sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1a134db3703f0cda6a2d2a50189e7fb1129476e286ab7ca2fc4acc12dd42ddb2 | Shell | 83 | 5 | #!/bin/bash
echo -e "#Running ./ex_ChiAnglesDefinition"
./ex_ChiAnglesDefinition
|
44f1072b05661045132d5d6fe12ea100abad82ef03d30d0360ec309cbb64ddd4 | Shell | 83 | 4 | #!/bin/bash
echo -e "Running ./ex_BoundedPriorityQueue"
./ex_BoundedPriorityQueue
|
cdc7d3f158b3b930f9ec36d75898680c73f0c2ba55d1a9bcfccce7944d7450e4 | Shell | 83 | 4 | #!/bin/bash
echo -e "# Running ./ex_simpson_integration"
./ex_simpson_integration
|
2411c9c42bba84f8d8d1a9c2c622bdf50247930cc6aeac17cdcd0010f1987ffe | Shell | 85 | 4 | #! /bin/tcsh
{path_software}/cafemol/bin/cafemol input.inp -machinefile > run1.log
|
3bac1af9c25e0afcaa866752a4374c39571ca90ee433d20f339bcb3e9ade1ba3 | Shell | 85 | 4 | #!/bin/bash
echo -e "Running ./ex_InterpolatePeriodic1D"
./ex_InterpolatePeriodic1D
|
c043edeca535f5acb066010a8ed2aca632a94428ecb458869ce52861fd9e71ee | Shell | 85 | 6 | #!/bin/sh
sh mpld.sh
sh mpld_voxelwise.sh
sh mpld_pvc.sh
sh mpld_region_analysis.sh
|
d7735a269eba36e5169261bf05e627bafa2af669fe76e64b3937b2e450d51067 | Shell | 85 | 4 | #!/bin/bash
echo -e "Running ./ex_InterpolatePeriodic2D"
./ex_InterpolatePeriodic2D
|
237c85ae7021120b4d84c7370d4a8d56570fd3d52ae29ed66b34e70b4d5bd47f | Shell | 86 | 5 | #!/bin/bash
for i in $(seq $4)
do
orfm -m $3 -t "$2/orfm_d" $1 > "$2/orfm_p"
done
|
61eb134ea51457836d7a2fa9cf24eaf8ea89a78cd906448ba535b60267f1a954 | Shell | 87 | 2 | export OPENAI_API_KEY='OPENAI_API_KEY'
gunicorn synthesis_parser:server -b 0.0.0.0:8000 |
781074090b0d7edd0e2a6abc16be7d5dcb442e0bd7d18973669902bcf6fe18a2 | Shell | 87 | 3 | #! /bin/bash
docker push bransonlabapt/apt_docker:apt-20260506-tf215-pytorch21-hopper
|
917b9c5b04d19cb1b51cf1e4a2504bf3f61c1b65c2edbb815d37c2299ed3e7eb | Shell | 87 | 4 | #!/bin/bash
echo -e "# Running ./ex_z_matrix_to_cartesian"
./ex_z_matrix_to_cartesian
|
f71b76aca59b037ad46db8804dcb0db153d3a62e63b59185e131c65fc5335b8f | Shell | 87 | 3 | echo Starting kernel module bcm2835_spi_display.ko
sudo insmod bcm2835_spi_display.ko
|
00cf206a34cfa9adc9a457d99c6343e0024dfe85afbe34e0944d51d1b8db6f19 | Shell | 88 | 5 | #!/bin/bash
echo -e "Running ./ex_HierarchicalClustering"
./ex_HierarchicalClustering
|
8665f609474fab9170c1aaed513ae7bf1b2a2f08b6f3ff92db3b39235d1ba18e | Shell | 88 | 5 | cd QM
~/Developer/sharc/bin/SHARC_PYSCF.py QM.in >> QM.log 2>> QM.err
err=$?
exit $err
|
9f37579ffa729246448d5bf5be9b690e9e7dabc9067e54899ed1d34c05d5fcf6 | Shell | 88 | 3 | #! /bin/bash
docker push bransonlabapt/apt_docker:apt-20260506-tf211-pytorch113-ampere
|
ae2f611ca861f024a85d9977aa679006d09e3bf16091ab232a7db4c8e1197e28 | Shell | 88 | 2 | $OVDIR/../bin/wfoverlap.x > ciovl.out
$OVDIR/../bin/wfoverlap.x -f dyson.in > dyson.out
|
fafe31fde06ed1fa43fc9bd9ef24ac64d9670b046769bc625a2ff3b82d4fc22d | Shell | 88 | 4 | #!/bin/bash
. /opt/conda/etc/profile.d/conda.sh
conda activate chexpert-label
exec "$@"
|
d7a687ce0a63c7afe1d483a2fb5441f9acd32ccebd11bff8dc01801a97bf764d | Shell | 89 | 4 | #!/bin/bash
conda activate ./4conda
export RUN_MODE=STUB
python ./src/cal_denoise_app.py
|
9bed3c1c42002eb1c653c3146989ce5fe26b007eb3ffd1fbdfb86eff42d87b40 | Shell | 90 | 2 | #!/bin/bash
CONDA_SUBDIR=osx-64 conda env create --prefix ./4conda -f environment-cpu.yml |
ba2499c620140f0b4ea5cf7cfe440a796fd466b113574cc69ec19e58a83d1539 | Shell | 90 | 2 | #! /bin/bash
PIP_NO_DEPS=1 CONDA_OVERRIDE_CUDA="12.4" conda env create -f environment.yml
|
f538d00cfff6f41efd0d9a2316775ea187756bf12b3a6816bf79ed45b0e61316 | Shell | 90 | 4 | #!/bin/bash
echo -e "#Running ./ex_random_vector_on_sphere"
./ex_random_vector_on_sphere
|
19b4234c860097f48b260c374c153085640547bfb5f59290d2cc2d689bab6aed | Shell | 91 | 5 | #!/bin/bash
# Train model
python3 main.py
# Predict using test data
python3 test_predict.py |
3fd235fbfffce86bedfc1eac3486b995ce585de8ef0560c49f078363df7dcb63 | Shell | 91 | 3 | #!/bin/bash
echo "$DOCKER_PASSWORD" | docker login -u "$DOCKER_USERNAME" --password-stdin
|
eee62e9cd6156596b399b23c57f440b643d6d8664386cc4245548291907a057f | Shell | 91 | 5 | # install PlatformIO
sudo pip install -U platformio
# update PlatformIO
platformio update
|
80142c224c565769bd7567f4d69f55ae3b6a4a57caef3bb936f419da8c553c45 | Shell | 92 | 5 | #!/bin/bash
echo -e "Running ./ex_expectation_maximization"
./ex_expectation_maximization
|
39a6df362bffb95753d0d7c71b40977d71f1d949df5249f28b1a032d82411ac1 | Shell | 96 | 5 | #!/usr/bin/env sh
set -ex
uv run ruff format bayes_opt tests
uv run ruff check bayes_opt --fix
|
b7ce8bd64adb173ab594bbff95a23cfe519202e25037f73592aef531e6d4f87c | Shell | 98 | 4 | #!/bin/bash
echo -e "# Running ./ex_VonMissesDistribution 10000"
./ex_VonMisesDistribution 10000
|
351ed88804983c9ee1c58d912af394a6192c9bdbc68aa80f26f7c9ff3d92d1e1 | Shell | 99 | 8 | #!/bin/bash
if [ -f pop.out ]
then
rm pop.out
fi
$SHARC/populations.py < KEYSTROKES.populations |
806c919226948db3059a461e12cb1b2927e94b4fbcf4c8889759c6c8655ea92c | Shell | 100 | 4 | #!/bin/bash
echo -e "Running ./ex_seq_io ./test_inputs/2gb1.seq"
./ex_seq_io ./test_inputs/2gb1.seq |
80fbfac9cb8748f1eb0387e139801f6d41abbbf6f5e517aa6af0c3141f946fe0 | Shell | 100 | 5 | #!/bin/bash
echo -e "# Running ./ex_RobustDistributionDecorator"
./ex_RobustDistributionDecorator
|
36a32259d292c23be53c9f7df5c87ff09c20e5932555b9b070d6610214e6abdb | Shell | 101 | 8 | #!/bin/bash
if [ -d State_2 ];
then
rm -r State_2
fi
$SHARC/setup_traj.py < KEYSTROKES.setup_traj |
2e0cb97bb11373126bae6a145460c686831b0b81bc5ec0e28a2c0a4525033b70 | Shell | 102 | 4 | #!/bin/sh
Rscript ../utils/4-prep-celda-modules.R "pbmc"
julia -p 31 ../utils/4-celda-pidc.jl "pbmc"
|
3009fd1960bd126f368d31a6345f10a2513f2951f9caaafe49099d6ab7eb666f | Shell | 102 | 3 | docker build -t hornet .
# docker tag hornet ghcr.io/hdegen/hornet
# docker push ghcr.io/hdegen/hornet |
31914a6c83e17ad2fb2dfb9297d7ba74f33b6932761872b80809949090117e5f | Shell | 102 | 4 | #!/bin/sh
Rscript ../utils/4-prep-celda-modules.R "wang"
julia -p 31 ../utils/4-celda-pidc.jl "wang"
|
baac3e26359c68fecc2405f9f315646cda3aac0324ef066dedcd0c205ee1e088 | Shell | 102 | 6 | #!/bin/bash
for FILE in *.py ; do
echo "TESTING:" $FILE
pytest $FILE
[ $? -eq 0 ] || exit 1
done |
40331e25dd6e1c00ba0b4fde9ff74f9dd4c235cccf10b346b71b6d291c8f1e93 | Shell | 103 | 4 | #!/bin/bash
echo -e "# Running ./ex_OptionParser -n=4 -nn=1,2,3,4"
./ex_OptionParser -n=4 -nn=1,2,3,4
|
b6eca8c1fa875c9ca73315f17fcbc315c6841f0fe63218be4502447b1d59af08 | Shell | 103 | 8 | #!/bin/bash
if [ -f crossing.xyz ]
then
rm crossing.xyz
fi
$SHARC/crossing.py < KEYSTROKES.crossing |
d593d4c8881388a5339f4afe63e900dfb88e9171a95f3567cfda3a69831ab20d | Shell | 103 | 2 | #! /usr/bin/env bash
ELEPHANT_PROFILE= kernprof -l -v -o ~/train.py.lprof /opt/elephant/script/eval.py
|
d240bcc5de042160462fd32802278144aee60b6d3d6d709bb574cb8661e3dd5f | Shell | 104 | 5 | #!/usr/bin/env sh
set -ex
uv run ruff format --check bayes_opt tests
uv run ruff check bayes_opt tests
|
6e117bb46af018e288d6888cd9bfb719f15f69026164151d4527f797616d3d19 | Shell | 105 | 4 | #!/bin/bash
echo -e "# Running ./ex_DsspData test_inputs/5edw.dssp"
./ex_DsspData test_inputs/5edw.dssp
|
a9a9f6ab63c6db47cd53e077aeef7e9e4702df32dfa3c3e2036bf70a382466fa | Shell | 107 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_Monomer"
./ex_Monomer
|
ba26dcd5452154752d058cec46d5a8affd2dff1590a211fd1342f83bb0622bc1 | Shell | 107 | 6 | #!/bin/bash
for i in $(seq $4)
do
orfipy --min $3 --bed orfipy_bed --outdir $2 --between-stop $1
done
|
bfdbe1c4b650ca2714d30183359599ba1c9621a63f617b5d81efe456ce70727f | Shell | 108 | 7 | #!/bin/bash
if [ -f initconds.excited ]
then
rm initconds.excited
fi
$SHARC/excite.py < KEYSTROKES.excite |
7dca885a191c1d99774becafb9d1af3f0c05f9d61a4d3b9868d2fec50bfe037d | Shell | 109 | 4 | #!/bin/bash
echo -e "Running ./ap_dssp_to_ss2 test_inputs/5edw.dssp"
./ap_dssp_to_ss2 test_inputs/5edw.dssp
|
5c554154999c5244423d3b56da09b077c62f8c2ba8b48d197f6e41635586e62d | Shell | 110 | 5 | #!/usr/bin/env sh
set -ex
uv run pre-commit install
uv run pre-commit run --all-files --show-diff-on-failure
|
75b3f107bd048ef451b53d052db10a0b1a9156d18ab38bd5db27a05a6e1ad1c1 | Shell | 110 | 4 | cd Extenrnal/SpaOTsc
pip install --user --requirement requirements.txt
pip install --user .
pip install scanpy |
180a20fb047c90b58f73be28ecd31a36c666b824cfa7b099ff870db92f4c151b | Shell | 111 | 1 | python -m grpc_tools.protoc -I./protos --python_out=. --pyi_out=. --grpc_python_out=. ./protos/trans_rpc.proto
|
ab2424cb44dde6d7ed53b694df463dc145ae633d313ab9b62d54f361cdb3cb1d | Shell | 112 | 7 | #!/bin/bash
for FILE in *.py ; do
echo "TESTING:" $FILE
pytest $FILE
[ $? -eq 0 ] || exit 1
sleep 1
done |
4968d670224aa8b99802a2c1d3c3e3a3a553207a14935f934a697291acd11648 | Shell | 113 | 3 | #!/bin/sh
seq 1 11 | parallel -j 3 './evalModel{}.py win500'
seq 1 11 | parallel -j 3 './evalModel{}.py win1000'
|
0dc36734f873f97732bde6d67d2884d852c48bdf5ab1e25fb5581dd02b249626 | Shell | 114 | 3 | #! /bin/bash
docker build --file Dockerfile --tag bransonlabapt/apt_docker:apt-20250626-tf215-pytorch21-hopper .
|
8e7a5ad9c2124e422c77a564da4cbf5032a0c73e802b862da564917d365d358c | Shell | 114 | 3 | #! /bin/bash
docker build --file Dockerfile --tag bransonlabapt/apt_docker:apt-20260506-tf215-pytorch21-hopper .
|
ad3800691001ced2e82edaa0fd070f78d29f4a4fe6bbb29e2036e7c4302fd7a7 | Shell | 114 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
./ap_blastxml_to_hsp test_inputs/1K25_01+PBP_C2.psi
|
da0aefd24e447826fb966b15130e2c64178239fa66f689a537018e84f6742480 | Shell | 114 | 3 | #! /bin/bash
docker build --file Dockerfile --tag bransonlabapt/apt_docker:apt-20250505-tf215-pytorch21-hopper .
|
02dae17efd7f5da7d945f3bc44cbb586ace512e356bdedbd772984c98462a7d9 | Shell | 115 | 1 | singularity exec -e -B /tmp -B `pwd` Docker/trinotate.simg /usr/local/src/Trinotate/run_TrinotateWebserver.pl 8088
|
25434a3cd2f9d3bd954870ffcf656087b032bbf6113191194cb0b073039afce9 | Shell | 115 | 7 | #!/bin/bash
set -e
cd /data
sudo service nginx restart
exec jupyter notebook --no-browser --NotebookApp.token=""
|
893c268f723edf07fc46ed473e5bb4c087443b47dcba183b59015d8ff549a848 | Shell | 115 | 3 | #! /bin/bash
docker build --file Dockerfile --tag bransonlabapt/apt_docker:apt-20260506-tf211-pytorch113-ampere .
|
ad738e6fc66f3b4304a68acc1ad4a9e213abed98cb6f9beb82e1b925f4ed6446 | Shell | 115 | 3 | #!/bin/sh
seq 1 10 | parallel -j 1 './trainModel{}.py win500'
seq 1 10 | parallel -j 1 './trainModel{}.py win1000'
|
64b55fb1c99ffc7158f55551ad920aae50627c751012b1303452587a53c2de4b | Shell | 116 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running: ./ex_alignment_io"
./ex_alignment_io
|
ab0c3360e7fdac3180987da6f7a8a196a602580ce5cca7761990bea275f994bc | Shell | 116 | 7 | #!/bin/bash
echo -e "# Running ./ex_WL_Ising"
./ex_WL_Ising
mkdir -p outputs_from_test
mv *dat outputs_from_test
|
2b6c45e9a0d061295db2c48f8f58cabd97916a416cdbaf80113c3f561231d2a2 | Shell | 117 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_AtomSelector"
./ex_AtomSelector
|
d7d494455ec48a2d44b652bba9ff002834a00032da5371a6bb7ece5880188756 | Shell | 117 | 4 | #!/bin/bash
echo -e "#Running ./ap_chi1_rotamers_estimation"
./ap_chi1_rotamers_estimation test_inputs/THR_chi1.dat
|
bf9a9d182dce018c251ae9891c0442d1664de49047a395323632e7b0f0217cc0 | Shell | 118 | 3 | #!/bin/bash
pip install -r requirements.txt
(cd ./topological_sampling/common/toposample_utilities && pip install .)
|
c6a3132dc6ac8cb1542a0e23cd8a7c48394ec39e1078abfcfca064d7c126cd16 | Shell | 120 | 7 | #!/bin/bash
echo -e "# Running ./ex_REMC_Ising"
./ex_REMC_Ising
mkdir -p outputs_from_test
mv *dat outputs_from_test
|
dc3310426f546339e609912f5bd934bffa1f5aab72a0fa410e1503233c83fdbe | Shell | 120 | 6 | #!/bin/bash
for i in $(seq $4)
do
orfipy --min $3 --dna orfipy_d --pep orfipy_p --outdir $2 --between-stop $1
done
|
e7881894aa00f71c74b28688966c8c5b04705ac012eb487d302987f20fbc9a4d | Shell | 121 | 1 | rsync -av --files-from=passed_256_5.txt vkzohj@172.16.1.100:/PBshare/SEU-ALLEN/Users/zuohan/data/enhanced_soma_images/ ./ |
d7d1b1baa94c1a36e0995a692db304a53c8f28410dc6e4aff5807b107db0850f | Shell | 122 | 4 | #!/bin/bash
echo -e "Running: ./ex_Interpolate1D test_inputs/input.txt 100"
./ex_Interpolate1D test_inputs/input.txt 100
|
2d68dd9f4e0f19fc630390f7ec214cd7dafb666e2cef1fd99ae94b7ca9c75621 | Shell | 124 | 4 | #!/bin/bash
git log --graph --full-history --all --color \
--pretty=format:"%x1b[31m%h%x09%x1b[32m%d%x1b[0m%x20%s"
|
ae1ea15969724711fe923069ccb8d478313c34f01532d6d5b1e20546841af9c4 | Shell | 124 | 4 | set -e
pandoc --from=markdown --to=rst --output=README.rst README.md
python3 setup.py sdist bdist_wheel
twine upload dist/*
|
d413dbcb01ccda02c8a143180e768618f28afc687e558f7917707c66e839f9a3 | Shell | 124 | 1 | CUDA_VISIBLE_DEVICES=0 python phi4_video_audio_SI_baseline_audio2text_conv_all_graph.py --signal graph_100_H --frame_num 10
|
656631ed3235d69ac005a32ace06190d4f59a0704fea73d2496e0e5fd9ca6106 | Shell | 125 | 4 | IK=2
NU=10
NP=5
/Applications/MATLAB_R2021a.app/bin/matlab -nodesktop -nosplash -nodisplay -r "run test1(${IK},${NU},${NP})"
|
afa31fc87aa1d212f001889f9773b147f97e7856665f2ac942f7e3b72ae82fc4 | Shell | 126 | 1 | /pkg/matlab/bin/matlab -nodisplay -nosplash -nodesktop -r "bioMarker='$1';projectId='$2';run('source/step5_stemness.m');exit;" |
cbeec81350842d6a24c58b442de3845ea3d5304e9ead962a616d6429a15ea942 | Shell | 126 | 4 | mkdir -p 3rdparty
cd 3rdparty
wget https://github.com/isl-org/Open3D/archive/refs/tags/v0.13.0.tar.gz
tar -xvzf v0.13.0.tar.gz |
a157b4e43a2efd6cc8406189dc0acf63ef5e01f2b2dfcbc6b2a333fa3766bd83 | Shell | 127 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_web_client"
./ex_web_client > stdout.out
|
23894fcc3671d4fab03a461ff591102690ee26b4d9bfa2197411cf4243d44cc8 | Shell | 128 | 8 | #!/bin/bash
mkdir -p outputs_from_test
echo -e "# Running ./ap_REMC_Rubik -s=wl"
./ap_REMC_Rubik
mv *.dat outputs_from_test
|
9472ba315456f465c85de0f3ef3ccd7271292ed7ddb32c38a5b9b1db1d025560 | Shell | 128 | 3 | #!/bin/bash
echo "Re" | $SHARC/amber_to_initconds.py -t 0.5 molecule.prmtop step_001.rst step_001.rst step_002.rst step_003.rst |
9ee7cd2338a872f5c5133e50bf65bbb75efdb005f331723cf958570cdd360339 | Shell | 128 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "# Running ./ex_SemiglobalAligner "
./ex_SemiglobalAligner
|
aeb270db0ceb92b10df7128bd2298c8b74426ef91519665ace64e749993fb790 | Shell | 128 | 7 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_SelectResidueRange"
./ex_SelectResidueRange
|
156760c425a004dbdfb4d3c4ff15262aa58f87adcd1db3d548aa72567b71b1bd | Shell | 129 | 4 | export nnUNet_raw="your_path"
export nnUNet_preprocessed="your_path"
export nnUNet_results="your_path"
export PATH=$PATH:/usr/bin |
1b7426dc09340bc4db9a5b3802474b4d93e6254a2a1d7dff463f9dd19e92d391 | Shell | 129 | 1 | docker run --rm -it -v `pwd`:/data -p 8088:8088 trinityrnaseq/trinotate /usr/local/src/Trinotate/run_TrinotateWebserver.pl 8088
|
cf0edc3a74a4e8749f009c2f5f27c736ac130d46b7d5bd776df404157ab4ab6d | Shell | 129 | 1 | /pkg/matlab/bin/matlab -nodisplay -nosplash -nodesktop -r "bioMarker='$1';projectId='$2';run('source/step5_nonstemness.m');exit;" |
191ed993f95df7c69a74c35f700643ab0b45d9ddeeca7aecf3371871bb6213b9 | Shell | 131 | 6 | #!/bin/bash
dockerfile=${1}
tag=${2}
docker build -t ${DOCKER_USERNAME}/fuzzy:${tag} -f fuzzy/docker/${dockerfile} fuzzy/docker/
|
381db9f7d83206241dfb9a3fbad73a8fdd84acab4eb6e0c3b49e6042be719e51 | Shell | 131 | 7 | #! user/bin/bash
cd /u/68/trianaa1/unix/Documents/rr/embraceplus/
ls
source config
~/bin/aws s3 sync ${ACCESS_URL} ${LOCAL_PATH}
|
489662666b17fa74064f878731dc46ad8974a3287d09648b6f3bb0be83a9c6bc | Shell | 131 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running ./ex_CartesianToSpherical"
./ex_CartesianToSpherical
|
b655f3a0fbc8ab68f26a20e596416fd4d46a1ea21a89d1c142c2d701a1da8c30 | Shell | 131 | 2 | cp -r input output
python ../DeepH-hybrid/refinerc_DeepH-hybrid.py --input_dir "output" --config "output/rc_config.json" --only_S 0 |
bc8e0ac33677e5b2aeb20f91dbfde85157c705fdbaed9647c4f87d9abefffd3a | Shell | 131 | 6 | #!/bin/bash
VERSION=`cat VERSION.txt`
docker push trinityrnaseq/trinotate:${VERSION}
docker push trinityrnaseq/trinotate:latest
|
385f7373a3b8d7265c182592f9f194f7e4fdc70d75d9afbbadea419a4b241577 | Shell | 133 | 2 | #! /usr/bin/env bash
python /opt/elephant/script/train.py seg /opt/elephant/script/train_configs/check_overfitting_Fluo-N3DH-CE.json
|
cf849a79ef0b36abaeedcfb6928b8ce135c18a73dc328c9255c91f45ce597959 | Shell | 133 | 6 | #!/bin/bash
for i in $(seq $4)
do
orfipy --min $3 --dna orfipy_3_d --pep orfipy_3_p --outdir $2 --start ATG --partial-3 $1
done
|
85bc93927d6058be0aaf4dc67930cf90327d614a38939c30b43d6b72ca065c02 | Shell | 135 | 6 | #!/bin/bash
mkdir -p outputs_from_test
echo -e "Running ./ap_download_pdb 2gb1"
./ap_download_pdb 2gb1
mv 2gb1.pdb outputs_from_test/
|
1c3154f46823ac64756579f29b7a95af978a974672307b3c1b3ca20a4f7aad7c | Shell | 136 | 2 | for i in strc seqc alignc str_align hist clust blast_analyse acorr str_calc ; do $i -hmd -v=CRITICAL 2> t; tail -n +4 t > $i.md; done
|
c05b5d84524628e3f432873c148e4f538e069e90222cd0322d2170147f9ab64f | Shell | 136 | 9 | #!/bin/bash
if [ $# -ne 1 ]
then
echo "Please, give input bam file (full name)"
exit
fi
python ${path2scripts}/tablator.py $1
|
74d27b008f268c255ddf00d6e7533029f97b2ff3a2b13b91ca56565ed29427b4 | Shell | 137 | 2 | echo "Building"
$PYTHON setup.py install --single-version-externally-managed --record=record.txt # Python command to install the script. |
44fa46ec6e38fb454674a2c9615ee13b2ae3d54545d5afb8ef67ac75b2cded1d | Shell | 138 | 6 | #!/bin/bash
export BIOSHELL_DATA_DIR="../../../../../data"
echo -e "Running: ./ex_Cif test_inputs/AA3.cif"
./ex_Cif test_inputs/AA3.cif
|
2624c4e77095415fe464501921fdd207b71effb30bf72b45ba5ae6b38bc6946e | Shell | 139 | 4 | #!/bin/bash
echo -e "# Running ./ex_count_residues_by_type test_inputs/CYP109B1.aln"
./ex_count_residues_by_type test_inputs/CYP109B1.aln
|
2a6f888f69f9a73d42a645f9efc421870dd06e1e29425692f69eecb9ff528445 | Shell | 139 | 3 | #! /bin/bash
apptainer pull apt-20250626-tf215-pytorch21-hopper.sif docker://bransonlabapt/apt_docker:apt-20250626-tf215-pytorch21-hopper
|
560d6593b165f6c694564ebdfae8a2792fe5fc4301cfcd8deaf0650af08b0a50 | Shell | 139 | 6 | #! /usr/bin/env bash
echo "set RUN_ON_FLASK"
export RUN_ON_FLASK=""
echo "#!/usr/bin/env bash\necho RabbitMQ is disabled." > /rabbitmq.sh |
63d2e3891ecc753d0a51a4d782c3699023a785ade7726cda54489922448036d0 | Shell | 139 | 3 | #! /bin/bash
apptainer pull apt-20250505-tf215-pytorch21-hopper.sif docker://bransonlabapt/apt_docker:apt-20250505-tf215-pytorch21-hopper
|
79196312a2aa7e705f402cfefae67cd5129d95d479770aeb2f6f676aa5ffe364 | Shell | 139 | 3 | #! /bin/bash
apptainer pull apt-20260506-tf215-pytorch21-hopper.sif docker://bransonlabapt/apt_docker:apt-20260506-tf215-pytorch21-hopper
|
34aee786cf35ab7a8ade59f3ad735789969ad2abdecfd9b15e00f59f1a2b87ac | Shell | 140 | 2 | #! /usr/bin/env bash
python /opt/elephant/script/train.py seg /opt/elephant/script/train_configs/check_overfitting_Fluo-N3DH-CE_no-aug.json
|
116188e83fb235ba407b2d07d2a9d8a8737a9c12fe6792ceda0fec1247a03fc8 | Shell | 141 | 3 | #! /bin/bash
apptainer pull apt-20260506-tf211-pytorch113-ampere.sif docker://bransonlabapt/apt_docker:apt-20260506-tf211-pytorch113-ampere
|
5ae5dd3e87becc80a174d07bb27d099b7d2d8775824b3b98e28910a5cb3de5ac | Shell | 141 | 4 | #!/bin/bash
echo -e "Running ./ex_read_properties_file test_inputs/input.properties"
./ex_read_properties_file test_inputs/input.properties
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.