbdata/app/bioconductor-genomeinfodbdata_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-genomicalignments,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-genomicalignments/app/bioconductor-genomicalignments_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-genomicfeatures,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-genomicfeatures/app/bioconductor-genomicfeatures_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-genomicranges,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-genomicranges/app/bioconductor-genomicranges_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-geomxtools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-geomxtools/app/bioconductor-geomxtools_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-ggsc,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-ggsc/app/bioconductor-ggsc_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-ggspavis,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-ggspavis/app/bioconductor-ggspavis_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-ggtree,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-ggtree/app/bioconductor-ggtree_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-glmgampoi,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-glmgampoi/app/bioconductor-glmgampoi_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-go.db,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-go.db/app/bioconductor-go.db_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-gosemsim,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-gosemsim/app/bioconductor-gosemsim_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-graph,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-graph/app/bioconductor-graph_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-gsva,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-gsva/app/bioconductor-gsva_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-hcatonsildata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-hcatonsildata/app/bioconductor-hcatonsildata_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-hdf5array,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-hdf5array/app/bioconductor-hdf5array_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-hoodscanr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-hoodscanr/app/bioconductor-hoodscanr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-humanhippocampus2024,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-humanhippocampus2024/app/bioconductor-humanhippocampus2024_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-imcdatasets,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-imcdatasets/app/bioconductor-imcdatasets_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-imcrtools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-imcrtools/app/bioconductor-imcrtools_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-impute,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-impute/app/bioconductor-impute_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-infercnv,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-infercnv/app/bioconductor-infercnv_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-interactivedisplaybase,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-interactivedisplaybase/app/bioconductor-interactivedisplaybase_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-iranges,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-iranges/app/bioconductor-iranges_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-irisfgm,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-irisfgm/app/bioconductor-irisfgm_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-jazzpanda,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-jazzpanda/app/bioconductor-jazzpanda_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-keggrest,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-keggrest/app/bioconductor-keggrest_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-limma,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-limma/app/bioconductor-limma_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-lisaclust,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-lisaclust/app/bioconductor-lisaclust_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-mastr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-mastr/app/bioconductor-mastr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-matrixgenerics,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-matrixgenerics/app/bioconductor-matrixgenerics_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-merfishdata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-merfishdata/app/bioconductor-merfishdata_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-metabolomicsworkbenchr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-metabolomicsworkbenchr/app/bioconductor-metabolomicsworkbenchr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-metapod,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-metapod/app/bioconductor-metapod_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-mia,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-mia/app/bioconductor-mia_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-moleculeexperiment,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-moleculeexperiment/app/bioconductor-moleculeexperiment_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-mosim,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-mosim/app/bioconductor-mosim_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-mousegastrulationdata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-mousegastrulationdata/app/bioconductor-mousegastrulationdata_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-mspurity,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-mspurity/app/bioconductor-mspurity_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-multiassayexperiment,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-multiassayexperiment/app/bioconductor-multiassayexperiment_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-multtest,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-multtest/app/bioconductor-multtest_shim_server.py,none,True,none,True
False,,,,,,,,bioconductor-mzr,,,,,
True,,no_command_literal,,False,False,none,True,bioconductor-nebulosa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-nebulosa/app/bioconductor-nebulosa_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-nnsvg,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-nnsvg/app/bioconductor-nnsvg_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-noiseq,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-noiseq/app/bioconductor-noiseq_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-orfhunter,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-orfhunter/app/bioconductor-orfhunter_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-org.ce.eg.db,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-org.ce.eg.db/app/bioconductor-org.ce.eg.db_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-org.hs.eg.db,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-org.hs.eg.db/app/bioconductor-org.hs.eg.db_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-org.mm.eg.db,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-org.mm.eg.db/app/bioconductor-org.mm.eg.db_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-partcnv,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-partcnv/app/bioconductor-partcnv_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-phemd,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-phemd/app/bioconductor-phemd_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-phyloseq,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-phyloseq/app/bioconductor-phyloseq_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-pipecomp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-pipecomp/app/bioconductor-pipecomp_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-poem,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-poem/app/bioconductor-poem_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-preprocesscore,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-preprocesscore/app/bioconductor-preprocesscore_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-proteomicsannotationhubdata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-proteomicsannotationhubdata/app/bioconductor-proteomicsannotationhubdata_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,runtime_exception,False,bioconductor-protgenerics,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-protgenerics/app/bioconductor-protgenerics_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-qvalue,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-qvalue/app/bioconductor-qvalue_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-rbgl,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-rbgl/app/bioconductor-rbgl_shim_server.py,none,True,none,True
True,which,none,--help,True,True,none,True,bioconductor-reactomegsa.data,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-reactomegsa.data/app/bioconductor-reactomegsa.data_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-regionalst,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-regionalst/app/bioconductor-regionalst_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-rforproteomics,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-rforproteomics/app/bioconductor-rforproteomics_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-rgraphviz,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-rgraphviz/app/bioconductor-rgraphviz_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-rhdf5,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-rhdf5/app/bioconductor-rhdf5_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-rhdf5filters,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-rhdf5filters/app/bioconductor-rhdf5filters_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-rhdf5lib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-rhdf5lib/app/bioconductor-rhdf5lib_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-rhtslib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-rhtslib/app/bioconductor-rhtslib_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-rsamtools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-rsamtools/app/bioconductor-rsamtools_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-rsubread,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-rsubread/app/bioconductor-rsubread_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-rtracklayer,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-rtracklayer/app/bioconductor-rtracklayer_shim_server.py,none,True,none,True
False,,,,,,,,bioconductor-rtracklayer copy,,,,,
False,,,,,,,,bioconductor-s4vectors,,,,,
True,,no_command_literal,,False,False,none,True,bioconductor-scaledmatrix,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scaledmatrix/app/bioconductor-scaledmatrix_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scalign,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scalign/app/bioconductor-scalign_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scarray.sat,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scarray.sat/app/bioconductor-scarray.sat_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scater,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scater/app/bioconductor-scater_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scbfa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scbfa/app/bioconductor-scbfa_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scbubbletree,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scbubbletree/app/bioconductor-scbubbletree_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-sccb2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-sccb2/app/bioconductor-sccb2_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scclassifr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scclassifr/app/bioconductor-scclassifr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scdataviz,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scdataviz/app/bioconductor-scdataviz_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scdotplot,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scdotplot/app/bioconductor-scdotplot_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scfeatures,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scfeatures/app/bioconductor-scfeatures_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scider,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scider/app/bioconductor-scider_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scmageck,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scmageck/app/bioconductor-scmageck_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scqtltools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scqtltools/app/bioconductor-scqtltools_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scran,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scran/app/bioconductor-scran_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-screpertoire,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-screpertoire/app/bioconductor-screpertoire_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scrnaseq,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scrnaseq/app/bioconductor-scrnaseq_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-sctreeviz,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-sctreeviz/app/bioconductor-sctreeviz_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scuttle,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scuttle/app/bioconductor-scuttle_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-scvir,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-scvir/app/bioconductor-scvir_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-seraster,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-seraster/app/bioconductor-seraster_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-shortread,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-shortread/app/bioconductor-shortread_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-signifinder,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-signifinder/app/bioconductor-signifinder_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-singlecellexperiment,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-singlecellexperiment/app/bioconductor-singlecellexperiment_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-singlecellmultimodal,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-singlecellmultimodal/app/bioconductor-singlecellmultimodal_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-smoothclust,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-smoothclust/app/bioconductor-smoothclust_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-smoppix,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-smoppix/app/bioconductor-smoppix_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-sosta,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-sosta/app/bioconductor-sosta_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spacetrooper,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spacetrooper/app/bioconductor-spacetrooper_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spaniel,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spaniel/app/bioconductor-spaniel_shim_server.py,none,True,none,True
True,spari,missing_executable_or_file,,False,True,none,True,bioconductor-spari,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spari/app/bioconductor-spari_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-sparsematrixstats,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-sparsematrixstats/app/bioconductor-sparsematrixstats_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spatialcpie,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spatialcpie/app/bioconductor-spatialcpie_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spatialdatasets,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spatialdatasets/app/bioconductor-spatialdatasets_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spatialdecon,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spatialdecon/app/bioconductor-spatialdecon_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spatialdmelxsim,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spatialdmelxsim/app/bioconductor-spatialdmelxsim_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spatialexperiment,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spatialexperiment/app/bioconductor-spatialexperiment_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spatialexperimentio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spatialexperimentio/app/bioconductor-spatialexperimentio_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spatialfda,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spatialfda/app/bioconductor-spatialfda_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spatialfeatureexperiment,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spatialfeatureexperiment/app/bioconductor-spatialfeatureexperiment_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spatialheatmap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spatialheatmap/app/bioconductor-spatialheatmap_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spatialomicsoverlay,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spatialomicsoverlay/app/bioconductor-spatialomicsoverlay_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-speckle,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-speckle/app/bioconductor-speckle_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spoon,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spoon/app/bioconductor-spoon_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spotclean,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spotclean/app/bioconductor-spotclean_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-spotsweeper,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-spotsweeper/app/bioconductor-spotsweeper_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-standr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-standr/app/bioconductor-standr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-statial,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-statial/app/bioconductor-statial_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-stjoincount,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-stjoincount/app/bioconductor-stjoincount_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-summarizedexperiment,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-summarizedexperiment/app/bioconductor-summarizedexperiment_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-svp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-svp/app/bioconductor-svp_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-tenxvisiumdata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-tenxvisiumdata/app/bioconductor-tenxvisiumdata_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-tenxxeniumdata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-tenxxeniumdata/app/bioconductor-tenxxeniumdata_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-tidyomics,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-tidyomics/app/bioconductor-tidyomics_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-tidyspatialexperiment,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-tidyspatialexperiment/app/bioconductor-tidyspatialexperiment_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-treesummarizedexperiment,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-treesummarizedexperiment/app/bioconductor-treesummarizedexperiment_shim_server.py,none,True,none,True
True,conda,none,--help,True,True,none,True,bioconductor-tximport,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-tximport/app/bioconductor-tximport_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-variantannotation,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-variantannotation/app/bioconductor-variantannotation_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-vectrapolarisdata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-vectrapolarisdata/app/bioconductor-vectrapolarisdata_shim_server.py,none,True,none,True
True,read,missing_executable_or_file,,False,True,none,True,bioconductor-visiumio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-visiumio/app/bioconductor-visiumio_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,schema_or_argument_error,False,bioconductor-weberdivechalcdata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-weberdivechalcdata/app/bioconductor-weberdivechalcdata_shim_server.py,none,True,none,True
True,cp,none,--help,True,True,none,True,bioconductor-xcms,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-xcms/app/bioconductor-xcms_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-xenlite,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-xenlite/app/bioconductor-xenlite_shim_server.py,none,True,none,True
True,which,none,--help,True,True,none,True,bioconductor-xvector,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-xvector/app/bioconductor-xvector_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,bioconductor-zlibbioc,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bioconductor-zlibbioc/app/bioconductor-zlibbioc_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,biopython,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_biopython/app/biopython_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,blast,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_blast/app/blast_shim_server.py,none,True,none,True
True,blastall,missing_executable_or_file,,False,True,none,True,blast-legacy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_blast-legacy/app/blast-legacy_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,bowtie,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bowtie/app/bowtie_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,bowtie2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bowtie2/app/bowtie2_shim_server.py,none,True,none,True
True,bpipe,missing_executable_or_file,,False,True,none,True,bpipe,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bpipe/app/bpipe_shim_server.py,none,True,none,True
True,brooklyn_plot,missing_executable_or_file,,False,True,none,True,brooklyn_plot,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_brooklyn_plot/app/brooklyn_plot_shim_server.py,none,True,none,True
True,busco,missing_executable_or_file,,False,True,none,True,busco,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_busco/app/busco_shim_server.py,none,True,none,True
True,bwa,missing_executable_or_file,,False,True,none,True,bwa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bwa/app/bwa_shim_server.py,none,True,none,True
True,bed_intersect,missing_executable_or_file,,False,True,none,True,bx-python,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_bx-python/app/bx-python_shim_server.py,none,True,none,True
True,adig,none,--help,True,True,none,True,c-ares,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_c-ares/app/c-ares_shim_server.py,none,True,none,True
True,cascade-reg,missing_executable_or_file,,False,True,none,True,cascade-reg,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cascade-reg/app/cascade-reg_shim_server.py,none,True,none,True
True,cd-hit,missing_executable_or_file,,False,True,none,True,cd-hit,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cd-hit/app/cd-hit_shim_server.py,none,True,none,True
True,cdbfasta,missing_executable_or_file,,False,True,none,True,cdbtools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cdbtools/app/cdbtools_shim_server.py,none,True,none,True
True,cell2cell,missing_executable_or_file,,False,True,none,True,cell2cell,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cell2cell/app/cell2cell_shim_server.py,none,True,none,True
True,cellitac,missing_executable_or_file,,False,True,none,True,cellitac,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cellitac/app/cellitac_shim_server.py,none,True,none,True
True,cellqc,missing_executable_or_file,,False,True,none,True,cellqc,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cellqc/app/cellqc_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,cellrank,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cellrank/app/cellrank_shim_server.py,none,True,none,True
True,cellsnake,missing_executable_or_file,,False,True,none,True,cellsnake,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cellsnake/app/cellsnake_shim_server.py,none,True,none,True
True,celltypist,missing_executable_or_file,,False,True,none,True,celltypist,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_celltypist/app/celltypist_shim_server.py,none,True,none,True
True,celltypist,missing_executable_or_file,,False,True,none,True,celltypist-so,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_celltypist-so/app/celltypist-so_shim_server.py,none,True,none,True
True,checkatlas,missing_executable_or_file,,False,True,none,True,checkatlas,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_checkatlas/app/checkatlas_shim_server.py,none,True,none,True
True,bin_set,missing_executable_or_file,,False,True,none,True,checkm-genome,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_checkm-genome/app/checkm-genome_shim_server.py,none,True,none,True
True,CIRCexplorer2,missing_executable_or_file,,False,True,none,True,circexplorer2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_circexplorer2/app/circexplorer2_shim_server.py,none,True,none,True
True,circos,missing_executable_or_file,,False,True,none,True,circos,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_circos/app/circos_shim_server.py,none,True,none,True
True,clustalo,missing_executable_or_file,,False,True,none,True,clustalo,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_clustalo/app/clustalo_shim_server.py,none,True,none,True
True,clustalw,missing_executable_or_file,,False,True,none,True,clustalw,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_clustalw/app/clustalw_shim_server.py,none,True,none,True
True,concat_gct,missing_executable_or_file,,False,True,none,True,cmappy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cmappy/app/cmappy_shim_server.py,none,True,none,True
True,cnmf,missing_executable_or_file,,False,True,none,True,cnmf,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cnmf/app/cnmf_shim_server.py,none,True,none,True
True,cnvkit.py,missing_executable_or_file,,False,True,none,True,cnvkit,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cnvkit/app/cnvkit_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,comebin,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_comebin/app/comebin_shim_server.py,none,True,none,True
True,comet,missing_executable_or_file,,False,True,none,True,comet-ms,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_comet-ms/app/comet-ms_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,constellations,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_constellations/app/constellations_shim_server.py,none,True,none,True
True,cooler,missing_executable_or_file,,False,True,none,True,cooler,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cooler/app/cooler_shim_server.py,none,True,none,True
True,cooltools,missing_executable_or_file,,False,True,none,True,cooltools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cooltools/app/cooltools_shim_server.py,none,True,none,True
True,cat,none,--help,True,True,none,True,coreutils,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_coreutils/app/coreutils_shim_server.py,none,True,none,True
True,cosg,missing_executable_or_file,,False,True,none,True,cosg,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cosg/app/cosg_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,cospar,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cospar/app/cospar_shim_server.py,none,True,none,True
True,CRISPResso,missing_executable_or_file,,False,True,none,True,crispresso2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_crispresso2/app/crispresso2_shim_server.py,none,True,none,True
True,CRISPRitz,missing_executable_or_file,,False,True,none,True,crispritz,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_crispritz/app/crispritz_shim_server.py,none,True,none,True
True,crisprme,missing_executable_or_file,,False,True,none,True,crisprme,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_crisprme/app/crisprme_shim_server.py,none,True,none,True
True,java,none,--help,True,True,none,True,cromwell,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cromwell/app/cromwell_shim_server.py,none,True,none,True
True,csvtk,missing_executable_or_file,,False,True,none,True,csvtk,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_csvtk/app/csvtk_shim_server.py,none,True,none,True
False,,,,,,,,csvtk copy,,,,,
True,cutadapt,missing_executable_or_file,,False,True,none,True,cutadapt,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cutadapt/app/cutadapt_shim_server.py,none,True,none,True
True,cwltool,missing_executable_or_file,,False,True,none,True,cwltool,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cwltool/app/cwltool_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,cytoscape,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cytoscape/app/cytoscape_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,cytotrace2-python,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cytotrace2-python/app/cytotrace2-python_shim_server.py,none,True,none,True
True,cyvcf2,missing_executable_or_file,,False,True,none,True,cyvcf2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_cyvcf2/app/cyvcf2_shim_server.py,none,True,none,True
True,dca,missing_executable_or_file,,False,True,none,True,dca,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_dca/app/dca_shim_server.py,none,True,none,True
True,dDocent,missing_executable_or_file,,False,True,none,True,ddocent,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ddocent/app/ddocent_shim_server.py,none,True,none,True
True,deblur,missing_executable_or_file,,False,True,none,True,deblur,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_deblur/app/deblur_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,decoupler,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_decoupler/app/decoupler_shim_server.py,none,True,none,True
True,deeptools,missing_executable_or_file,,False,True,none,True,deeptools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_deeptools/app/deeptools_shim_server.py,none,True,none,True
True,deeptoolsintervals,missing_executable_or_file,,False,True,none,True,deeptoolsintervals,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_deeptoolsintervals/app/deeptoolsintervals_shim_server.py,none,True,none,True
True,delly,missing_executable_or_file,,False,True,none,True,delly,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_delly/app/delly_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,dendropy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_dendropy/app/dendropy_shim_server.py,none,True,none,True
True,diamond,missing_executable_or_file,,False,True,none,True,diamond,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_diamond/app/diamond_shim_server.py,none,True,none,True
False,,,,,,,,diamond copy,,,,,
True,,no_command_literal,,False,False,none,True,disease-gene-qa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_disease-gene-qa/app/disease-gene-qa_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,dnaio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_dnaio/app/dnaio_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,doubletdetection,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_doubletdetection/app/doubletdetection_shim_server.py,none,True,none,True
True,dropkick,missing_executable_or_file,,False,True,none,True,dropkick,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_dropkick/app/dropkick_shim_server.py,none,True,none,True
True,java,none,--help,True,True,none,True,dsh-bio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_dsh-bio/app/dsh-bio_shim_server.py,none,True,none,True
True,dx,missing_executable_or_file,,False,True,none,True,dxpy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_dxpy/app/dxpy_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,easy_vitessce,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_easy_vitessce/app/easy_vitessce_shim_server.py,none,True,none,True
True,echidna_runner,missing_executable_or_file,,False,True,none,True,echidna,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_echidna/app/echidna_shim_server.py,none,True,none,True
True,backtranseq,missing_executable_or_file,,False,True,none,True,emboss,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_emboss/app/emboss_shim_server.py,none,True,none,True
True,java,none,--help,True,True,none,True,ena-webin-cli,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ena-webin-cli/app/ena-webin-cli_shim_server.py,none,True,none,True
True,haplo,missing_executable_or_file,,False,True,none,True,ensembl-vep,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ensembl-vep/app/ensembl-vep_shim_server.py,none,True,none,True
True,efetch,missing_executable_or_file,,False,True,none,True,entrez-direct,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_entrez-direct/app/entrez-direct_shim_server.py,none,True,none,True
True,epic2,missing_executable_or_file,,False,True,none,True,epic,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_epic/app/epic_shim_server.py,none,True,none,True
True,episcanpy,missing_executable_or_file,,False,True,none,True,episcanpy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_episcanpy/app/episcanpy_shim_server.py,none,True,none,True
True,eva-sub-cli,missing_executable_or_file,,False,True,none,True,eva-sub-cli,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_eva-sub-cli/app/eva-sub-cli_shim_server.py,none,True,none,True
True,f5c,missing_executable_or_file,,False,True,none,True,f5c,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_f5c/app/f5c_shim_server.py,none,True,none,True
True,famsa,missing_executable_or_file,,False,True,none,True,famsa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_famsa/app/famsa_shim_server.py,none,True,none,True
True,f5ls,missing_executable_or_file,,False,True,none,True,fast5,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_fast5/app/fast5_shim_server.py,none,True,none,True
True,fastANI,missing_executable_or_file,,False,True,none,True,fastani,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_fastani/app/fastani_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,fastdtw,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_fastdtw/app/fastdtw_shim_server.py,none,True,none,True
True,fastp,missing_executable_or_file,,False,True,none,True,fastp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_fastp/app/fastp_shim_server.py,none,True,none,True
False,,,,,,,,fastqc,,,,,
True,,no_command_literal,,False,False,none,True,fasttree,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_fasttree/app/fasttree_shim_server.py,none,True,none,True
True,fermi2,missing_executable_or_file,,False,True,none,True,fermi2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_fermi2/app/fermi2_shim_server.py,none,True,none,True
True,fgbio,missing_executable_or_file,,False,True,none,True,fgbio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_fgbio/app/fgbio_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,filechunkio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_filechunkio/app/filechunkio_shim_server.py,none,True,none,True
True,flagx,missing_executable_or_file,,False,True,none,True,flagx,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_flagx/app/flagx_shim_server.py,none,True,none,True
True,flye,missing_executable_or_file,,False,True,none,True,flye,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_flye/app/flye_shim_server.py,none,True,none,True
False,,,,,,,,foldseek,,,,,
True,freebayes,missing_executable_or_file,,False,True,none,True,freebayes,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_freebayes/app/freebayes_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,missing_python_dependency,False,ftputil,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ftputil/app/ftputil_shim_server.py,none,True,none,True
True,fwdpy11,missing_executable_or_file,,False,True,none,True,fwdpy11,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_fwdpy11/app/fwdpy11_shim_server.py,none,True,none,True
True,galaxy-json-to-xml,missing_executable_or_file,,False,True,none,True,galaxy-lib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_galaxy-lib/app/galaxy-lib_shim_server.py,none,True,none,True
True,gatk,missing_executable_or_file,,False,True,none,True,gatk,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gatk/app/gatk_shim_server.py,none,True,none,True
True,gatk,missing_executable_or_file,,False,True,none,True,gatk4,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gatk4/app/gatk4_shim_server.py,none,True,none,True
True,gatk,missing_executable_or_file,,False,True,none,True,gatk4-spark,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gatk4-spark/app/gatk4-spark_shim_server.py,none,True,none,True
True,gdk-pixbuf-csource,none,--help,True,True,none,True,gdk-pixbuf,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gdk-pixbuf/app/gdk-pixbuf_shim_server.py,none,True,none,True
True,fzn-gecode,missing_executable_or_file,,False,True,none,True,gecode,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gecode/app/gecode_shim_server.py,none,True,none,True
False,,,,,,,,gemini,,,,,
True,,no_command_literal,,False,False,none,True,gene-trajectory-python,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gene-trajectory-python/app/gene-trajectory-python_shim_server.py,none,True,none,True
True,genecircuitry,missing_executable_or_file,,False,True,none,True,genecircuitry,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_genecircuitry/app/genecircuitry_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,geneimpacts,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_geneimpacts/app/geneimpacts_shim_server.py,none,True,none,True
False,,,,,,,,genenotebook,,,,,
True,genenotebook,missing_executable_or_file,,False,True,none,True,genoboo,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_genoboo/app/genoboo_shim_server.py,none,True,none,True
False,,,,,,,,genomad,,,,,
True,genomepy,missing_executable_or_file,,False,True,none,True,genomepy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_genomepy/app/genomepy_shim_server.py,none,True,none,True
True,gt,missing_executable_or_file,,False,True,none,True,genometools-genometools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_genometools-genometools/app/genometools-genometools_shim_server.py,none,True,none,True
True,gffread,missing_executable_or_file,,False,True,none,True,gffread,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gffread/app/gffread_shim_server.py,none,True,none,True
True,gffutils-cli,missing_executable_or_file,,False,True,none,True,gffutils,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gffutils/app/gffutils_shim_server.py,none,True,none,True
True,gs,missing_executable_or_file,,False,True,none,True,ghostscript,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ghostscript/app/ghostscript_shim_server.py,none,True,none,True
True,gimme,missing_executable_or_file,,False,True,none,True,gimmemotifs,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gimmemotifs/app/gimmemotifs_shim_server.py,none,True,none,True
True,glimmerhmm,missing_executable_or_file,,False,True,none,True,glimmerhmm,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_glimmerhmm/app/glimmerhmm_shim_server.py,none,True,none,True
True,gff3_exons,missing_executable_or_file,,False,True,none,True,gmap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gmap/app/gmap_shim_server.py,none,True,none,True
True,gneiss,missing_executable_or_file,,False,True,none,True,gneiss,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gneiss/app/gneiss_shim_server.py,none,True,none,True
True,gnuplot,missing_executable_or_file,,False,True,none,True,gnuplot,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gnuplot/app/gnuplot_shim_server.py,none,True,none,True
True,gofasta,missing_executable_or_file,,False,True,none,True,gofasta,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gofasta/app/gofasta_shim_server.py,none,True,none,True
True,goleft,missing_executable_or_file,,False,True,none,True,goleft,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_goleft/app/goleft_shim_server.py,none,True,none,True
False,,,,,,,,gridss,,,,,
True,gmx,missing_executable_or_file,,False,True,none,True,gromacs,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gromacs/app/gromacs_shim_server.py,none,True,none,True
True,gseapy,none,--help,True,True,none,True,gseapy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gseapy/app/gseapy_shim_server.py,none,True,none,True
True,gsmap,missing_executable_or_file,,False,True,none,True,gsmap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gsmap/app/gsmap_shim_server.py,none,True,none,True
True,gtdbtk,missing_executable_or_file,,False,True,none,True,gtdbtk,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_gtdbtk/app/gtdbtk_shim_server.py,none,True,none,True
True,harpy,missing_executable_or_file,,False,True,none,True,harpy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_harpy/app/harpy_shim_server.py,none,True,none,True
True,hhblits,missing_executable_or_file,,False,True,none,True,hhsuite,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_hhsuite/app/hhsuite_shim_server.py,none,True,none,True
True,hicBuildMatrix,missing_executable_or_file,,False,True,none,True,hicexplorer,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_hicexplorer/app/hicexplorer_shim_server.py,none,True,none,True
True,hifiasm,missing_executable_or_file,,False,True,none,True,hifiasm,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_hifiasm/app/hifiasm_shim_server.py,none,True,none,True
True,hisat2,missing_executable_or_file,,False,True,none,True,hisat2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_hisat2/app/hisat2_shim_server.py,none,True,none,True
True,hmmalign,missing_executable_or_file,,False,True,none,True,hmmer,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_hmmer/app/hmmer_shim_server.py,none,True,none,True
True,htseq-count,missing_executable_or_file,,False,True,none,True,htseq,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_htseq/app/htseq_shim_server.py,none,True,none,True
True,annot-tsv,missing_executable_or_file,,False,True,none,True,htslib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_htslib/app/htslib_shim_server.py,none,True,none,True
False,,,,,,,,humann,,,,,
True,humann2,missing_executable_or_file,,False,True,none,True,humann2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_humann2/app/humann2_shim_server.py,none,True,none,True
False,,,,,,,,hyphy,,,,,
True,igvtools,missing_executable_or_file,,False,True,none,True,igv,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_igv/app/igv_shim_server.py,none,True,none,True
True,igv-reports,missing_executable_or_file,,False,True,none,True,igv-reports,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_igv-reports/app/igv-reports_shim_server.py,none,True,none,True
True,illumina-interop,missing_executable_or_file,,False,True,none,True,illumina-interop,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_illumina-interop/app/illumina-interop_shim_server.py,none,True,none,True
True,cmalign,missing_executable_or_file,,False,True,none,True,infernal,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_infernal/app/infernal_shim_server.py,none,True,none,True
True,iss,missing_executable_or_file,,False,True,none,True,insilicoseq,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_insilicoseq/app/insilicoseq_shim_server.py,none,True,none,True
True,IntaRNA,missing_executable_or_file,,False,True,none,True,intarna,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_intarna/app/intarna_shim_server.py,none,True,none,True
True,involucro,missing_executable_or_file,,False,True,none,True,involucro,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_involucro/app/involucro_shim_server.py,none,True,none,True
True,bp,missing_executable_or_file,,False,True,none,True,iow,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_iow/app/iow_shim_server.py,none,True,none,True
True,ipyrad,missing_executable_or_file,,False,True,none,True,ipyrad,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ipyrad/app/ipyrad_shim_server.py,none,True,none,True
True,ipython-cluster-helper,missing_executable_or_file,,False,True,none,True,ipython-cluster-helper,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ipython-cluster-helper/app/ipython-cluster-helper_shim_server.py,none,True,none,True
True,iqtree2,missing_executable_or_file,,False,True,none,True,iqtree,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_iqtree/app/iqtree_shim_server.py,none,True,none,True
True,itsxpress,missing_executable_or_file,,False,True,none,True,itsxpress,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_itsxpress/app/itsxpress_shim_server.py,none,True,none,True
True,ivar,missing_executable_or_file,,False,True,none,True,ivar,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ivar/app/ivar_shim_server.py,none,True,none,True
True,jalview,missing_executable_or_file,,False,True,none,True,jalview,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_jalview/app/jalview_shim_server.py,none,True,none,True
True,java,none,--help,True,True,none,True,java-jdk,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_java-jdk/app/java-jdk_shim_server.py,none,True,none,True
True,jbrowse,missing_executable_or_file,,False,True,none,True,jbrowse2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_jbrowse2/app/jbrowse2_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,jcvi,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_jcvi/app/jcvi_shim_server.py,none,True,none,True
True,bc,missing_executable_or_file,,False,True,none,True,jellyfish,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_jellyfish/app/jellyfish_shim_server.py,none,True,none,True
True,jq,none,--help,True,True,none,True,jq,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_jq/app/jq_shim_server.py,none,True,none,True
True,k8,missing_executable_or_file,,False,True,none,True,k8,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_k8/app/k8_shim_server.py,none,True,none,True
True,kaiju,missing_executable_or_file,,False,True,none,True,kaiju,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_kaiju/app/kaiju_shim_server.py,none,True,none,True
True,kalign2,missing_executable_or_file,,False,True,none,True,kalign2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_kalign2/app/kalign2_shim_server.py,none,True,none,True
True,kallisto,missing_executable_or_file,,False,True,none,True,kallisto,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_kallisto/app/kallisto_shim_server.py,none,True,none,True
True,kb,missing_executable_or_file,,False,True,none,True,kb-python,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_kb-python/app/kb-python_shim_server.py,none,True,none,True
True,khipu,missing_executable_or_file,,False,True,none,True,khipu-metabolomics,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_khipu-metabolomics/app/khipu-metabolomics_shim_server.py,none,True,none,True
False,,,,,,,,kma,,,,,
True,kmc,missing_executable_or_file,,False,True,none,True,kmc,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_kmc/app/kmc_shim_server.py,none,True,none,True
True,jellyfish,missing_executable_or_file,,False,True,none,True,kmer-jellyfish,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_kmer-jellyfish/app/kmer-jellyfish_shim_server.py,none,True,none,True
True,kraken2,missing_executable_or_file,,False,True,none,True,kraken2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_kraken2/app/kraken2_shim_server.py,none,True,none,True
True,ktClassifyBLAST,missing_executable_or_file,,False,True,none,True,krona,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_krona/app/krona_shim_server.py,none,True,none,True
True,last,none,--help,True,True,none,True,last,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_last/app/last_shim_server.py,none,True,none,True
True,lastz,missing_executable_or_file,,False,True,none,True,lastz,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_lastz/app/lastz_shim_server.py,none,True,none,True
False,,,,,,,,liana,,,,,
True,cif-diff,missing_executable_or_file,,False,True,none,True,libcifpp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_libcifpp/app/libcifpp_shim_server.py,none,True,none,True
False,,,,,,,,libdb,,,,,
True,benchmark,missing_executable_or_file,,False,True,none,True,libdeflate,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_libdeflate/app/libdeflate_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,libsequence,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_libsequence/app/libsequence_shim_server.py,none,True,none,True
True,locarna,missing_executable_or_file,,False,True,none,True,locarna,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_locarna/app/locarna_shim_server.py,none,True,none,True
True,macs2,missing_executable_or_file,,False,True,none,True,macs2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_macs2/app/macs2_shim_server.py,none,True,none,True
True,mafft,missing_executable_or_file,,False,True,none,True,mafft,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mafft/app/mafft_shim_server.py,none,True,none,True
True,mageck,missing_executable_or_file,,False,True,none,True,mageck,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mageck/app/mageck_shim_server.py,none,True,none,True
True,scshiba.py,missing_executable_or_file,,False,True,none,True,mameshiba,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mameshiba/app/mameshiba_shim_server.py,none,True,none,True
True,minimap2,missing_executable_or_file,,False,True,none,True,mappy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mappy/app/mappy_shim_server.py,none,True,none,True
True,markerrepo,missing_executable_or_file,,False,True,none,True,markerrepo,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_markerrepo/app/markerrepo_shim_server.py,none,True,none,True
True,mash,missing_executable_or_file,,False,True,none,True,mash,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mash/app/mash_shim_server.py,none,True,none,True
True,mono,missing_executable_or_file,,False,True,none,True,maxquant,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_maxquant/app/maxquant_shim_server.py,none,True,none,True
False,,,,,,,,mcl,,,,,
True,medaka,missing_executable_or_file,,False,True,none,True,medaka,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_medaka/app/medaka_shim_server.py,none,True,none,True
True,megahit,missing_executable_or_file,,False,True,none,True,megahit,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_megahit/app/megahit_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,meme,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_meme/app/meme_shim_server.py,none,True,none,True
True,mentalist,missing_executable_or_file,,False,True,none,True,mentalist,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mentalist/app/mentalist_shim_server.py,none,True,none,True
True,atlas,missing_executable_or_file,,False,True,none,True,metagenome-atlas,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_metagenome-atlas/app/metagenome-atlas_shim_server.py,none,True,none,True
True,merge_metaphlan_tables.py,missing_executable_or_file,,False,True,none,True,metaphlan,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_metaphlan/app/metaphlan_shim_server.py,none,True,none,True
True,merge_metaphlan_tables.py,missing_executable_or_file,,False,True,none,True,metaphlan2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_metaphlan2/app/metaphlan2_shim_server.py,none,True,none,True
True,mikado,missing_executable_or_file,,False,True,none,True,mikado,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mikado/app/mikado_shim_server.py,none,True,none,True
True,minced,missing_executable_or_file,,False,True,none,True,minced,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_minced/app/minced_shim_server.py,none,True,none,True
True,miniasm,missing_executable_or_file,,False,True,none,True,miniasm,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_miniasm/app/miniasm_shim_server.py,none,True,none,True
True,minimap2,missing_executable_or_file,,False,True,none,True,minimap2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_minimap2/app/minimap2_shim_server.py,none,True,none,True
True,minvar,missing_executable_or_file,,False,True,none,True,minvar,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_minvar/app/minvar_shim_server.py,none,True,none,True
True,mitos_check_ref.py,missing_executable_or_file,,False,True,none,True,mitos,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mitos/app/mitos_shim_server.py,none,True,none,True
False,,,,,,,,mlst,,,,,
True,,no_command_literal,,False,False,none,True,mmtf-python,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mmtf-python/app/mmtf-python_shim_server.py,none,True,none,True
True,mobivision-M,missing_executable_or_file,,False,True,none,True,mobivision-m,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mobivision-m/app/mobivision-m_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,moments,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_moments/app/moments_shim_server.py,none,True,none,True
True,mosdepth,missing_executable_or_file,,False,True,none,True,mosdepth,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mosdepth/app/mosdepth_shim_server.py,none,True,none,True
True,mothur,missing_executable_or_file,,False,True,none,True,mothur,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mothur/app/mothur_shim_server.py,none,True,none,True
True,msisensor-pro,missing_executable_or_file,,False,True,none,True,msisensor-pro,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_msisensor-pro/app/msisensor-pro_shim_server.py,none,True,none,True
True,tric,missing_executable_or_file,,False,True,none,True,msproteomicstools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_msproteomicstools/app/msproteomicstools_shim_server.py,none,True,none,True
True,msstitch,missing_executable_or_file,,False,True,none,True,msstitch,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_msstitch/app/msstitch_shim_server.py,none,True,none,True
True,multiqc,missing_executable_or_file,,False,True,none,True,multiqc,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_multiqc/app/multiqc_shim_server.py,none,True,none,True
True,multiqc,missing_executable_or_file,,False,True,none,True,multiqc-bcbio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_multiqc-bcbio/app/multiqc-bcbio_shim_server.py,none,True,none,True
True,multiqc,missing_executable_or_file,,False,True,none,True,multiqc-xenium-extra,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_multiqc-xenium-extra/app/multiqc-xenium-extra_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,multivelo,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_multivelo/app/multivelo_shim_server.py,none,True,none,True
True,mummer,missing_executable_or_file,,False,True,none,True,mummer,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mummer/app/mummer_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,munkres,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_munkres/app/munkres_shim_server.py,none,True,none,True
True,muscle,missing_executable_or_file,,False,True,none,True,muscle,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_muscle/app/muscle_shim_server.py,none,True,none,True
True,mysql_config,missing_executable_or_file,,False,True,none,True,mysql-connector-c,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mysql-connector-c/app/mysql-connector-c_shim_server.py,none,True,none,True
True,mztosqlite,missing_executable_or_file,,False,True,none,True,mztosqlite,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_mztosqlite/app/mztosqlite_shim_server.py,none,True,none,True
True,NanoComp,missing_executable_or_file,,False,True,none,True,nanocomp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_nanocomp/app/nanocomp_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,nanoget,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_nanoget/app/nanoget_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,nanomath,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_nanomath/app/nanomath_shim_server.py,none,True,none,True
False,,,,,,,,nanoplot,,,,,
True,nanopolish,missing_executable_or_file,,False,True,none,True,nanopolish,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_nanopolish/app/nanopolish_shim_server.py,none,True,none,True
False,,,,,,,,ncbi-amrfinderplus,,,,,
True,dataformat,missing_executable_or_file,,False,True,none,True,ncbi-datasets-pylib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ncbi-datasets-pylib/app/ncbi-datasets-pylib_shim_server.py,none,True,none,True
True,ncbi-genome-download,missing_executable_or_file,,False,True,none,True,ncbi-genome-download,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ncbi-genome-download/app/ncbi-genome-download_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,ncbi-ngs-sdk,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ncbi-ngs-sdk/app/ncbi-ngs-sdk_shim_server.py,none,True,none,True
True,ncbi-vdb,missing_executable_or_file,,False,True,none,True,ncbi-vdb,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ncbi-vdb/app/ncbi-vdb_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,ncls,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ncls/app/ncls_shim_server.py,none,True,none,True
True,nextalign,missing_executable_or_file,,False,True,none,True,nextalign,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_nextalign/app/nextalign_shim_server.py,none,True,none,True
True,nextclade,missing_executable_or_file,,False,True,none,True,nextclade,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_nextclade/app/nextclade_shim_server.py,none,True,none,True
True,nextflow,missing_executable_or_file,,False,True,none,True,nextflow,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_nextflow/app/nextflow_shim_server.py,none,True,none,True
True,nf-core,missing_executable_or_file,,False,True,none,True,nf-core,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_nf-core/app/nf-core_shim_server.py,none,True,none,True
True,nglview,missing_executable_or_file,,False,True,none,True,nglview,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_nglview/app/nglview_shim_server.py,none,True,none,True
True,ngmlr,missing_executable_or_file,,False,True,none,True,ngmlr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ngmlr/app/ngmlr_shim_server.py,none,True,none,True
True,ngs-smap,missing_executable_or_file,,False,True,none,True,ngs-smap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ngs-smap/app/ngs-smap_shim_server.py,none,True,none,True
True,ngs-tools,missing_executable_or_file,,False,True,none,True,ngs-tools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ngs-tools/app/ngs-tools_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,novae,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_novae/app/novae_shim_server.py,none,True,none,True
True,novoalign,missing_executable_or_file,,False,True,none,True,novoalign,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_novoalign/app/novoalign_shim_server.py,none,True,none,True
True,compress_fast5,missing_executable_or_file,,False,True,none,True,ont-fast5-api,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ont-fast5-api/app/ont-fast5-api_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,openms-thirdparty,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_openms-thirdparty/app/openms-thirdparty_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,timeout,False,opticlust,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_opticlust/app/opticlust_shim_server.py,none,True,none,True
True,orthofinder,missing_executable_or_file,,False,True,none,True,orthofinder,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_orthofinder/app/orthofinder_shim_server.py,none,True,none,True
False,,,,,,,,ourotools,,,,,
True,pairix,missing_executable_or_file,,False,True,none,True,pairix,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pairix/app/pairix_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,palantir,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_palantir/app/palantir_shim_server.py,none,True,none,True
True,chi2,missing_executable_or_file,,False,True,none,True,paml,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_paml/app/paml_shim_server.py,none,True,none,True
False,,,,,,,,pandaseq,,,,,
True,,no_command_literal,,False,False,none,True,pango-designation,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pango-designation/app/pango-designation_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,schema_or_argument_error,False,pangolearn,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pangolearn/app/pangolearn_shim_server.py,none,True,none,True
False,,,,,,,,pangolin,,,,,
True,parasail_aligner,missing_executable_or_file,,False,True,none,True,parasail-python,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_parasail-python/app/parasail-python_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,pasta,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pasta/app/pasta_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,paste-bio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_paste-bio/app/paste-bio_shim_server.py,none,True,none,True
True,pcdl_get_anndata,missing_executable_or_file,,False,True,none,True,pcdl,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pcdl/app/pcdl_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,peakqc,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_peakqc/app/peakqc_shim_server.py,none,True,none,True
True,java,none,--help,True,True,none,True,peptide-shaker,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_peptide-shaker/app/peptide-shaker_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-aceperl,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-aceperl/app/perl-aceperl_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-algorithm-diff,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-algorithm-diff/app/perl-algorithm-diff_shim_server.py,none,True,none,True
False,,,,,,,,perl-algorithm-munkres,,,,,
False,,,,,,,,perl-alien-build,,,,,
True,cpanm,missing_executable_or_file,,False,True,none,True,perl-alien-libxml2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-alien-libxml2/app/perl-alien-libxml2_shim_server.py,none,True,none,True
True,cpanm,missing_executable_or_file,,False,True,none,True,perl-app-cpanminus,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-app-cpanminus/app/perl-app-cpanminus_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-appconfig,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-appconfig/app/perl-appconfig_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-archive-tar,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-archive-tar/app/perl-archive-tar_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-autoloader,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-autoloader/app/perl-autoloader_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-base,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-base/app/perl-base_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-bio-asn1-entrezgene,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-bio-asn1-entrezgene/app/perl-bio-asn1-entrezgene_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-bio-coordinate,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-bio-coordinate/app/perl-bio-coordinate_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-bio-featureio,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-bio-featureio/app/perl-bio-featureio_shim_server.py,none,True,none,True
False,,,,,,,,perl-bio-phylo,,,,,
True,perl,none,--help,True,True,none,True,perl-bio-samtools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-bio-samtools/app/perl-bio-samtools_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-bio-searchio-hmmer,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-bio-searchio-hmmer/app/perl-bio-searchio-hmmer_shim_server.py,none,True,none,True
True,paml_parser.pl,missing_executable_or_file,,False,True,none,True,perl-bio-tools-phylo-paml,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-bio-tools-phylo-paml/app/perl-bio-tools-phylo-paml_shim_server.py,none,True,none,True
True,clustalw,missing_executable_or_file,,False,True,none,True,perl-bio-tools-run-alignment-clustalw,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-bio-tools-run-alignment-clustalw/app/perl-bio-tools-run-alignment-clustalw_shim_server.py,none,True,none,True
False,,,,,,,,perl-bioperl,,,,,
True,bp_genbank2gff3.pl,missing_executable_or_file,,False,True,none,True,perl-bioperl-core,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-bioperl-core/app/perl-bioperl-core_shim_server.py,none,True,none,True
False,,,,,,,,perl-bioperl-run,,,,,
True,isbn_tool.pl,missing_executable_or_file,,False,True,none,True,perl-business-isbn,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-business-isbn/app/perl-business-isbn_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-business-isbn-data,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-business-isbn-data/app/perl-business-isbn-data_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-capture-tiny,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-capture-tiny/app/perl-capture-tiny_shim_server.py,none,True,none,True
False,,,,,,,,perl-carp,,,,,
True,perl,none,--help,True,True,none,True,perl-cgi,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-cgi/app/perl-cgi_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,schema_or_argument_error,False,perl-class-inspector,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-class-inspector/app/perl-class-inspector_shim_server.py,none,True,none,True
False,,,,,,,,perl-class-load,,,,,
False,,,,,,,,perl-class-load-xs,,,,,
True,perl,none,--help,True,True,none,True,perl-common-sense,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-common-sense/app/perl-common-sense_shim_server.py,none,True,none,True
True,pigz,missing_executable_or_file,,False,True,none,True,perl-compress-raw-zlib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-compress-raw-zlib/app/perl-compress-raw-zlib_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-config-general,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-config-general/app/perl-config-general_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-constant,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-constant/app/perl-constant_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-convert-binary-c,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-convert-binary-c/app/perl-convert-binary-c_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-convert-binhex,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-convert-binhex/app/perl-convert-binhex_shim_server.py,none,True,none,True
False,,,,,,,,perl-cpan-meta,,,,,
True,perl,none,--help,True,True,none,True,perl-cpan-meta-requirements,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-cpan-meta-requirements/app/perl-cpan-meta-requirements_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-crypt-rc4,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-crypt-rc4/app/perl-crypt-rc4_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-data-dumper,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-data-dumper/app/perl-data-dumper_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-data-optlist,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-data-optlist/app/perl-data-optlist_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-date-format,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-date-format/app/perl-date-format_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-dbi,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-dbi/app/perl-dbi_shim_server.py,none,True,none,True
False,,,,,,,,perl-devel-globaldestruction,,,,,
True,perl,none,--help,True,True,none,True,perl-devel-overloadinfo,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-devel-overloadinfo/app/perl-devel-overloadinfo_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-devel-stacktrace,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-devel-stacktrace/app/perl-devel-stacktrace_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-digest-md5,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-digest-md5/app/perl-digest-md5_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-digest-perl-md5,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-digest-perl-md5/app/perl-digest-perl-md5_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-digest-sha1,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-digest-sha1/app/perl-digest-sha1_shim_server.py,none,True,none,True
False,,,,,,,,perl-dist-checkconflicts,,,,,
False,,,,,,,,perl-dynaloader,,,,,
True,perl,none,--help,True,True,none,True,perl-encode,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-encode/app/perl-encode_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-encode-locale,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-encode-locale/app/perl-encode-locale_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,schema_or_argument_error,False,perl-error,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-error/app/perl-error_shim_server.py,none,True,none,True
False,,,,,,,,perl-eval-closure,,,,,
True,perl,none,--help,True,True,none,True,perl-exception-class,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-exception-class/app/perl-exception-class_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-exporter,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-exporter/app/perl-exporter_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-extutils-cbuilder,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-extutils-cbuilder/app/perl-extutils-cbuilder_shim_server.py,none,True,none,True
True,make,none,--help,True,True,none,True,perl-extutils-makemaker,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-extutils-makemaker/app/perl-extutils-makemaker_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-ffi-checklib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-ffi-checklib/app/perl-ffi-checklib_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-file-sort,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-file-sort/app/perl-file-sort_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-file-spec,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-file-spec/app/perl-file-spec_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-file-which,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-file-which/app/perl-file-which_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-font-afm,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-font-afm/app/perl-font-afm_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-getopt-long,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-getopt-long/app/perl-getopt-long_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,schema_or_argument_error,False,perl-graph,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-graph/app/perl-graph_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,perl-graphviz,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-graphviz/app/perl-graphviz_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-html-element-extended,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-html-element-extended/app/perl-html-element-extended_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-html-formatter,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-html-formatter/app/perl-html-formatter_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,schema_or_argument_error,False,perl-html-parser,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-html-parser/app/perl-html-parser_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-html-tableextract,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-html-tableextract/app/perl-html-tableextract_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-html-tagset,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-html-tagset/app/perl-html-tagset_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-html-tidy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-html-tidy/app/perl-html-tidy_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-html-tree,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-html-tree/app/perl-html-tree_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-html-treebuilder-xpath,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-html-treebuilder-xpath/app/perl-html-treebuilder-xpath_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-http-cookies,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-http-cookies/app/perl-http-cookies_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-http-daemon,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-http-daemon/app/perl-http-daemon_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-http-date,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-http-date/app/perl-http-date_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-http-negotiate,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-http-negotiate/app/perl-http-negotiate_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-image-info,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-image-info/app/perl-image-info_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,perl-image-size,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-image-size/app/perl-image-size_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-importer,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-importer/app/perl-importer_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-io-compress,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-io-compress/app/perl-io-compress_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-io-html,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-io-html/app/perl-io-html_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-io-sessiondata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-io-sessiondata/app/perl-io-sessiondata_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-io-string,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-io-string/app/perl-io-string_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-io-stringy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-io-stringy/app/perl-io-stringy_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-io-tty,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-io-tty/app/perl-io-tty_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-io-zlib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-io-zlib/app/perl-io-zlib_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-ipc-cmd,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-ipc-cmd/app/perl-ipc-cmd_shim_server.py,none,True,none,True
False,,,,,,,,perl-ipc-run,,,,,
True,perl,none,--help,True,True,none,True,perl-ipc-sharelite,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-ipc-sharelite/app/perl-ipc-sharelite_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-jcode,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-jcode/app/perl-jcode_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-json,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-json/app/perl-json_shim_server.py,none,True,none,True
True,json_pp,none,--help,True,True,none,True,perl-json-pp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-json-pp/app/perl-json-pp_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-json-xs,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-json-xs/app/perl-json-xs_shim_server.py,none,True,none,True
True,vcf-annotate,missing_executable_or_file,,False,True,none,True,perl-lib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-lib/app/perl-lib_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-libwww-perl,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-libwww-perl/app/perl-libwww-perl_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-libxml-perl,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-libxml-perl/app/perl-libxml-perl_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-list-moreutils,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-list-moreutils/app/perl-list-moreutils_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-list-moreutils-xs,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-list-moreutils-xs/app/perl-list-moreutils-xs_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-locale-maketext-simple,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-locale-maketext-simple/app/perl-locale-maketext-simple_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-lwp-mediatypes,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-lwp-mediatypes/app/perl-lwp-mediatypes_shim_server.py,none,True,none,True
False,,,,,,,,perl-lwp-simple,,,,,
True,perl,none,--help,True,True,none,True,perl-mailtools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-mailtools/app/perl-mailtools_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-math-bezier,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-math-bezier/app/perl-math-bezier_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-math-derivative,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-math-derivative/app/perl-math-derivative_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-math-random,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-math-random/app/perl-math-random_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-math-round,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-math-round/app/perl-math-round_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-math-spline,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-math-spline/app/perl-math-spline_shim_server.py,none,True,none,True
True,fragment-annotation.pl,missing_executable_or_file,,False,True,none,True,perl-metabolomics-fragment-annotation,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-metabolomics-fragment-annotation/app/perl-metabolomics-fragment-annotation_shim_server.py,none,True,none,True
False,,,,,,,,perl-mime-base64,,,,,
True,perl,none,--help,True,True,none,True,perl-mime-lite,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-mime-lite/app/perl-mime-lite_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,schema_or_argument_error,False,perl-mime-types,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-mime-types/app/perl-mime-types_shim_server.py,none,True,none,True
True,chmod,none,--help,True,True,none,True,perl-module-build,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-module-build/app/perl-module-build_shim_server.py,none,True,none,True
True,corelist,none,--help,True,True,none,True,perl-module-corelist,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-module-corelist/app/perl-module-corelist_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-module-load-conditional,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-module-load-conditional/app/perl-module-load-conditional_shim_server.py,none,True,none,True
True,perl-module-metadata,missing_executable_or_file,,False,True,none,True,perl-module-metadata,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-module-metadata/app/perl-module-metadata_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,perl-module-runtime,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-module-runtime/app/perl-module-runtime_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-module-runtime-conflicts,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-module-runtime-conflicts/app/perl-module-runtime-conflicts_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-moo,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-moo/app/perl-moo_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-moose,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-moose/app/perl-moose_shim_server.py,none,True,none,True
False,,,,,,,,perl-mozilla-ca,,,,,
True,perl,none,--help,True,True,none,True,perl-net-http,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-net-http/app/perl-net-http_shim_server.py,none,True,none,True
True,ssleay-version,missing_executable_or_file,,False,True,none,True,perl-net-ssleay,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-net-ssleay/app/perl-net-ssleay_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-number-format,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-number-format/app/perl-number-format_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-ole-storage_lite,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-ole-storage_lite/app/perl-ole-storage_lite_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,perl-package-deprecationmanager,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-package-deprecationmanager/app/perl-package-deprecationmanager_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-package-stash,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-package-stash/app/perl-package-stash_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-params-check,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-params-check/app/perl-params-check_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,perl-params-util,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-params-util/app/perl-params-util_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-params-validate,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-params-validate/app/perl-params-validate_shim_server.py,none,True,none,True
True,samtools,missing_executable_or_file,,False,True,none,True,perl-parent,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-parent/app/perl-parent_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-parse-recdescent,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-parse-recdescent/app/perl-parse-recdescent_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-pod-escapes,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-pod-escapes/app/perl-pod-escapes_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-pod-usage,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-pod-usage/app/perl-pod-usage_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-postscript,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-postscript/app/perl-postscript_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-regexp-common,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-regexp-common/app/perl-regexp-common_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-role-tiny,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-role-tiny/app/perl-role-tiny_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-sereal,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-sereal/app/perl-sereal_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-sereal-decoder,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-sereal-decoder/app/perl-sereal-decoder_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-set-intervaltree,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-set-intervaltree/app/perl-set-intervaltree_shim_server.py,none,True,none,True
False,,,,,,,,perl-set-intspan,,,,,
False,,,,,,,,perl-set-scalar,,,,,
True,perl,none,--help,True,True,none,True,perl-soap-lite,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-soap-lite/app/perl-soap-lite_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-sort-naturally,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-sort-naturally/app/perl-sort-naturally_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-spreadsheet-parseexcel,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-spreadsheet-parseexcel/app/perl-spreadsheet-parseexcel_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-spreadsheet-writeexcel,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-spreadsheet-writeexcel/app/perl-spreadsheet-writeexcel_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-sub-exporter,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-sub-exporter/app/perl-sub-exporter_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-sub-exporter-progressive,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-sub-exporter-progressive/app/perl-sub-exporter-progressive_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-sub-identify,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-sub-identify/app/perl-sub-identify_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,perl-sub-name,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-sub-name/app/perl-sub-name_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-sub-quote,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-sub-quote/app/perl-sub-quote_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-sub-uplevel,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-sub-uplevel/app/perl-sub-uplevel_shim_server.py,none,True,none,True
False,,,,,,,,perl-svg,,,,,
True,perl,none,--help,True,True,none,True,perl-task-weaken,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-task-weaken/app/perl-task-weaken_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-template-toolkit,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-template-toolkit/app/perl-template-toolkit_shim_server.py,none,True,none,True
True,perl-test,missing_executable_or_file,,False,True,none,True,perl-test,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-test/app/perl-test_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-test-deep,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-test-deep/app/perl-test-deep_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-test-differences,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-test-differences/app/perl-test-differences_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-test-exception,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-test-exception/app/perl-test-exception_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-test-fatal,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-test-fatal/app/perl-test-fatal_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-test-harness,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-test-harness/app/perl-test-harness_shim_server.py,none,True,none,True
False,,,,,,,,perl-test-most,,,,,
True,perl,none,--help,True,True,none,True,perl-test-warn,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-test-warn/app/perl-test-warn_shim_server.py,none,True,none,True
False,,,,,,,,perl-text-diff,,,,,
False,,,,,,,,perl-text-parsewords,,,,,
True,perl,none,--help,True,True,none,True,perl-tie-ixhash,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-tie-ixhash/app/perl-tie-ixhash_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-time-hires,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-time-hires/app/perl-time-hires_shim_server.py,none,True,none,True
False,,,,,,,,perl-timedate,,,,,
True,perl,none,--help,True,True,none,True,perl-tree-dag_node,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-tree-dag_node/app/perl-tree-dag_node_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-try-tiny,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-try-tiny/app/perl-try-tiny_shim_server.py,none,True,none,True
False,,,,,,,,perl-types-serialiser,,,,,
True,perl,none,--help,True,True,none,True,perl-unicode-map,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-unicode-map/app/perl-unicode-map_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-uri,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-uri/app/perl-uri_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-url-encode,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-url-encode/app/perl-url-encode_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-version,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-version/app/perl-version_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-www-robotrules,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-www-robotrules/app/perl-www-robotrules_shim_server.py,none,True,none,True
False,,,,,,,,perl-xml-dom-xpath,,,,,
True,perl,none,--help,True,True,none,True,perl-xml-filter-buffertext,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-filter-buffertext/app/perl-xml-filter-buffertext_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-xml-libxml,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-libxml/app/perl-xml-libxml_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,schema_or_argument_error,False,perl-xml-libxslt,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-libxslt/app/perl-xml-libxslt_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-xml-namespacesupport,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-namespacesupport/app/perl-xml-namespacesupport_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-xml-parser,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-parser/app/perl-xml-parser_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-xml-regexp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-regexp/app/perl-xml-regexp_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-xml-sax,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-sax/app/perl-xml-sax_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-xml-sax-base,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-sax-base/app/perl-xml-sax-base_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-xml-sax-expat,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-sax-expat/app/perl-xml-sax-expat_shim_server.py,none,True,none,True
True,xml_grep,missing_executable_or_file,,False,True,none,True,perl-xml-twig,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-twig/app/perl-xml-twig_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-xml-xpath,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-xpath/app/perl-xml-xpath_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-xml-xpathengine,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xml-xpathengine/app/perl-xml-xpathengine_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-xsloader,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-xsloader/app/perl-xsloader_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,perl-yaml,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_perl-yaml/app/perl-yaml_shim_server.py,none,True,none,True
True,phyml,missing_executable_or_file,,False,True,none,True,phyml,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_phyml/app/phyml_shim_server.py,none,True,none,True
True,piaso,missing_executable_or_file,,False,True,none,True,piaso,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_piaso/app/piaso_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,picard,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_picard/app/picard_shim_server.py,none,True,none,True
False,,,,,,,,picard copy,,,,,
False,,,,,,,,picard-slim,,,,,
False,,,,,,,,pilon,,,,,
True,pixelator,missing_executable_or_file,,False,True,none,True,pixelator,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pixelator/app/pixelator_shim_server.py,none,True,none,True
False,,,,,,,,planemo,,,,,
False,,,,,,,,plink,,,,,
False,,,,,,,,poa,,,,,
True,junctools,missing_executable_or_file,,False,True,none,True,portcullis,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_portcullis/app/portcullis_shim_server.py,none,True,none,True
False,,,,,,,,pplacer,,,,,
True,prank,missing_executable_or_file,,False,True,none,True,prank,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_prank/app/prank_shim_server.py,none,True,none,True
True,ntmtt,missing_executable_or_file,,False,True,none,True,primer3,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_primer3/app/primer3_shim_server.py,none,True,none,True
False,,,,,,,,primer3-py,,,,,
True,prodigal,missing_executable_or_file,,False,True,none,True,prodigal,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_prodigal/app/prodigal_shim_server.py,none,True,none,True
True,prokka,missing_executable_or_file,,False,True,none,True,prokka,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_prokka/app/prokka_shim_server.py,none,True,none,True
True,prophyle,missing_executable_or_file,,False,True,none,True,prophyle,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_prophyle/app/prophyle_shim_server.py,none,True,none,True
True,proteinortho,missing_executable_or_file,,False,True,none,True,proteinortho,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_proteinortho/app/proteinortho_shim_server.py,none,True,none,True
True,proteomiqon-peptidedb,missing_executable_or_file,,False,True,none,True,proteomiqon-peptidedb,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_proteomiqon-peptidedb/app/proteomiqon-peptidedb_shim_server.py,none,True,none,True
True,proteomiqon-peptidespectrummatching,missing_executable_or_file,,False,True,none,True,proteomiqon-peptidespectrummatching,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_proteomiqon-peptidespectrummatching/app/proteomiqon-peptidespectrummatching_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,pubchempy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pubchempy/app/pubchempy_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,py2bit,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_py2bit/app/py2bit_shim_server.py,none,True,none,True
True,bedtools,missing_executable_or_file,,False,True,none,True,pybedtools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pybedtools/app/pybedtools_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,pybigwig,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pybigwig/app/pybigwig_shim_server.py,none,True,none,True
False,,,,,,,,pybiolib,,,,,
True,pycistopic,missing_executable_or_file,,False,True,none,True,pycistopic,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pycistopic/app/pycistopic_shim_server.py,none,True,none,True
False,,,,,,,,pyfaidx,,,,,
True,pyfastx,missing_executable_or_file,,False,True,none,True,pyfastx,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pyfastx/app/pyfastx_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,missing_python_dependency,False,pyhmmer,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pyhmmer/app/pyhmmer_shim_server.py,none,True,none,True
True,pyranger,missing_executable_or_file,,False,True,none,True,pyranges,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pyranges/app/pyranges_shim_server.py,none,True,none,True
False,,,,,,,,pyrle,,,,,
True,pyrodigal,missing_executable_or_file,,False,True,none,True,pyrodigal,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pyrodigal/app/pyrodigal_shim_server.py,none,True,none,True
True,pyroe,missing_executable_or_file,,False,True,none,True,pyroe,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pyroe/app/pyroe_shim_server.py,none,True,none,True
False,,,,,,,,pyrovelocity,,,,,
True,bcftools,missing_executable_or_file,,False,True,none,True,pysam,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pysam/app/pysam_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,pysftp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pysftp/app/pysftp_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,pyspoa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pyspoa/app/pyspoa_shim_server.py,none,True,none,True
True,bgzip,missing_executable_or_file,,False,True,none,True,pytabix,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pytabix/app/pytabix_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,pyteomics,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pyteomics/app/pyteomics_shim_server.py,none,True,none,True
True,edlib-aligner,missing_executable_or_file,,False,True,none,True,python-edlib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_python-edlib/app/python-edlib_shim_server.py,none,True,none,True
False,,,,,,,,pyvcf,,,,,
True,,no_command_literal,,False,False,none,True,pyvcf3,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_pyvcf3/app/pyvcf3_shim_server.py,none,True,none,True
True,qcatch,missing_executable_or_file,,False,True,none,True,qcatch,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_qcatch/app/qcatch_shim_server.py,none,True,none,True
False,,,,,,,,qiime,,,,,
True,qualimap,missing_executable_or_file,,False,True,none,True,qualimap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_qualimap/app/qualimap_shim_server.py,none,True,none,True
False,,,,,,,,quast,,,,,
True,,no_command_literal,,False,False,none,True,r-abdiv,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-abdiv/app/r-abdiv_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-acidbase,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-acidbase/app/r-acidbase_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-archr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-archr/app/r-archr_shim_server.py,none,True,none,True
True,R,missing_executable_or_file,,False,True,none,True,r-azimuth,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-azimuth/app/r-azimuth_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-basejump,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-basejump/app/r-basejump_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-beyondcell,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-beyondcell/app/r-beyondcell_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-cdseq,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-cdseq/app/r-cdseq_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-dwls,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-dwls/app/r-dwls_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-epitrace,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-epitrace/app/r-epitrace_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-flanders,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-flanders/app/r-flanders_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-goalie,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-goalie/app/r-goalie_shim_server.py,none,True,none,True
True,r-mams,missing_executable_or_file,,False,True,none,True,r-mams,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-mams/app/r-mams_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-redeemr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-redeemr/app/r-redeemr_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-restfulr,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-restfulr/app/r-restfulr_shim_server.py,none,True,none,True
False,,,,,,,,r-saige,,,,,
True,,no_command_literal,,False,False,none,True,r-sceasy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-sceasy/app/r-sceasy_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-scopfunctions,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-scopfunctions/app/r-scopfunctions_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-scpred,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-scpred/app/r-scpred_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-seurat,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-seurat/app/r-seurat_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-seurat-data,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-seurat-data/app/r-seurat-data_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-seurat-disk,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-seurat-disk/app/r-seurat-disk_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-seurat-scripts,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-seurat-scripts/app/r-seurat-scripts_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,r-signac,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_r-signac/app/r-signac_shim_server.py,none,True,none,True
False,,,,,,,,racon,,,,,
True,raxmlHPC,missing_executable_or_file,,False,True,none,True,raxml,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_raxml/app/raxml_shim_server.py,none,True,none,True
False,,,,,,,,recognizer,,,,,
True,RepeatMasker,missing_executable_or_file,,False,True,none,True,repeatmasker,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_repeatmasker/app/repeatmasker_shim_server.py,none,True,none,True
True,rgi,missing_executable_or_file,,False,True,none,True,rgi,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_rgi/app/rgi_shim_server.py,none,True,none,True
True,DuplexFold,missing_executable_or_file,,False,True,none,True,rnastructure,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_rnastructure/app/rnastructure_shim_server.py,none,True,none,True
True,rnftools,missing_executable_or_file,,False,True,syntax_error,False,rnftools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_rnftools/app/rnftools_shim_server.py,none,True,none,True
False,,,,,,,,rpsbproc,,,,,
True,pyrsa-decrypt,none,--help,True,True,none,True,rsa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_rsa/app/rsa_shim_server.py,none,True,none,True
True,rscape,missing_executable_or_file,,False,True,none,True,rscape,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_rscape/app/rscape_shim_server.py,none,True,none,True
True,rsem-calculate-expression,missing_executable_or_file,,False,True,none,True,rsem,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_rsem/app/rsem_shim_server.py,none,True,none,True
True,FPKM-UQ.py,missing_executable_or_file,,False,True,none,True,rseqc,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_rseqc/app/rseqc_shim_server.py,none,True,none,True
False,,,,,,,,rtg-tools,,,,,
True,rbt,missing_executable_or_file,,False,True,none,True,rust-bio-tools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_rust-bio-tools/app/rust-bio-tools_shim_server.py,none,True,none,True
True,sage,missing_executable_or_file,,False,True,none,True,sage-proteomics,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sage-proteomics/app/sage-proteomics_shim_server.py,none,True,none,True
False,,,,,,,,salmon,,,,,
True,map_genes.sh,missing_executable_or_file,,False,True,none,True,samap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_samap/app/samap_shim_server.py,none,True,none,True
True,sambamba,missing_executable_or_file,,False,True,none,True,sambamba,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sambamba/app/sambamba_shim_server.py,none,True,none,True
True,samblaster,missing_executable_or_file,,False,True,none,True,samblaster,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_samblaster/app/samblaster_shim_server.py,none,True,none,True
True,samsift,missing_executable_or_file,,False,True,none,True,samsift,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_samsift/app/samsift_shim_server.py,none,True,none,True
True,cat,none,--help,True,True,none,True,samtools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_samtools/app/samtools_shim_server.py,none,True,none,True
True,sc-musketeers,missing_executable_or_file,,False,True,none,True,sc-musketeers,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sc-musketeers/app/sc-musketeers_shim_server.py,none,True,none,True
True,scaden,missing_executable_or_file,,False,True,none,True,scaden,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scaden/app/scaden_shim_server.py,none,True,none,True
True,scanpy,missing_executable_or_file,,False,True,none,True,scanpy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scanpy/app/scanpy_shim_server.py,none,True,none,True
True,scanpy,missing_executable_or_file,,False,True,none,True,scanpy-cli,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scanpy-cli/app/scanpy-cli_shim_server.py,none,True,none,True
True,scanpy-cli,missing_executable_or_file,,False,True,none,True,scanpy-scripts,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scanpy-scripts/app/scanpy-scripts_shim_server.py,none,True,none,True
True,scar,missing_executable_or_file,,False,True,none,True,scar,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scar/app/scar_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,scarches,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scarches/app/scarches_shim_server.py,none,True,none,True
True,sccaf,missing_executable_or_file,,False,True,none,True,sccaf,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sccaf/app/sccaf_shim_server.py,none,True,none,True
True,sccellfie,missing_executable_or_file,,False,True,none,True,sccellfie,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sccellfie/app/sccellfie_shim_server.py,none,True,none,True
True,scelvis,missing_executable_or_file,,False,True,none,True,scelvis,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scelvis/app/scelvis_shim_server.py,none,True,none,True
True,scepia,missing_executable_or_file,,False,True,none,True,scepia,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scepia/app/scepia_shim_server.py,none,True,none,True
True,scglue,missing_executable_or_file,,False,True,none,True,scglue,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scglue/app/scglue_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,scib,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scib/app/scib_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,timeout,False,scirpy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scirpy/app/scirpy_shim_server.py,none,True,none,True
True,pip,none,--help,True,True,none,True,scmeta,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scmeta/app/scmeta_server.py,none,True,none,True
True,scmidas,missing_executable_or_file,,False,True,none,True,scmidas,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scmidas/app/scmidas_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,scpred-cli,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scpred-cli/app/scpred-cli_shim_server.py,none,True,none,True
True,cdna-generator,missing_executable_or_file,,False,True,none,True,scrnasim-toolz,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scrnasim-toolz/app/scrnasim-toolz_shim_server.py,none,True,none,True
True,scspectra,missing_executable_or_file,,False,True,none,True,scspectra,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scspectra/app/scspectra_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,timeout,False,scstem,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scstem/app/scstem_shim_server.py,none,True,none,True
True,sctriangulate,missing_executable_or_file,,False,True,none,True,sctriangulate,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sctriangulate/app/sctriangulate_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,scvelo,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scvelo/app/scvelo_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,scvi,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scvi/app/scvi_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,runtime_exception,False,scvi-tools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scvi-tools/app/scvi-tools_shim_server.py,none,True,none,True
True,scvis,missing_executable_or_file,,False,True,none,True,scvis,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scvis/app/scvis_shim_server.py,none,True,none,True
True,scvis,missing_executable_or_file,,False,True,none,True,scvis_galaxy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scvis_galaxy/app/scvis_galaxy_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,scxmatch,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_scxmatch/app/scxmatch_shim_server.py,none,True,none,True
True,runDeconvolution,missing_executable_or_file,,False,True,none,True,sdeper,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sdeper/app/sdeper_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,seacells,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_seacells/app/seacells_shim_server.py,none,True,none,True
True,searchgui,missing_executable_or_file,,False,True,none,True,searchgui,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_searchgui/app/searchgui_shim_server.py,none,True,none,True
True,segemehl.x,missing_executable_or_file,,False,True,none,True,segemehl,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_segemehl/app/segemehl_shim_server.py,none,True,none,True
True,which,none,--help,True,True,none,True,sentieon,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sentieon/app/sentieon_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,sepp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sepp/app/sepp_shim_server.py,none,True,none,True
True,seq2science,missing_executable_or_file,,False,True,none,True,seq2science,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_seq2science/app/seq2science_shim_server.py,none,True,none,True
True,seqcluster,missing_executable_or_file,,False,True,none,True,seqcluster,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_seqcluster/app/seqcluster_shim_server.py,none,True,none,True
True,seqfu,missing_executable_or_file,,False,True,none,True,seqfu,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_seqfu/app/seqfu_shim_server.py,none,True,none,True
True,seqkit,missing_executable_or_file,,False,True,none,True,seqkit,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_seqkit/app/seqkit_shim_server.py,none,True,none,True
True,seqtk,missing_executable_or_file,,False,True,none,True,seqtk,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_seqtk/app/seqtk_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,sequence-operations,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sequence-operations/app/sequence-operations_server.py,none,True,none,True
True,seurat-filter-cells.R,missing_executable_or_file,,False,True,none,True,seurat-scripts,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_seurat-scripts/app/seurat-scripts_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,sevenbridges-python,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sevenbridges-python/app/sevenbridges-python_shim_server.py,none,True,none,True
True,scshiba.py,missing_executable_or_file,,False,True,none,True,shiba,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_shiba/app/shiba_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,simo-omics,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_simo-omics/app/simo-omics_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,simplejson,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_simplejson/app/simplejson_shim_server.py,none,True,none,True
True,sina,missing_executable_or_file,,False,True,none,True,sina,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sina/app/sina_shim_server.py,none,True,none,True
True,sincei,missing_executable_or_file,,False,True,none,True,sincei,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sincei/app/sincei_shim_server.py,none,True,none,True
True,slow5tools,missing_executable_or_file,,False,True,none,True,slow5tools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_slow5tools/app/slow5tools_shim_server.py,none,True,none,True
True,snakemake,missing_executable_or_file,,False,True,none,True,snakemake,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snakemake/app/snakemake_shim_server.py,none,True,none,True
False,,,,,,,,snakemake-interface-common,,,,,
True,,no_command_literal,,False,False,none,True,snakemake-interface-executor-plugins,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snakemake-interface-executor-plugins/app/snakemake-interface-executor-plugins_shim_server.py,none,True,none,True
False,,,,,,,,snakemake-interface-logger-plugins,,,,,
True,,no_command_literal,,False,False,none,True,snakemake-interface-report-plugins,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snakemake-interface-report-plugins/app/snakemake-interface-report-plugins_shim_server.py,none,True,none,True
True,pip,none,--help,True,True,none,True,snakemake-interface-storage-plugins,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snakemake-interface-storage-plugins/app/snakemake-interface-storage-plugins_shim_server.py,none,True,none,True
True,snakemake,missing_executable_or_file,,False,True,none,True,snakemake-minimal,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snakemake-minimal/app/snakemake-minimal_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,snakemake-wrapper-utils,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snakemake-wrapper-utils/app/snakemake-wrapper-utils_shim_server.py,none,True,none,True
True,snakeSV,missing_executable_or_file,,False,True,none,True,snakesv,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snakesv/app/snakesv_shim_server.py,none,True,none,True
False,,,,,,,,snap-aligner,,,,,
True,snippy,missing_executable_or_file,,False,True,none,True,snippy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snippy/app/snippy_shim_server.py,none,True,none,True
True,snp2cell,missing_executable_or_file,,False,True,none,True,snp2cell,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snp2cell/app/snp2cell_shim_server.py,none,True,none,True
True,snpEff,missing_executable_or_file,,False,True,none,True,snpeff,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snpeff/app/snpeff_shim_server.py,none,True,none,True
True,perl,none,--help,True,True,none,True,snpsift,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_snpsift/app/snpsift_shim_server.py,none,True,none,True
True,sopa,missing_executable_or_file,,False,True,none,True,sopa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sopa/app/sopa_shim_server.py,none,True,none,True
False,,,,,,,,sorted_nearest,,,,,
True,sortmerna,missing_executable_or_file,,False,True,none,True,sortmerna,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sortmerna/app/sortmerna_shim_server.py,none,True,none,True
True,sourmash,missing_executable_or_file,,False,True,none,True,sourmash,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sourmash/app/sourmash_shim_server.py,none,True,none,True
True,biosyntheticspades.py,missing_executable_or_file,,False,True,none,True,spades,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_spades/app/spades_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,spagrn,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_spagrn/app/spagrn_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,spapros,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_spapros/app/spapros_shim_server.py,none,True,none,True
True,spatialleiden,missing_executable_or_file,,False,True,none,True,spatialleiden,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_spatialleiden/app/spatialleiden_shim_server.py,none,True,none,True
True,fasterq-dump,missing_executable_or_file,,False,True,none,True,sra-tools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_sra-tools/app/sra-tools_shim_server.py,none,True,none,True
True,clone_filter,missing_executable_or_file,,False,True,none,True,stacks,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_stacks/app/stacks_shim_server.py,none,True,none,True
True,STAR,missing_executable_or_file,,False,True,none,True,star,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_star/app/star_shim_server.py,none,True,none,True
True,STAR-Fusion,missing_executable_or_file,,False,True,none,True,star-fusion,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_star-fusion/app/star-fusion_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,stream,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_stream/app/stream_shim_server.py,none,True,none,True
True,stringtie,missing_executable_or_file,,False,True,none,True,stringtie,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_stringtie/app/stringtie_shim_server.py,none,True,none,True
True,exactSNP,missing_executable_or_file,,False,True,none,True,subread,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_subread/app/subread_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,switchtfi,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_switchtfi/app/switchtfi_shim_server.py,none,True,none,True
True,t_coffee,missing_executable_or_file,,False,True,none,True,t-coffee,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_t-coffee/app/t-coffee_shim_server.py,none,True,none,True
True,t_coffee,missing_executable_or_file,,False,True,none,True,t_coffee,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_t_coffee/app/t_coffee_shim_server.py,none,True,none,True
True,tabix,missing_executable_or_file,,False,True,none,True,tabix,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_tabix/app/tabix_shim_server.py,none,True,none,True
True,tabixpp,missing_executable_or_file,,False,True,none,True,tabixpp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_tabixpp/app/tabixpp_shim_server.py,none,True,none,True
True,talon,missing_executable_or_file,,False,True,none,True,talon,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_talon/app/talon_shim_server.py,none,True,none,True
True,taxonkit,missing_executable_or_file,,False,True,none,True,taxonkit,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_taxonkit/app/taxonkit_shim_server.py,none,True,none,True
True,tb-profiler,missing_executable_or_file,,False,True,none,True,tb-profiler,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_tb-profiler/app/tb-profiler_shim_server.py,none,True,none,True
False,,,,,,,,thapbi-pict,,,,,
True,tidyp,missing_executable_or_file,,False,True,none,True,tidyp,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_tidyp/app/tidyp_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,tirank,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_tirank/app/tirank_shim_server.py,none,True,none,True
True,MMalign,missing_executable_or_file,,False,True,none,True,tmalign,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_tmalign/app/tmalign_shim_server.py,none,True,none,True
False,,,,,,,,tobias,,,,,
False,,,,,,,,toil,,,,,
False,,,,,,,,transdecoder,,,,,
True,treetime,missing_executable_or_file,,False,True,none,True,treetime,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_treetime/app/treetime_shim_server.py,none,True,none,True
False,,,,,,,,trf,,,,,
True,trim_galore,missing_executable_or_file,,False,True,none,True,trim-galore,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_trim-galore/app/trim-galore_shim_server.py,none,True,none,True
True,trimadap,missing_executable_or_file,,False,True,none,True,trimadap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_trimadap/app/trimadap_shim_server.py,none,True,none,True
False,,,,,,,,trimal,,,,,
True,trimmomatic,missing_executable_or_file,,False,True,none,True,trimmomatic,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_trimmomatic/app/trimmomatic_shim_server.py,none,True,none,True
True,Trinity,missing_executable_or_file,,False,True,none,True,trinity,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_trinity/app/trinity_shim_server.py,none,True,none,True
True,EufindtRNA,missing_executable_or_file,,False,True,none,True,trnascan-se,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_trnascan-se/app/trnascan-se_shim_server.py,none,True,none,True
False,,,,,,,,ucsc-bedgraphtobigwig,,,,,
True,bedToBigBed,missing_executable_or_file,,False,True,none,True,ucsc-bedtobigbed,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ucsc-bedtobigbed/app/ucsc-bedtobigbed_shim_server.py,none,True,none,True
True,cellbrowser,missing_executable_or_file,,False,True,none,True,ucsc-cell-browser,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ucsc-cell-browser/app/ucsc-cell-browser_shim_server.py,none,True,none,True
True,ucsc-fatotwobit,missing_executable_or_file,,False,True,none,True,ucsc-fatotwobit,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ucsc-fatotwobit/app/ucsc-fatotwobit_shim_server.py,none,True,none,True
True,gtfToGenePred,missing_executable_or_file,,False,True,none,True,ucsc-gtftogenepred,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ucsc-gtftogenepred/app/ucsc-gtftogenepred_shim_server.py,none,True,none,True
True,liftOver,missing_executable_or_file,,False,True,none,True,ucsc-liftover,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ucsc-liftover/app/ucsc-liftover_shim_server.py,none,True,none,True
True,ucsc-nibfrag,missing_executable_or_file,,False,True,none,True,ucsc-nibfrag,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ucsc-nibfrag/app/ucsc-nibfrag_shim_server.py,none,True,none,True
True,twoBitInfo,missing_executable_or_file,,False,True,none,True,ucsc-twobitinfo,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ucsc-twobitinfo/app/ucsc-twobitinfo_shim_server.py,none,True,none,True
True,ucsc-twobittofa,missing_executable_or_file,,False,True,none,True,ucsc-twobittofa,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_ucsc-twobittofa/app/ucsc-twobittofa_shim_server.py,none,True,none,True
False,,,,,,,,ucsc-wigtobigwig,,,,,
False,,,,,,,,umi_tools,,,,,
True,umis,missing_executable_or_file,,False,True,none,True,umis,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_umis/app/umis_shim_server.py,none,True,none,True
True,unicycler,missing_executable_or_file,,False,True,none,True,unicycler,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_unicycler/app/unicycler_shim_server.py,none,True,none,True
True,faithpd,missing_executable_or_file,,False,True,none,True,unifrac,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_unifrac/app/unifrac_shim_server.py,none,True,none,True
False,,,,,,,,unifrac-binaries,,,,,
False,,,,,,,,upimapi,,,,,
True,,no_command_literal,,False,False,none,True,urllib3,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_urllib3/app/urllib3_shim_server.py,none,True,none,True
True,RIPPLES,missing_executable_or_file,,False,True,none,True,usher,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_usher/app/usher_shim_server.py,none,True,none,True
False,,,,,,,,vardict,,,,,
True,VarDict,missing_executable_or_file,,False,True,none,True,vardict-java,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_vardict-java/app/vardict-java_shim_server.py,none,True,none,True
False,,,,,,,,varlociraptor,,,,,
False,,,,,,,,varscan,,,,,
False,,,,,,,,vcflib,,,,,
True,,no_command_literal,,False,False,none,True,vcfpy,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_vcfpy/app/vcfpy_shim_server.py,none,True,none,True
True,vcftools,missing_executable_or_file,,False,True,none,True,vcftools,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_vcftools/app/vcftools_shim_server.py,none,True,none,True
True,vcontact2,missing_executable_or_file,,False,True,none,True,vcontact2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_vcontact2/app/vcontact2_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,viennarna,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_viennarna/app/viennarna_shim_server.py,none,True,none,True
True,,no_command_literal,,False,False,none,True,vitessce-python,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_vitessce-python/app/vitessce-python_shim_server.py,none,True,none,True
True,vpt,missing_executable_or_file,,False,True,none,True,vpt,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_vpt/app/vpt_shim_server.py,none,True,none,True
False,,,,,,,,vsearch,,,,,
True,vt,missing_executable_or_file,,False,True,none,True,vt,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_vt/app/vt_shim_server.py,none,True,none,True
True,wasp2-analyze,missing_executable_or_file,,False,True,none,True,wasp2,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_wasp2/app/wasp2_shim_server.py,none,True,none,True
True,whatshap,missing_executable_or_file,,False,True,none,True,whatshap,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_whatshap/app/whatshap_shim_server.py,none,True,none,True
True,java,none,--help,True,True,none,True,womtool,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_womtool/app/womtool_shim_server.py,none,True,none,True
True,xclone-baf,missing_executable_or_file,,False,True,none,True,xclone,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_xclone/app/xclone_shim_server.py,none,True,none,True
False,,,,,,,,xopen,,,,,
True,yacrd,missing_executable_or_file,,False,True,none,True,yacrd,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_yacrd/app/yacrd_shim_server.py,none,True,none,True
True,zdb,missing_executable_or_file,,False,True,none,True,zdb,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_zdb/app/zdb_shim_server.py,none,True,none,True
True,zol-suite,missing_executable_or_file,,False,True,none,True,zol,/225040511/project/Beyond Prompt-Based Planning/Biomanus/biomni_web/backend/data/mcp_generated/mcp_zol/app/zol_shim_server.py,none,True,none,True