sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
bdde256cf3b10398716d299365e9baa59d48c1de1fc21b85e709a1826ddfb15a | Shell | 821 | 25 | #!/bin/bash
## These mkdir steps + ln -s + "mkdir -p logs/NAc_genes" were typically done
## outside the loop at
## https://github.com/LieberInstitute/twas/blob/master/bsp2/compute_weights_indv.sh
## To avoid having to change the file permissions later
## From https://twitter.com/fellgernon/status/1258455434073124865?... |
da203b1b5e4211b9d84b348da6bb0fd08386cc758abf71d2e8f35ae99baef77c | Shell | 825 | 25 | #!/bin/bash
dx login --token TOKEN
subset_num=$1
my_cmd="wget https://www.kingrelatedness.com/Linux-king.tar.gz && \
tar -xzvf Linux-king.tar.gz && \
./king -b subset${subset_num}.bed --kinship --degree 3 --cpus 90 --prefix subset${subset_num}"
bed_file="/notebooks/wes/sample_qc/relatedness/subset$... |
938c256145b0ad2e96657702196eedeef0478ea2f6459ff6a394247d0b5dd95c | Shell | 826 | 22 | #!/bin/bash
dx login --token TOKEN
my_cmd="plink2 --bfile ukb_c1-22_GRCh38_full_analysis_set_plus_decoy_hla_merged \
--out final_array_snps_GRCh38_qc_pass \
--mac 100 --maf 0.01 --hwe 1e-15 --mind 0.1 --geno 0.1 \
--write-snplist --write-samples --no-id-header \
--threads 32"
bed_file=... |
29c2d4985d0d2265be1507b7056a1e70f662007dd827eba33c6914e26db24e8f | Shell | 828 | 32 | #!/usr/bin/env bash
set -e
# Get the directory where the current script is located
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
# Source the common setup file
source "$SCRIPT_DIR/common_setup.sh"
test_container_simple() {
setup_environment
setup_unique_directory
setup_data_directories
... |
3f54a7019076b009da62352ccb0ba9d66cdf44593867766709b8a70a6fb45ec4 | Shell | 828 | 47 | # Adding a fake registration folder containing an identity matrix for group feat analyses - loop through all subjects
# Author: Valeria Oliva
echo -n "where did you mount the Project folder? write path (e.g. for vale it is /home/valeo/) >"
read projectpath
cd ../../../data/BIDS/derivatives/
echo -n "session? 01 o... |
a588402e062627dcc34335982d7490eb8b3946bb52d869617d4234a4820a7422 | Shell | 829 | 38 | #!/bin/bash
# Siwei 09 Dec 2022
# Count BAMs at exon level
featureCounts_path="/home/zhangs3/Data/Tools/subread-2.0.3-Linux-x86_64/bin/featureCounts"
star_ref_genome="/home/zhangs3/Data/Databases/Genomes/CellRanger_10x/refdata-cellranger-arc-GRCh38-2020-A/fasta/genome.fa"
# gencode_v35_gtf="/home/zhangs3/Data/Databas... |
fbeea80a83fffe850718e965388e72cc66b014fa1bfa615ff029a7157df979fd | Shell | 829 | 19 | #!/bin/bash
# SetBackground.sh
#Code adapted from code on Taylor lab github site
export NA=$1
cd ${NA}
# calculate inbetween position for wig
#perl ../inbetween_cpd_format.pl <${NA}_dipy_sorted_minusstrand.bed >${NA}_dipy_inbetween_minusstrand.wig
#perl ../inbetween_cpd_format.pl <${NA}_dipy_sorted_plusstrand.bed >... |
e87363c8875aeb6028f393539d356f286cd44ec39acb08bb522c21edcb4025a3 | Shell | 831 | 22 | #!/usr/bin/env bash
# Regenerate the clubSandwich reference values PyMARE's alignment test reads.
#
# Run from the repository root:
#
# validation/clubsandwich/regenerate.sh
#
# Rewrites pymare/tests/data/clubsandwich_reference.json in place. The
# alignment workflow runs this script and then compares the result nu... |
0cb2675715ecdccf6cbfa80ba7e2307f75be710f7eceb0dc0a8d8015ad3ec5ce | Shell | 832 | 25 | #!/bin/bash
#BSUB -J random_baseline # Job name
#BSUB -n 20 # number of processors
#BSUB -q long # Select queue
#BSUB -o logs_shpc/output-PC3-%J.out # Output file
#BSUB -e logs_shpc/output-PC3-%J.err # Error file
#BSUB -M 5G #... |
50fbe0cffaf1ac6959a3c448c8eadfecd5ee7ed2fa957d22716d94d2d6ed0350 | Shell | 835 | 16 | #!/bin/bash
# You must have Java Development Kit (JDK) 8 (1.8). If higher (>8) then it must
# support --release flag to pin down the version when compiling.
# Always compile with 8 (1.8) to keep backward compatibility.
# In conda, you can get a JDK version that supports --release flag:
# conda install openjdk
javac --... |
b7d90251a1f4c97cd00b9000fa67ecba872b83a4f3b544cc44c6100a1e51ebb6 | Shell | 835 | 24 | # TODO make tutorial_dev_spectral_libraries.ipynb work
DOCS_NBS=$(find ../docs/nbs -name "*.ipynb" | grep -v tutorial_dev_spectral_libraries.ipynb)
# TODO make test_isotope_mp.ipynb work
# Note: multiprocessing in ipynb sometimes suspended on some versions of Windows, ignore the
# corresponding notebook(s) if this occ... |
65eff94f74f004b9dc4b3f9f2e55848f19586a9148a457e0dd10e2eb548c93ad | Shell | 836 | 25 | #!/bin/bash
# python -u "/home/lthpc/zhongzh/RFD4Hist/train_teacher.py" \
# --model ResNet50 \
# --batch_size 64 \
# --learning_rate 0.01 \
# --dataset ivygap \
# > 12_25_ResNet50_lr0.01_teacher.log &
# python -u "/home/lthpc/zhongzh/RFD4Hist/train_teacher.py" \
# --model ResNet18 \
# --batc... |
5cb460564505f823fef716599db853c9efa6432cbb4f98eb19e5ba9e4386eb8e | Shell | 838 | 21 |
for subid in wlsubj049 wlsubj079 wlsubj122 wlsubj123 wlsubj127 wlsubj135 wlsubj138 wlsubj141
do
export SUBJID=$subid
for foldername in mgzfiles niftiles
do
export FLDR=$foldername
DEST_DIR=et2160@greene.hpc.nyu.edu:/scratch/et2160/attentionpRF/derivatives/GLMdenoise/main/sub-${SUBJID}/ses-nyu3t99/
DATA_DIR=/V... |
8b1033dfcd01a1c8a39aa631411636e123ca0a355819510068f6fd8d6b1b2253 | Shell | 841 | 39 | # Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# arg1 = file, arg2 = file it depends on
# enforce using portable C locale
LC_ALL=C
export LC_ALL
action () {
if (test $mode = 0) then
rm -f ../$1
elif (! cmp -s $1 ../$1) then
if (test -z "$2" || test -e ../... |
80e3193748a6650702574401913e726f3ae228a360708bf78129a8746cf224ba | Shell | 843 | 34 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=3G
#SBATCH --job-name=05_deconvolution_hspe_random_subset
#SBATCH -c 1
#SBATCH -o logs/05_deconvolution_hspe_random_subset_%a.txt
#SBATCH -e logs/05_deconvolution_hspe_random_subset_%a.txt
#SBATCH --array=418,429,853,859,863,882,918,924,935,953,958,964,969,983,988,992,996,999... |
04d30004339c0cf08426b2fc57c2b87fe4a0df37e17194e973c0c1080e6c53cb | Shell | 845 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=09_deconvolution_Mathys_hspe_MeanRatio_top25
#SBATCH -c 1
#SBATCH -o logs/09_deconvolution_Mathys_hspe_MeanRatio_top25.txt
#SBATCH -e logs/09_deconvolution_Mathys_hspe_MeanRatio_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date... |
605d1ad3f28ccfd3ebae0b69acf1db0f6bfc02850682f455bd61aed89a87f3c9 | Shell | 847 | 37 | #!/bin/bash
# - Blue Brain Project -
# This script builds the mod extensions to neurodamus. The folder gets named _lib
set -euxo pipefail
CORE_DIR="$1"
if [ -d _lib ]; then
exit 0
fi
# Get the common synapses
COMMON_DIR=_common
if [ -d "$COMMON_DIR" ]; then
( cd "$COMMON_DIR" && git pull --quiet )
else
... |
39ddf643d4cca08f042365dc6e645d828d927ecead82c49e0d151eba3525bfbd | Shell | 848 | 26 | #!/bin/bash
# Description: Downloads and unzips all pdb files
pdb_download_dir="../data/download_dir"
mkdir -p "$pdb_download_dir"
echo "Downloading PDB database"
rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 rsync.rcsb.org::ftp_data/structures/divided/pdb/ "$pdb_download... |
9473833d34414330ce893b2dfd24d850df003fb1239a073f57cac02b73e1d1e9 | Shell | 848 | 13 | s=$1 # with ${s}_R1.fq.gz and ${s}_R2.fq.gz in the working directory
p="path-to-cell-id-reference" # build a bowtie index on cell_id_full.fa
reachtools combine2 ${s} ## reachtools combine3 ${s} if use 384-plex format
### version for bowtie will chage for use of this step
zcat ${s}_combined.fq.gz | bowtie ${p} - --norc... |
68c4287fe65826104fa8fb2692726ea0e1c8486b988d06526e9bc3d5e8344a14 | Shell | 849 | 24 | #!/usr/bin/env bash
ROOT_DIR=examples/deep-activity-rec/ibrahim16-cvpr
# Phase 1 artifacts
rm -r $ROOT_DIR/p1-network1/test-leveldb
rm -r $ROOT_DIR/p1-network1/trainval-leveldb
rm $ROOT_DIR/p1-network1/mean.binaryproto
rm $ROOT_DIR/p1-network1/z_log_dataset_net1.txt
rm $ROOT_DIR/p1-network1/z_trainval-test-log.txt
rm... |
4cd8de677a9edaef2d772b4c793e87aa3ce1e56b2d632da0fe726e39983bb5e9 | Shell | 856 | 24 | #!/usr/bin/env bash
ROOT_DIR=examples/deep-activity-rec/ibrahim16-cvpr-simple
# Phase 1 artifacts
rm -r $ROOT_DIR/p1-network1/test-leveldb
rm -r $ROOT_DIR/p1-network1/trainval-leveldb
rm $ROOT_DIR/p1-network1/mean.binaryproto
rm $ROOT_DIR/p1-network1/z_log_dataset_net1.txt
rm $ROOT_DIR/p1-network1/z_trainval-test-log... |
c644ec9b50f78e4f8e541e04882bf86b0b5752e22e9bd2339e0bd0e9abedac16 | Shell | 856 | 26 | #!/bin/bash
# Define the path to the settings.xml file
SETTINGS_FILE="/tmp/settings.xml"
# Check if HTTP_PROXY is set and not equal to "false"
if [ -n "$HTTP_PROXY" ] && [ "$HTTP_PROXY" != "false" ]; then
# Extract host and port from HTTP_PROXY
PROXY_HOST=$(echo "${HTTP_PROXY#*//}" | cut -d ':' -f 1)
PROXY_PORT... |
cefa22c48347dc8df96562ec814f1dd58d80f96d77f14ce2b2fb6c35709c08d5 | Shell | 860 | 18 | #!/bin/bash
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -p ph... |
aa596cc10fd6a2db8db5e34205a9c7196be1de4d8a366c5b1d59c13d53987dc8 | Shell | 863 | 29 | #!/bin/bash
IDENTIFIERS=$( jq -r '.data_form.identifiers[]' ${WORKFLOW_DIR}/conf/conf.json )
SELECTED_MODELS=$( jq -r '.workflow_form.models[]' ${WORKFLOW_DIR}/conf/conf.json )
TOTAL_SELECTED=false
for MODEL in $SELECTED_MODELS; do
if [ "$MODEL" = "total" ]; then
TOTAL_SELECTED=true
break
fi
do... |
b01c02aa8c299f80af0ef51397055b986c26473c8b6cbe03eb721e8b90d5f733 | Shell | 863 | 27 | # Write subject batch script to run DSIStudio.sh on Amarel
subj=$1
scriptsDir="/projects/f_mc1689_1/ReliableFC/docs/scripts/diffusion"
batchDir="${scriptsDir}/batchScripts/"
cd ${batchDir}
batchFilename=DSI-${subj}.sh
echo "#!/bin/bash" > $batchFilename
echo "#SBATCH --nodes=1" >> $batchFilename
echo "#SBATCH --nt... |
cde4bd42dfd0494c0cf263a288180ad9c56e100d88ba567204eae7635e7c614b | Shell | 863 | 33 | #!/bin/bash -e
lmpbin=$1
if [ ! -f $lmpbin ]; then
echo "LAMMPS binary '$lmpbin' is not a file"
exit 1
fi
ref_out="plate_cap.csv"
ref_mix_out="plate_cap_eta_mix.csv"
if [ ! -f $ref_out ] || [ ! -f $ref_mix_out ]; then
echo "Generating reference data"
python3 plate_cap.py
fi
echo "Running Lammps input... |
12dd931517605eb3200c1b285888426ed8d18d1699f32e337612651fb14e0d83 | Shell | 864 | 23 | #!/bin/bash
#3_count.sh
#cjm 2024/12/05
#job submission script for making count tables from reads for scRNAseq analysis.
#define some variables to make this more reuseable
#transcriptome index path
txome="/work/cjm124/scRNAanalysis/Lvar3"
#data directory path
fastqs="/work/cjm124/scRNAanalysis/reads"
cd $fastqs... |
1e4ed7e98dc8eaacea81d5f8b96b7d7f0773b15e36787ba0c0cd1dd22a5e0d8b | Shell | 865 | 38 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
# source activate /SAN/vyplab/vyplab_reference_genomes/conda_envs/splicing_env/
WORKFLOW="workflows/${1}.smk"
if [ "$2" != "... |
c3f3702615b683bd3c9a5a24eb8886e8719dc589396e6720f840f41f2f72eac5 | Shell | 867 | 41 | #!/bin/bash
# set our directories
cd ..
dir_out=$(pwd)
dir_res="$dir_out/results_tstt/"
dir_hel="$dir_out/helpers/"
for FILE in $dir_res/*_tfce_corrp_*.nii.gz
do
:
echo $FILE >> "$dir_hel/out_results.txt"
fslstats $FILE -l 0.95 -V >> "$dir_hel/out_results.txt"
done
dir_res="$dir_out/results_ostt/"
for FILE... |
487586d97bc01b261c56c845881b2136ace9e0f88d8e2aa224e434653674cbab | Shell | 868 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=04_deconvolution_DWLS_1vALL_top25
#SBATCH -c 1
#SBATCH -o logs/04_deconvolution_DWLS_1vALL_top25.txt
#SBATCH -e logs/04_deconvolution_DWLS_1vALL_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
ech... |
a875e697f4c78681a9feccb252102a67f6670c697403ccf684088fd343a3ffd0 | Shell | 870 | 39 | #!/bin/bash
#SBATCH --job-name=rss_script_slurm
#SBATCH --partition=q48,q40,q36,q28,q24
#SBATCH --mem=10G
#SBATCH --nodes=1
#SBATCH --time=01:00:00
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --array=1-50%50
echo "========= Job started at `date` =========="
echo "My jobid: $SLURM_JOB_ID"
echo "My ar... |
ad76520b8beb7cdd2f82d3cf862cba7fec12bce052ec51edbdb88b7a8bee228e | Shell | 870 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=02_deconvolution_MuSiC_1vALL_top25
#SBATCH -c 1
#SBATCH -o logs/02_deconvolution_MuSiC_1vALL_top25.txt
#SBATCH -e logs/02_deconvolution_MuSiC_1vALL_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
... |
ceb17925eda69e0bc98da83d39578a6a5e2fb9cb47cf07e95ed55034c5ff324b | Shell | 870 | 27 | #!/bin/zsh
# set up to run on the mac studio
#!/bin/zsh
WORK_DIRECTORY=/Volumes/LaCie/
export PATH=$PATH:/Users/paulinoramirez/program/samtools-1.16.1/
for R1 in *.fastq.gz;do
#code to skip aligning sample fastq files if a corresponding sample bam file exists
if [ -e $WORK_DIRECTORY/DRS_compairison/results/fl... |
73f450d6f711818103c85e937886de974a58524262e61772bc00e81cbd4260ec | Shell | 871 | 12 | #!/bin/bash
AFNI SurfFWHM \
-input /data/p_02495/dhcp_derivatives/dhcp_surface/sub-CC00058XX09/ses-11300/func/sub-CC00058XX09_ses-11300_hemi-L_space-T2w_desc-simulatedsmoothed_bold_tmp.func.gii \
-i_gii /data/p_02495/dhcp_derivatives/dhcp_anat_pipeline/sub-CC00058XX09/ses-11300/anat/sub-CC00058XX09_ses-11300_h... |
e42583332e745f3607313016194bd0f5012054caf87138e32d466f56f260ee6a | Shell | 871 | 8 | ~/bin/blast-2.2.18/bin/megablast -d ~/genomes/CDS_sequence_hg19_06272013 -i $1 -e 1 -D 3 -v 3 > $2_reads_vs_CDS.tab
~/bin/blast-2.2.18/bin/megablast -d ~/genomes/mRNA_sequence_hg19_06272013 -i $1 -e 1 -D 3 -v 3 > $2_reads_vs_mRNA.tab
~/bin/blast-2.2.18/bin/megablast -d ~/genomes/rnaseq_contaminants_07312013 -i $1 -e... |
1d0c26e8dd2ba4899895ccd8a48c8758711ea2ecdf87e267c04c7e68ba86458b | Shell | 873 | 44 | #!/bin/bash
# Siwei 01 Jun 2023
# Count BAMs use the unified peakset used in Kosoy et al., Nat Genet 2022
# use an SAF file
featureCounts_path="/home/zhangs3/Data/Tools/subread-2.0.3-Linux-x86_64/bin/featureCounts"
ref_genome="/home/zhangs3/Data/Databases/Genomes/CellRanger_10x/refdata-cellranger-arc-GRCh38-2020-A/fa... |
877079c8982d3836477c8917e509bb0f1d87395533bc9ee34df5861cbf775d2f | Shell | 876 | 36 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=40G
#SBATCH --job-name=08_bisque_donor_subset
#SBATCH -c 4
#SBATCH -t 3:00:00
#SBATCH -o logs/08_bisque_donor_subset_%a.txt
#SBATCH -e /dcs04/lieber/lcolladotor/deconvolution_LIBD4030/Human_DLPFC_Deconvolution/code/13_PEC_deconvolution/logs/08_bisque_donor_subset_%a.txt
#SBAT... |
f5de4c5ff50200f28be3bf0d5fbd83af015437c7422d06febfb42a5e2c299061 | Shell | 876 | 26 | #!/bin/bash
# This file takes a mol2 and uses tleap to convert to PDB, then OpenBabel to
# convert to SMILES. This is done because these mol2 files use AMBER types and
# don't have any element names, so e.g. Os is parsed incorrectly as Osmium.
to_smi=$(realpath lib/to_smi.sh)
cd smi/PhEthOH
echo "Unzipping PhEthOH... |
13ca3ef35f63aa909eb8946524de8d8a3783a9a770f8c18eff455c763a52942b | Shell | 879 | 23 | #!/bin/bash
#K. Castellano
module load Trimmomatic/v0.39
fileList="5FBS_D20_S276 5FBS_D182_S279 5FBS_D313_S282 5FBS_D445_S285 5FBS_D738_S288 10FBS_D20_S277 10FBS_D182_S280 10FBS_D313_S283 10FBS_D445_S286 10FBS_D738_S289 15FBS_D20_S278 15FBS_D182_S281 15FBS_D313_S284 15FBS_D445_S287 15FBS_D738_S290"
path=<path to file... |
aed55df5c884db44a5f7f0005742d3abc2c90f0b4f7dcd90dfff899de7d7e02e | Shell | 879 | 29 | #!/bin/bash
# brew install boost
# Py35: compatibility issue during conda installation with py35, so version ignored
# Py36: issue during compilation with py36, so version ignored
# conda create --name cp37 python=3.7 pip wheel swig numpy delocate twine
# conda create --name cp38 python=3.8 pip wheel swig numpy deloca... |
df7bd34884e82e5e2ef0eac247435fb9e962bdf9254b12299186f3b7663e1d5b | Shell | 879 | 36 | #!/bin/bash
# Siwei 19 Jan 2023
# Direct count for 20 SNP sites designed for ABE/CBE multiplex editing
# Use CombineGVCFs and GenotypeGVCFs to jointly genotype all gvcf files produced from the previous step
vcf_suffix="_12Nov_use_known_genotyping.g.vcf"
gatk4="/home/zhangs3/Data/Tools/gatk-4.2.6.1/gatk"
ref_path="/h... |
fae5b838b48b4e629beea8c22a7ef5e5869994f1f96659164df2ad1285afe079 | Shell | 879 | 23 | #!/bin/bash
#BSUB -J figure_3_stats # Job name
#BSUB -n 20 # number of processors
#BSUB -q long # Select queue
#BSUB -o logs_shpc/output-figure3-%J.out # Output file
#BSUB -e logs_shpc/output-figure3-%J.err # Error file
#BSUB -M 5G ... |
8957b96591f1a0800b1d4f80f94f6339fd50025f036c20b3afb642cccb96c326 | Shell | 880 | 9 | #!/usr/bin/env bash
echo 'iCLIP coverage for spliced exon starts, SH-SY5Y expressed background'
Rscript scripts/cl_iclip_coverage.R -r processed/iclip_regions/2023-12-14_papa_cryptic_spliced.background_shsy5y.le_start.bed -i data/iCLIP/tardbp-shsy5y.concat.sort.chr.bed -c data/GRCh38.primary_assembly.genome.chromsize... |
e666875f0c4b76ab9d67f34fbb1356343c4f33d159347c9a37f06b7ea395d0d5 | Shell | 880 | 20 | #!/bin/bash
# First arg is the bam file to process
# Get the directory where the script is located
SCRIPT_DIR=$(dirname "$0")
if samtools quickcheck $1; then
echo "$(date) Found new file, Index"
samtools index -@ 4 $1
echo "$(date) Pileup"
modkit pileup --ref $SCRIPT_DIR/files/hg19.fa --include-bed $SCRIPT_DIR/f... |
49d8015f37958e7d47b4eae8a14ca73c7e72636c45729e0ca1a855652acf303b | Shell | 882 | 32 | #!/bin/bash
### Window requires pyinstall v2.1
wine msiexec -i python-2.7.8.msi
wine pywin32-218.win32-py2.7.exe
wine PyQt4-4.11.4-gpl-Py2.7-Qt4.8.7-x32.exe
wine lxml-3.7.3.win32-py2.7.exe
THIS_SCRIPT_PATH=`readlink -f $0`
THIS_SCRIPT_DIR=`dirname ${THIS_SCRIPT_PATH}`
cd pyinstaller
git checkout v2.1
cd ${THIS_SCRIPT_... |
b1b83570dc80f372082718b1fa9264aa192f73382357e8289120fc1aee536ce6 | Shell | 883 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=04_deconvolution_DWLS_MeanRatio_MAD3
#SBATCH -c 1
#SBATCH -o logs/04_deconvolution_DWLS_MeanRatio_MAD3.txt
#SBATCH -e logs/04_deconvolution_DWLS_MeanRatio_MAD3.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ... |
808a534499cfd4ba0f3a0fc8f17cf7c2174754a56118ab40dcd17b2150deba5e | Shell | 884 | 23 | #!/bin/bash
#BSUB -J plot_figure_4_stats # Job name
#BSUB -n 20 # number of processors
#BSUB -q long # Select queue
#BSUB -o logs_shpc/output-figure3-%J.out # Output file
#BSUB -e logs_shpc/output-figure3-%J.err # Error file
#BSUB -M 5G ... |
0aca2e6325725f84c51b738e13a2062d36bf10851aba8eeb5d2522ede694fd5b | Shell | 885 | 35 | set -e
if [ "$DP_VARIANT" = "cuda" ]; then
CUDA_ARGS="-DUSE_CUDA_TOOLKIT=TRUE"
elif [ "$DP_VARIANT" = "rocm" ]; then
CUDA_ARGS="-DUSE_ROCM_TOOLKIT=TRUE"
fi
#------------------
SCRIPT_PATH=$(dirname $(realpath -s $0))
if [ -z "$INSTALL_PREFIX" ]; then
INSTALL_PREFIX=$(realpath -s ${SCRIPT_PATH}/../../dp)
fi
mkdir -... |
d9be883df936c243da4fbee79a445558c12b2e1a5fb53b811e3c7f4d030ba611 | Shell | 885 | 29 | #!/bin/bash
set -euf -o pipefail
TOKEN=$KAAPANA_READTHEDOCS_TOKEN
COMMIT=$CI_COMMIT_SHA
curl -sf -H "Authorization: Token $TOKEN" \
https://readthedocs.org/api/v3/projects/kaapana/builds/ -o builds.json
# Newest completed "latest" build for this commit; builds still running have
# success == null and are skipped... |
97e6070b5a9a7d9f01f2f957f5de43799e7bdfb1ba267b3649ae223fdfe3b41a | Shell | 887 | 28 | #!/bin/bash
# helper script to convert all jupyter notebooks in the preprocessing folder to python scripts without having to open up jupyter lab
# Get the directory of the script (preprocessing folder)
NOTEBOOK_DIR="$(dirname "$0")"
echo "Starting conversion of Jupyter notebooks to Python scripts in directory: $NOTEB... |
a0523702ddfc5620190d72dde07f8df5bb41b8c703328857c70f90612fe0d4b3 | Shell | 887 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=02_deconvolution_MuSiC_MeanRatio_MAD3
#SBATCH -c 1
#SBATCH -o logs/02_deconvolution_MuSiC_MeanRatio_MAD3.txt
#SBATCH -e logs/02_deconvolution_MuSiC_MeanRatio_MAD3.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE in... |
03a3b8c532f9433f4ed5d77f3d5e7939bc243587d0e26047c21839f65b1a5033 | Shell | 888 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=04_deconvolution_DWLS_MeanRatio_top25
#SBATCH -c 1
#SBATCH -o logs/04_deconvolution_DWLS_MeanRatio_top25.txt
#SBATCH -e logs/04_deconvolution_DWLS_MeanRatio_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE in... |
e0698a69e939689eba2c1de15572bce481c57fcebcb0966ee0ccfe5a74fa79dd | Shell | 888 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=04_deconvolution_DWLS_MeanRatio_over2
#SBATCH -c 1
#SBATCH -o logs/04_deconvolution_DWLS_MeanRatio_over2.txt
#SBATCH -e logs/04_deconvolution_DWLS_MeanRatio_over2.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE in... |
598f384ffcf3814bc5d1c198a2860c799286d4bc485f7a0c16a540c5f6357453 | Shell | 890 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=08_deconvolution_Mathys_Bisque
#SBATCH -c 1
#SBATCH -o logs/08_deconvolution_Mathys_Bisque.txt
#SBATCH -e logs/08_deconvolution_Mathys_Bisque.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ... |
dc663c488de9628b5f54171372832ba814bf645695ebdaaa3ea8d86867553ad0 | Shell | 890 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=02_deconvolution_MuSiC_MeanRatio_top25
#SBATCH -c 1
#SBATCH -o logs/02_deconvolution_MuSiC_MeanRatio_top25.txt
#SBATCH -e logs/02_deconvolution_MuSiC_MeanRatio_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE... |
dcf56ea11a1adf045ea228b9f5b496b6c66a53d09e2ee1781efc40f2b7edd3f6 | Shell | 891 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=01_deconvolution_Bisque_MeanRatio_MAD3
#SBATCH -c 1
#SBATCH -o logs/01_deconvolution_Bisque_MeanRatio_MAD3.txt
#SBATCH -e logs/01_deconvolution_Bisque_MeanRatio_MAD3.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE... |
36e6ab6ed61b210cefcf336a32d297423fe8b4638687f501abe96ebc8d0a7732 | Shell | 892 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=02_deconvolution_MuSiC_MeanRatio_over2
#SBATCH -c 1
#SBATCH -o logs/02_deconvolution_MuSiC_MeanRatio_over2.txt
#SBATCH -e logs/02_deconvolution_MuSiC_MeanRatio_over2.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE... |
55b7e606109526b2616ddae3c920cdc3c2cd3c0c11969f2bf439608527e71e8b | Shell | 893 | 29 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=80
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
#... |
20b05314275dea277272117c6bb57c7b894a577c0e2868aa70a9aa0e21ee5b94 | Shell | 895 | 35 | #!/bin/bash
traits=("scz" "bpd" "asd" "epilepsy")
for trait in "${traits[@]}"; do
snploc="./gwas_files/${trait}.magma.input.snp.chr.loc.txt"
ncbi38="./magma_files/geneloc/NCBI38.gene.loc"
# Annotate SNPs
~/tools/magma/magma --annotate \
--snp-loc ${snploc} \
--gene-loc ${ncbi38} \
... |
718c386cf12cb5d95719fd802f203be2c50fa20dd42d1f6ed96fa3cc2c426bf8 | Shell | 896 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=01_deconvolution_Bisque_MeanRatio_over2
#SBATCH -c 1
#SBATCH -o logs/01_deconvolution_Bisque_MeanRatio_over2.txt
#SBATCH -e logs/01_deconvolution_Bisque_MeanRatio_over2.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JH... |
20a38a9481475175173f127f6e202f86a18950cfb0d16b98721e6fd1e1af22c7 | Shell | 899 | 39 | #!/bin/bash
# Siwei 13 May 2021
# extract vcf files generated from WASPed bams and HaplotypeCaller,
# retain GT of 0/1 (isHet == 1) only
# init
gatk4="/home/zhangs3/Data/Tools/gatk-4.1.8.1/gatk"
ref_path="/home/zhangs3/Data/Databases/Genomes/hg38"
ref_genome="/home/zhangs3/Data/Databases/Genomes/hg38/INDEX/Homo_sapi... |
0206d947581f9275aaaddab3311c94483679289b6ce8688d86d242d06f694bad | Shell | 900 | 37 | #!/bin/bash
set -e
cd downloads
# Check if there are any split tar files in the current directory
if [ "$(ls 2>/dev/null -Ubad1 -- *.tar.gz.* | wc -l)" -gt 0 ]; then
# Declare an associative array to store unique tar file prefixes
declare -A tar_prefixes
# Populate the array with unique prefixes from the ... |
bddfb688ebcbf841a184521b314e92b1ec7616d28f338b00d252feac01d72a4f | Shell | 900 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=100G
#SBATCH --job-name=06_deconvolution_BayesPrism_1vALL_top25
#SBATCH -c 1
#SBATCH -o logs/06_deconvolution_BayesPrism_1vALL_top25.txt
#SBATCH -e logs/06_deconvolution_BayesPrism_1vALL_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** J... |
3dc1e9057642641b99d8385ff76cf645e9c7576edbe4d71c6fbe157cd8d2b26e | Shell | 902 | 20 | #!/bin/bash
#K. Castellano
module load htseq/v2.0.4
fileList="trim_10FBS_D445_S286 trim_10FBS_D738_S289 trim_15FBS_D182_S281 trim_15FBS_D20_S278 trim_15FBS_D313_S284 trim_15FBS_D445_S287 trim_15FBS_D738_S290 trim_5FBS_D182_S279 trim_5FBS_D20_S276 trim_5FBS_D313_S282 trim_5FBS_D445_S285 trim_5FBS_D738_S288 trim_10FBS_... |
0ef961e008327028257656e3371e174878f4cbf3614dc389b460189e74cecb2b | Shell | 903 | 24 | #!/bin/bash
if [ -z "$GAZEBO_MODEL_PATH" ]; then
bash -c 'echo "export GAZEBO_MODEL_PATH=$GAZEBO_MODEL_PATH:"`pwd`/../assets/models >> ~/.bashrc'
else
bash -c 'sed "s,GAZEBO_MODEL_PATH=[^;]*,'GAZEBO_MODEL_PATH=`pwd`/../assets/models'," -i ~/.bashrc'
fi
if [ -z "$ARDUPILOT_PATH" ]; then
bash -c 'echo "export ARD... |
94b59998d3d01f0492b4bd74b0ef1cf1df436e676ca82ffdc0854f3866e667b1 | Shell | 904 | 20 |
get_dynamic_contacts.py --topology dhfr_4m6l_top.psf --trajectory dhfr_4m6l_trj.dcd \
--itypes hb --sele "protein or resname 21V NAP" --output dhfr_4m6l_hb_contacts.tsv
get_contact_frequencies.py --input_files dhfr_4m6l_hb_contacts.tsv \
--itypes hbls hblb lwb lwb2 --label_file dhfr_4m6l_labels.tsv \
-... |
9bc74159d2ed668e54aedc3e09bd08366ae87d457a333d40d13c4edea82fdacd | Shell | 904 | 30 | #!/bin/sh
if [ $# != 2 ]
then
echo "usage: $0 <pngfile> <iconset name>"
exit 1
fi
png="$1"
ico="$2"
if [ ! -f ${png} ]
then
echo "PNG Image $1 not found"
fi
rm -rf ${ico}.iconset
mkdir ${ico}.iconset
sips -z 16 16 ${png} --out ${ico}.iconset/icon_16x16.png
sips -z 32 32 ${png} --out ${ico}.iconset/... |
3b328e2af3c90fca252acf8c2236c45f40ab180e69044dd8cadbdbe1a995094b | Shell | 912 | 16 | #!/bin/bash
set -eu
# Disable security token for Jupyter lab
sed -i "s/^.*ServerApp.token.*$/c.ServerApp.token = ''/g" /kaapana/app/.jupyter/jupyter_lab_config.py
sed -i "s+^.*ServerApp.base_url.*$+c.ServerApp.base_url = '$INGRESS_PATH'+g" /kaapana/app/.jupyter/jupyter_lab_config.py
sed -i "s+^.*ServerApp.root_dir.*$... |
dbaf1e1f521254f2306d26cfe54fd0b162a26b34f4ff38065bb3cf93087de09a | Shell | 913 | 31 | #!/bin/bash
# @author Marcus A. Triplett (2022), Columbia University
set -e
source activate neurocaas
userhome="/home/ubuntu/"
echo "---- DOWNLOADING DATA ----"
neurocaas-contrib workflow get-data
neurocaas-contrib workflow get-config
echo "---- PARSING PATHS ----"
datapath=$(neurocaas-contrib workflow get-datapath... |
e49fdeede0b2abf23f27640fcf8c344b6cabe4090da60792fbc9809907f452e7 | Shell | 914 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=75G
#SBATCH --job-name=06_deconvolution_BayesPrism_MeanRatio_MAD3
#SBATCH -c 1
#SBATCH -o logs/06_deconvolution_BayesPrism_MeanRatio_MAD3.txt
#SBATCH -e logs/06_deconvolution_BayesPrism_MeanRatio_MAD3.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo... |
7d6b2ba58b1400d6260c8d640c0be12336bda4eddfe1df5b85e7c06bd9086e79 | Shell | 915 | 34 | #!/bin/bash
# This script makes the _version table for each schema in BigQuery,
# Currently hard-coded to the status as of 2025-04-20.
export METADATA_TABLE="_metadata"
# create an array of target datasets and versions
# loop through them at the same time
datasets=(
"mimiciv_icu:3.1"
"mimiciv_hosp:3.1"
"mimiciv_... |
a6df07b3bcc802535d41c65ed5c9c6f4275dd68f26bc381b28d628adc56e9aaa | Shell | 916 | 39 | # Apply registration to the denoised brain images (single subject)
#Author: Valeria Oliva
echo -n "Which sub? Only type number >"
read subject
echo -n "session? 01 or 02 >"
read ses
cd ../../../data/BIDS/derivatives/sub-NSPilot${subject}/ses-${ses}brain/func/feat_analyses
for scan in FingerTap ForceAbs ForcePerce... |
3cf3a6134cce6331807c713c97bf292e76b627e30373f143feb1340ed6933a07 | Shell | 918 | 28 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=400
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
... |
ea7c8c88717ef0bdf0b9eaa185dae657a2e692f66cb9926fcb63df66a7ee9716 | Shell | 918 | 47 | #!/bin/bash
#PBS -q celltypes
#PBS -l walltime=24:00:00
#PBS -l nodes=16:ppn=16
#PBS -l mem=150g
#PBS -N dend_opt
#PBS -e /dev/null
#PBS -o /dev/null
#PBS -r n
#PBS -m bea
cd $PBS_O_WORKDIR
set -e
source activate ateam_opt
# Relaunch batch job if not finished
qsub -W depend=afternotok:$PBS_JOBID batch_job.sh
# C... |
ec6bd2fea9a57f7ae44a9e3a8caf3afd47b641e7d45bb1384060b4e12493fb3c | Shell | 919 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=75G
#SBATCH --job-name=06_deconvolution_BayesPrism_MeanRatio_over2
#SBATCH -c 1
#SBATCH -o logs/06_deconvolution_BayesPrism_MeanRatio_over2.txt
#SBATCH -e logs/06_deconvolution_BayesPrism_MeanRatio_over2.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
e... |
97394d5fdccb80054d3dd2359210463d6ea4475e9431edf1d99145fd4e91c8bf | Shell | 920 | 23 | # Create brain and spinal cord physiological regressors for PNM using Ken's script with appropriate arguments for the Neuromuscular Signature Pilot project
# Auhor: Valeria Oliva
echo -n "sub? Only insert number >"
read subject
echo -n "session? 01 or 02 >"
read ses
cd ../../../data/BIDS/derivatives/sub-NSPilot${su... |
9f794a20f5487cb20d5a60bb6326a480fc99fc99fabad3112bb296a7fcfa1796 | Shell | 920 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=100G
#SBATCH --job-name=06_deconvolution_BayesPrism_MeanRatio_top25
#SBATCH -c 1
#SBATCH -o logs/06_deconvolution_BayesPrism_MeanRatio_top25.txt
#SBATCH -e logs/06_deconvolution_BayesPrism_MeanRatio_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
... |
a9ee5749bb53df260125d1488c4966dc79d0bdbe61e722cd26f506b84c556ede | Shell | 920 | 38 | #!/bin/bash
# This script computes the framewise displacement (FD) that will be used for censoring.
# -----------------------------------------------------------
# Script written by Ludovico Coletta
# Nilab, FBK (2022)
# -----------------------------------------------------------
function compute_fd {
ts=$1
... |
32a90bae3c5935247ecaa520e53884e0887dab0301c4f234b3c2065a9d7a7b7b | Shell | 921 | 40 | #!/bin/bash
# Retry a command only when it was terminated by SIGTERM (128 + SIGTERM = 143).
#
# GitHub-hosted runners have intermittently terminated the LAMMPS pytest
# process without a Python, LAMMPS, or MPI error. Retrying only exit code 143
# masks that external transient while preserving every actionable test fa... |
7f7856eb6a357b15854e4884bd2df161ebfdf37be4d3b73b7a72d04f33184197 | Shell | 921 | 45 | #! /bin/bash
# collect BAM insert size (1 txt for eachfile)
[[ -d ./tss_sumstat ]] &&
rm -r tss_sumstats
mkdir -p tss_sumstats
# find all WASPed.bam files
mapfile -d $'\0' BAMs_to_count < <(find . -type f -name "*WASPed.bam" -print0)
for ((i=0; i<${#BAMs_to_count[@]}; i++))
do
echo ${BAMs_to_count[$i]}
## test... |
34f5dc0de29bac6ecc2f8d4d413b8884dcd6fce493f826846331892a63a2323a | Shell | 922 | 29 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=20
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
#... |
af3eb4c27b2b8848d98fc5217ef232edeb5662a529d6832e083352b080047a5a | Shell | 922 | 27 | # Write subject batch script to run createMasks_afni_subj.sh on Amarel
subj=$1
scriptsDir="/projects/f_mc1689_1/ReliableFC/docs/scripts/postprocessing"
batchDir="${scriptsDir}/batchScripts/"
cd ${batchDir}
batchFilename=createMasks-${subj}.sh
echo "#!/bin/bash" > $batchFilename
echo "#SBATCH --nodes=1" >> $batchFi... |
e2b7ba89ee832bbf1110f3fc2ebbdcb08a92a8f4c9ddadbd095a09a256034c07 | Shell | 922 | 32 | #!/bin/sh
# Prepare test-images
if [ ! -d tmp ]; then
echo building test image ...
mkdir tmp/
vips colourspace images/sample2.v tmp/t1.v srgb
vips replicate tmp/t1.v tmp/t2.v 20 15
vips extract_area tmp/t2.v tmp/x.tif[tile] 0 0 5000 5000
vips copy tmp/x.tif tmp/x.jpg
vipsheader tmp/x.tif
fi
# tune your syste... |
47ca48a9ab2e7a87acdfe9d032fabe3240b1c730887c7467dc51cf8d02601383 | Shell | 923 | 43 | #!/bin/bash
function reg_points_to_subj {
point=$1
path_to_sub=$2
sub_id=$(basename $path_to_sub)
point_name=$(basename $point .nii.gz)
flirt \
-in $point \
-ref ${path_to_sub}/anat/${sub_id}__T1w.nii.gz \
-interp nearestneighbour \
-applyxfm -init ${path_t... |
97246885af1f55e613f0b24d3a59272cc90434c2a477973b4549725f775a1524 | Shell | 926 | 22 | #!/bin/bash
# Orftcr.sh
export NA=$1
cd ${NA}
#lowres bin analysis first
#printf "${NA}_dipy_inbetween_bk_plus.wig\n${NA}_dipy_inbetween_bk_minus.wig\n" | perl ../cpd_inorf_bins.pl >${NA}_dipy_inbetween_bk_tcrbins_matrix.txt
#printf "${NA}_dipy_inbetween_bk_tcrbins_matrix.txt\n" | perl ../tcr_bins_allgenes.pl >${NA}... |
ac7c9494f6bf4ed7e47af15e20bb3d430cfd711b41c4579200301520e3787789 | Shell | 928 | 32 | #!/bin/bash
# This script is used to retry the uv command if a transient network error is encountered.
# See also:
# https://github.com/astral-sh/uv/issues/2586
# https://github.com/astral-sh/uv/issues/3456
# https://github.com/astral-sh/uv/issues/3514
# https://github.com/astral-sh/uv/issues/4402
tmpstderr=$(mktemp)
m... |
961e70834ef8754d1a5dffdd795674f7608fbb65869e8d8877de19fd19371145 | Shell | 930 | 18 | echo "Waiting for OpenSearch service to be available..."
until curl --insecure -sS https://opensearch-service.${SERVICES_NAMESPACE}.svc:9200; do
echo "OpenSearch not available yet, retrying..."
sleep 5
done
echo "OpenSearch is now available!"
CONFIG_DIR="/usr/share/opensearch/config/"
SECURITY_CONFIG_DIR="${CONFIG_DIR}... |
265dbc83117a2f3614c5f35086ed51ca7f4c4fa28befc6b587d62122f8afb110 | Shell | 931 | 33 | torchrun --rdzv-backend=c10d --rdzv-endpoint=localhost:0 repl/scripts/cli.py \
--dataset mouse \
--grayscale \
--seq_len 25 \
--encoder conv2d \
--use_bn \
--enc_n_layers 6 \
--enc_kernel_size 5,5 5,5 5,5 3,3 3,3 3,3 \
--enc_stride 2,2 2,2 2,2 1,1 1,1 1,1 \
--enc_padding 2,2 2,2 2,2 ... |
0463bf737627807e18bfc9f7eb772e3ccec9f702928020d2c710ecef5659ec5d | Shell | 933 | 22 | #!/bin/bash -e
set -o pipefail
# Versions of the datasets that CI downloads for the test suite, in a form usable
# in cache keys. These can be suffixed (e.g. TESTING_VERSION=${TESTING_VERSION}-1)
# to start fresh when a cache misbehaves.
TESTING_VERSION=`grep -o "testing=\"[0-9.]\+\"" mne/datasets/config.py | cut -d ... |
3932116da8ce48a3841cb6bd718ed09798c4a65f5c39fc4741c8cb591fbf3134 | Shell | 934 | 27 | #!/bin/bash
chr_num=$1
dx login --token TOKEN
my_cmd="plink2 --bfile chr${chr_num}_hqc \
--out chr${chr_num}_hqc_pruned \
--exclude chr${chr_num}_hqc.prune.out \
--make-bed --write-snplist \
--threads 16"
bed_file="/notebooks/wes/sample_qc/high_quality_variants/chr${chr_num}/chr${c... |
10356a14f028f79f356efdb2dc407a29745559a7de345e149ee9a4c85e6e68b3 | Shell | 936 | 26 | #!/usr/bin/env bash
# Generate events
mne_process_raw --raw test_raw.fif --eventsout test-eve.fif
# Averaging no filter
mne_process_raw --raw test_raw.fif --projon --filteroff \
--saveavetag -nf-ave --ave test-no-reject.ave
# Averaging 40Hz
mne_process_raw --raw test_raw.fif --lowpass 40 --projoff \
... |
6108b73a69f4c3e20a75e1d3a5e9ecb49b240dc36fd220953f71ff0c5573627a | Shell | 940 | 25 | #!/bin/bash
dx login --token TOKEN
my_cmd="plink2 --bfile ukb_c1-22_GRCh38_full_analysis_set_plus_decoy_hla_merged \
--out final_array_snps_GRCh38_qc_pass_pruned \
--extract final_array_snps_GRCh38_qc_pass.snplist \
--indep-pairwise 1000 100 0.9 \
--write-snplist \
--threads 32"... |
912ef7d921105f4a12fc01cfdf11dfe8f67ee858dbb7f650b0fc8b8a9f89cc78 | Shell | 941 | 10 | #awk '{print $4"\t"$5"\t"$5"\t"$10"\t"$11}' $1 > $1.5col
perl /home/yli4/bin/customizedDB/MFM_SNV/extract_5cols.pl $1 > $1.5col
perl ~/annovar/annotate_variation.pl -buildver hg19 -geneanno --seq_padding 30 -dbtype knowngene $1.5col /home/yli4/annovar/humandb/
perl /home/yli4/bin/customizedDB/MFM_SNV/seqpad2fas.pl $1.... |
621ac0386f66e89ad5cd3f542e62f249be24d1fdace0d6ff0c4a9d8e8e657b8d | Shell | 942 | 32 | #!/bin/bash
# Check if uv is installed
if ! command -v uv &> /dev/null; then
echo "uv not found. Installing..."
curl -LsSf https://astral.sh/uv/install.sh | sh
else
echo "uv is already installed."
fi
# Check if jq is installed
if ! command -v jq &> /dev/null; then
echo "jq not found. Installing..."
if co... |
ab10f25ee89c27dabff4c0663ed8985e9b339b7e70b5f7cba56eb987f22be2ae | Shell | 943 | 32 | #!/usr/bin/env bash
data_download_setup() {
setup_environment
echo "[DEBUG]: Testing general settings..."
# REMINDER: This only necessary if the runner doesn't have persistent storage
echo "[DEBUG]: data download from osf"
echo -e "[osf]\nproject = $OSF_PROJECT_ID\nusername = $OSF_USERNAM... |
88a4007bea8c8283ebcc35423110ec74c5a54429e4161ce22080ead215684d13 | Shell | 944 | 34 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=02_deconvolution_Bisque_MeanRatio_top25
#SBATCH -c 1
#SBATCH -o logs/02_deconvolution_Bisque_MeanRatio_top25.txt
#SBATCH -e logs/02_deconvolution_Bisque_MeanRatio_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JH... |
714dce09752992cc14dbd798387e53b2bf53d2886e41d5c8455391f4f6bd859b | Shell | 945 | 40 | #!/bin/bash
# Siwei 27 Apr 2021
# ldsc uses numpy, which optimizes threads on its own.
# if you wish to parallelize, set to 1
export OMP_NUM_THREADS=3
export MKL_NUM_THREADS=3
# parallel -j22 python ldsc.py \
# --bfile 1000G_EUR_Phase3_plink/1000G.EUR.QC.{1} \
# --l2 \
# --ld-wind-cm 1 \
# --out 1000G_EUR_P3_base... |
1e03a40b8f71b1cfe72374fd4abbb5a13b08273b8771971337051e63d1a538c6 | Shell | 947 | 23 | #!/bin/bash
# When missing dummy scan
# Select the timeseries without the first containing drop of signal
module load afni
root_dir='/project/4180000.19/multirat_stim/scratch/to_convert/test_marie/Shmuel/3dresample'
input_dir=$root_dir'/input'
output_dir=$root_dir'/output'
cd $root_dir
for file in "$input_dir"/*; ... |
53d41b101a2f24fc318c6659db0cb3ae40b4d8e3276b18d2f7054f8f76e053c3 | Shell | 947 | 36 | torchrun --rdzv-backend=c10d --rdzv-endpoint=localhost:0 repl/scripts/cli.py \
--dataset oddballs \
--grayscale \
--flatten_images \
--seq_len 64 \
--num_sequences 2000 \
--mnist_seqtype local_global_oddball \
--encoder mlp \
--enc_output_dim 64 \
--enc_n_layers 2 \
--integrator ... |
db081bbddb65c03d40e8a0637707be8768486c40c7d9610e9e9d5c7b8b9eef72 | Shell | 951 | 34 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=02_deconvolution_Bisque_MeanRatio_top25
#SBATCH -c 1
#SBATCH -o logs/02_deconvolution_Bisque_MeanRatio_top25.txt
#SBATCH -e logs/02_deconvolution_Bisque_MeanRatio_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JH... |
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