sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
0827c6c56ba0426a45af50f43b245e6f55ac982fbf5978328fda97c505fe2791 | Shell | 998 | 26 | #!/bin/bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); yo... |
442470cf7fe7662d0fc41fb9b14c102a90f19598c1a3f1f1e91586e2a8f1d293 | Shell | 999 | 20 | #!/bin/bash
###################################################################
#created by Davit Bzhalava on 2014-07-08 #
#compares two sequence database with each other #
###################################################################
#sudo nohup /media/StorageOne/HTS... |
6ab88919207ca68fd5f8f95ef45528eadf321515346b78672fc36ccf6e0a78a7 | Shell | 999 | 32 | #!/bin/bash
#SBATCH --job-name=d.merge
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=10
#SBATCH --mem=3GB # Job memory request
#SBATCH --time=0-2:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=d.merge.out
#SBTAC... |
5362c6e3114a383bc77cd017a772ee9ad89e41d27ec6aafc7b6c88278f461d76 | Shell | 1,000 | 18 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script is specific to CBIG HPC cluster.
rep_dir="${CBIG_CODE_DIR}/stable_projects/predict_phenotypes/Chen2024_MMM/replication/"
log_dir="${rep_dir}/log"
mkdir -p ${log_dir}
src_dataset=$1... |
6bb61bb830295b4364dd6a54dcc55a44c26fdeb4fba4c1280e0beb31a3360409 | Shell | 1,001 | 36 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=1
#PBS -N pooled
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# read variables for PBS jobs
var_list="${HOME}/project/multiomics/CallPeak/data/region_list.csv"
region=$(awk -F',' -v x=${PBS_ARRAYID} 'NR==x {print $1}' ${var_lis... |
0a3d049de10191a9c9d9b02673a054e749e31b1fcdcafacc989966bba706493b | Shell | 1,002 | 27 | #!/bin/bash
#SBATCH --job-name=get_data
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --cpus-per-task=1
#SBATCH --mem=20MB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=get_data.out
#SBATCH --error=get_data.err
# Title: Download scRNA data from... |
8542dce2acdef4a312b58cf289b3341426f2cac6f811c7dff4d2dfdfc0891854 | Shell | 1,002 | 23 | #!/bin/bash
#
# Prepare a run directory for somatic SV validations with the HCC2218 breast
# cancer cell line.
set -eu -o pipefail
mkdir -p config
cd config
wget -c https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/config/examples/HCC2218-sv.yaml
cd ../
mkdir -p input
cd input
wget -c --no-check-certifica... |
f3586cc9abae5311ed59cd54924839a70ca84e8303dd27af6bc65286cd2ae603 | Shell | 1,003 | 29 | #!/bin/bash
#SBATCH -c 2
#SBATCH -t 0-00:30
#SBATCH -p short
#SBATCH --mem=8G
#SBATCH -o /home/ab714/bancpipeline/jobs/install_bancr_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/install_bancr_%j.err
set -euo pipefail
cd /home/ab714/bancpipeline
source /home/ab714/bancpipeline/o2/o2_env.sh
ulimit -c 0
echo "=== Ins... |
40e1a560c8ca5f0cc6336c000977ae63d8944b2aa0cfc862e77b875e03a0c0b7 | Shell | 1,004 | 33 | #@title { display-mode: "code" }
#from http://wiki.ros.org/indigo/Installation/Ubuntu
#1.2 Setup sources.list
sudo sh -c 'echo "deb http://packages.ros.org/ros/ubuntu $(lsb_release -sc) main" > /etc/apt/sources.list.d/ros-latest.list'
# 1.3 Setup keys
sudo apt-key adv --keyserver 'hkp://keyserver.ubuntu.com:80' --r... |
2278671dff4e83e9fdbe8a56c0e24ea9db65661d672e6022e4794e2a7f7c6ff7 | Shell | 1,006 | 33 | #!/usr/bin/env bash
set -euo pipefail
# Submit CPU PBS job first, then submit GPU PBS job with dependency:
# GPU starts only when CPU job exits successfully (afterok).
#
# Usage:
# bash scripts/submit_cpu_then_gpu.sh
# bash scripts/submit_cpu_then_gpu.sh scripts/run_pipeline_pbs.sh scripts/run_nn_gpu_pbs.sh
ROOT=... |
25cf943e168403a2a3399096ea41fb58ff7ec1c7c55cd7891c645fcc82367728 | Shell | 1,007 | 38 | function build {
pyinstaller --noconfirm --clean ProcessWorker.spec
pyinstaller --noconfirm --clean TierpsyTracker.spec
}
function build_spec {
pyinstaller --noconfirm --clean \
--exclude-module PyQt4 \
--exclude-module PyQt4.QtCore \
--exclude-module PyQt4.QtGui \
--hidden-import=h5py.defs \
--hidden-import=h5py.u... |
71fe3b49d216939e410305ae6f29ca970a493eae172938530eb041078594b0c6 | Shell | 1,009 | 33 | #!/bin/sh
set -o allexport
sta_i_pCaLs=1
end_i_pCaLs=2
sta_i_Kir=1
end_i_Kir=2
sta_i_KM=1
end_i_KM=2
sta_N_i_batch=1
end_N_i_batch=1
for i_pCaLs in $(eval echo "{$sta_i_pCaLs..$end_i_pCaLs}")
do
echo "$i_pCaLs"
for i_Kir in $(eval echo "{$sta_i_Kir..$end_i_Kir}")
do
... |
1f4a16e5e87718127aab344bc760e4da9fdc3e9f4e2dc2c6b2782702de2e4f12 | Shell | 1,012 | 12 | #! bin/bash
num=$(ls -f1 results/kallisto/kallisto/aliquot/*/abundance.tsv | wc -l)
upper=$(echo "$((5 * $num))")
myseq=$(seq 4 5 $upper | sed 's/^\|$//g' | paste -sd,)
myseq=$(echo "1,2,"$myseq)
paste results/kallisto/kallisto/aliquot/*/abundance.tsv | cut -f $myseq > results/kallisto/kallisto/final/transcript_count_... |
8b8942c8c34cd7e45097f7461a34e1be594fa6cb25474ce8123a3dfaae38a1be | Shell | 1,013 | 36 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --exclude=cn10
#SBATCH --nodes=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=30000
#SBATCH --mail-type=BEGIN,END
#SBATCH --mail-user=alex.lepauvre@ae.mpg.de
#SBATCH --time 120:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/rsa/slurm-... |
a88db5b10c489624272672c6db435cf2c07a7dfd2539e16ef0e354cb5761647c | Shell | 1,014 | 25 | #!/bin/bash
#SBATCH --mem=40G
#SBATCH --ntasks=15
#SBATCH --job-name=DFIM_GenNet
#SBATCH --partition=short,long
#SBATCH --gres=gpu:1
#SBATCH -t 1-00:00:00
#SBATCH -o out.log
#SBATCH -e error.log
# Load the modules
module purge
source /trinity/home/avanhilten/miniconda3/etc/profile.d/conda.sh
conda init
conda activate... |
ad3515ef6a13690b5223f56325ff3031babd62907b064e582862abf3c7444681 | Shell | 1,016 | 25 | #!/bin/bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); yo... |
e21762db4f06579e816b326dce1c00b3eebdbf389ce95713cfeae2a071c109dd | Shell | 1,016 | 30 | #!/bin/bash
#SBATCH --get-user-env
#SBATCH --job-name=norlux_md5sums_%a
#SBATCH --chdir=/projects/verhaak-lab/USERS/johnsk/glass4
#SBATCH --output=/projects/verhaak-lab/USERS/johnsk/glass4/logs/md5/norlux_batch2_aligned_bams_md5_%a.log
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=kevin.c.johnson@jax.org
#SBATCH --ntask... |
f37d0581532f0af4a1dec55cb2e07d216965759e6f4ab46031c5892e3f774298 | Shell | 1,016 | 36 | #!/bin/bash
# Define the full training set size
TOTAL_TRAIN=4000
# Define the percentages to test
PERCENTAGES=(1 5 10 20 50 100 200 300)
# PERCENTAGES=(200 300)
echo "Starting batch experiments..."
for PCT in "${PERCENTAGES[@]}"
do
# Calculate limits (using bash arithmetic)
# train_limit = 4000 * PCT / 100
... |
31cb9464da13943400c6ad32edb91af78c9dfe5e16f807b01659644d081278f8 | Shell | 1,018 | 23 | #!/bin/bash
#SBATCH -p priority
#SBATCH -t 0-04:00
#SBATCH -c 1
#SBATCH --mem=16G
#SBATCH -J banc_wb_push
#SBATCH -o data/scheduled_runs/wb_push_%j.out
#SBATCH -e data/scheduled_runs/wb_push_%j.err
###############################################################################
# Live push of banc-alignment-update-seata... |
9ed61e074c8359e92806d0e1a86017ab8e96cb88ed9efb9142b3495f62e53103 | Shell | 1,018 | 16 | #!/bin/bash
cd /global/project/projectdirs/m2043/BigNeuron/Data/taiwan16k/img_anisosmooth/
var=0;
for filename in `ls -d *`
do
echo $filename
echo $var
i=25;
# mkdir /global/project/projectdirs/m2043/BigNeuron/Data/taiwan16k/reconstructions_for_img_anisosmooth/$filename
# for i... |
f07d5ac56eed09a11918926eecaa98c1eeb3f9e30fae32cca4993f9dc406c1cc | Shell | 1,018 | 41 | #!/usr/bin/env bash
# clean up the error and output files created by fsl_sub by deleting the ones
# without errors. You can specify a folder to search in.
# Lennart Verhagen
# give help
if [[ $# -eq 0 ]] || [[ $# -gt 1 ]] ; then
echo ""
echo "clean up the error and output files of fsl_sub"
echo ""
echo "clea... |
2a51f61be1191a1bc79f6947f1843d3612da7fdf1a4e414fba4d2a152b914b54 | Shell | 1,019 | 32 | #!/bin/bash
#SBATCH --job-name=st7
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st7.out
#SBTACH --error... |
58ec9d2163b08465c10f3c4637cf77b57f0feee22a0383c896b8f29117a3b96d | Shell | 1,019 | 32 | #!/bin/bash
#SBATCH --job-name=st4
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st4.out
#SBTACH --error... |
74263b0d188593d7eb5aa25925603d1a3d594833f353b1541c9bfbc734389a37 | Shell | 1,019 | 32 | #!/bin/bash
#SBATCH --job-name=st6
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st6.out
#SBTACH --error... |
909e2d45b3811a67ed2aafae9f75129f5862d5df63a8d3a79ce20adaae2f03ee | Shell | 1,019 | 22 | #!/bin/bash
#SBATCH -c 10 # cores per array task
#SBATCH -t 0-12:00 # 12h short (each shard fits)
#SBATCH -p short
#SBATCH --mem-per-cpu=8G # 80G per task
#SBATCH --array=0-9 # 10 disjoint shards
#SBATCH -o jobs/banc_native_arr_%A_%a.out
#SBA... |
c5e288d9b04c010038b2aac9e645f6f15ceb790fc7b4818549ce662b6d0aeb3e | Shell | 1,019 | 32 | #!/bin/bash
#SBATCH --job-name=st3
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st3.out
#SBTACH --error... |
dd1c15020502cf201857cbdb4e8a988d73118ec754228802fd579a2dff3e6390 | Shell | 1,019 | 32 | #!/bin/bash
#SBATCH --job-name=st8
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st8.out
#SBTACH --error... |
f60b8dd4e125e6e166b60cc0ef49ed7b129e1eb3f825edec853b15a5bea26429 | Shell | 1,019 | 32 | #!/bin/bash
#SBATCH --job-name=st5
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st5.out
#SBTACH --error... |
8fe31eb3c99c746c95ddc7d4d5fe3113ab3b08ad8d216a57904a8661d40cc95c | Shell | 1,020 | 30 | #!/bin/bash
#
# Cancer-like mixture of two Genome in a Bottle samples (NA12878 and NA24385)
# ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/use_cases/mixtures/UMCUTRECHT_NA12878_NA24385_mixture_10052016/
set -eu -o pipefail
mkdir -p config
cd config
wget -c https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/con... |
67fe593533c8f4feec45cc148dc469d38a141484aaf12918d7da692165a931a4 | Shell | 1,021 | 51 | #!/bin/bash
chr=$1
plink_ressources="--memory 32000 --threads 2"
workdir=data/heritability
ids_file=$workdir/final_ids.formatted
infile=$workdir/merged_beds/white_british_${chr}_snpfinal
outdir=$workdir/prep/filtered/
# run SNPs
outfile=$outdir/snps/${chr}_snps_filtered
mkdir -p $outdir/snps
plink --bfile $infile... |
b3d7b316a638d79b23c07b49d73648cdd88a390d07e5fcf91176b8706faad178 | Shell | 1,021 | 16 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/img_anisosmooth/
var=0;
for filename in `ls -d *`
do
echo $filename
echo $var
mkdir /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/reconstructions_for_img_anisosmooth/$filename
for i in {1..27... |
36680dc431904ce2bb390033e1197bce8209de4446ce079f5e2b42032b635884 | Shell | 1,022 | 36 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --exclude=cn10
#SBATCH --nodes=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=30000
#SBATCH --mail-type=BEGIN,END
#SBATCH --mail-user=alex.lepauvre@ae.mpg.de
#SBATCH --time 120:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/rsa/slurm-... |
adab899c9b82b25c56ee23e991eb5f71d1979f92a0a9aa84288992666c5370cc | Shell | 1,022 | 36 | #!/bin/bash
# Define the full training set size
TOTAL_TRAIN=4000
# Define the percentages to test
PERCENTAGES=(1 5 10 20 50 100 200 300)
# PERCENTAGES=(200 300)
echo "Starting batch experiments..."
for PCT in "${PERCENTAGES[@]}"
do
# Calculate limits (using bash arithmetic)
# train_limit = 4000 * PCT / 100
... |
861596ee37514f2dcef2e78300368ca99e0dbee409e078407a6e66143e2ca635 | Shell | 1,023 | 29 | #!/bin/bash
set -e ${DEBUG:+-x}
CUSTOM_CERTS_DIR="$OPT_DIR"/custom_certs_bundle
CUSTOM_CERTS_BUNDLE=$CUSTOM_CERTS_DIR/cacert.pm
if [ -n "${CUSTOM_CA_CERTS:-}" ] && [ ! -f "$CUSTOM_CERTS_BUNDLE" ]; then
CERTIFI_CA_FILE=$(python3 -m certifi | head -n1)
mkdir -p "$OPT_DIR"/custom_certs_bundle
cp "$CERTIFI_CA_FILE... |
110c40c5762f5a27df18d9a631ec145c7f3157555f67ab1ed52def95c0a3aa00 | Shell | 1,024 | 32 | #!/bin/bash
#SBATCH --job-name=st18
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st18.out
#SBTACH --err... |
1c517b0006b52682c31bb11e72e4808d8b35071f564691795d01ec7a6b2fe7b3 | Shell | 1,024 | 32 | #!/bin/bash
#SBATCH --job-name=st11
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st11.out
#SBTACH --err... |
23111cc0852c0c0173623d842229ddc65398320425c833731817ac3729e8f0d2 | Shell | 1,024 | 37 | #!/bin/bash
#SBATCH --partition=xnat
#SBATCH --exclude=cn12
#SBATCH --nodes=1
#SBATCH --cpus-per-task=64
#SBATCH --mem-per-cpu=8GB
#SBATCH --mail-type=BEGIN,END
#SBATCH --mail-user=simon.henin@nyumc.org
#SBATCH --time 1-24:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/synchron... |
4784fa5b8372003959a4d6d889b67af294eb4f296757049546e2d5594a066448 | Shell | 1,024 | 32 | #!/bin/bash
#SBATCH --job-name=st12
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st12.out
#SBTACH --err... |
688742975e15a6e90496f6623c32d88d50ca2d67fb889e1efc708b4bce5f95d6 | Shell | 1,024 | 32 | #!/bin/bash
#SBATCH --job-name=st17
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st17.out
#SBTACH --err... |
c9cd86ed32bbc70897f62e6b867ae58dcfb797c5ed954feb50e18b0e1689ed14 | Shell | 1,024 | 32 | #!/bin/bash
#SBATCH --job-name=st13
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st13.out
#SBTACH --err... |
da7b98c9a100121aeaa93650b54e6f9358333aa519be916452eaf2fa0c21c19f | Shell | 1,024 | 32 | #!/bin/bash
#SBATCH --job-name=st16
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=st16.out
#SBTACH --err... |
1d37eee7ee9d207d8b071184a75e063593025f5c5e7de185752479efddcd9d06 | Shell | 1,025 | 34 | #!/bin/sh
module load cesga/2020
module load whatshap/1.1
# pop
pop=${1}
# chr
chr=${2}
# vcfdir
vcfdir=/mnt/netapp2/Store_csebdjgl/lynx_genome/lynx_data/mLynRuf2.2_ref_vcfs
# i_vcf
i_vcf=${vcfdir}/lynxtrogression_v2.autosomic_scaffolds.filter4.${pop}_pop.${chr}.vcf
# o_vcf
o_vcf=${vcfdir}/lynxtrogression_v2.autosomi... |
6a4203d854d4e03d8fa978c8c8ed1864be06405220847c4b8803414e2e97b5e3 | Shell | 1,025 | 16 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/img_anisosmooth/
var=0;
for filename in `ls -d *`
do
echo $filename
echo $var
mkdir /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/reconstructions_for_img_anisosmooth/$filename
for i in {1..... |
fdd70cf44fc2ea39e411ac16a7b8752db227995d0cf4d84cf3cbe7b229d82416 | Shell | 1,026 | 18 | #!/bin/bash
# uncomment next line for interactive checking of generated output
PYTHON="ipython2 --pylab -i"
# non-interactive shell. Check results afterwards
PYTHON="python2.7"
# Attraction demo: two structures are grown
# Two subvolumes are used to indicates that environmental cues are not \
# limited to one Subvol... |
7df766adc315ad7efc6de3e767ee35d06c0961d2762020ea51764cd93399175d | Shell | 1,028 | 26 | #!/bin/bash
# export DEPS=$HOME/dependencies
export PERL5LIB=$DEPS/bioperl-live:$PWD/ensembl-test/modules:$PWD/ensembl/modules:$PWD/modules:$PWD/ensembl-io/modules:$PWD/ensembl-funcgen/modules:$PWD/ensembl-variation/modules:$DEPS/Bio-HTS/blib/lib:$DEPS/Bio-HTS/blib/arch:$PERL5LIB
# export HTSLIB_DIR=$DEPS/htslib
expor... |
858a6f2d3b41c90a4b436e6f6ad472dacba87d5398febe471b445f0e5dd62165 | Shell | 1,030 | 38 | #!/bin/bash
genome=$1
TF_subset=$2
base=/data/share/htp/hack_GRN/vlad/ATAC_Seq/cbust
PFMs=$base/PWMs/motifs/$TF_subset
fasta=$base/fastas/$genome #modify the path for different subsets
out_folder=$base/cbust_out/$genome/$TF_subset #modify the path for different subsets
mkdir -p $out_folder
mkdir -p $out_folder/slu... |
ea0542b25825a4acfb1b648b1e3c16e7acef68cfe4a4fe7ab5b0e19277ce07cb | Shell | 1,030 | 43 |
#!/bin/bash
set -e
microscope='ISM'
animal='38'
stain='mye'
what='mtbi'
# directory containing ndpi files
input_dir=".../data/${microscope}_${animal}/${stain}"
# file_prefix="${microscope}-${animal}-15 ${stain}"
file_prefix="${microscope}-${animal}"
# output directory
output_dir=".../AE/image_preprocessing/data/$... |
ea5bdfa27b0777179bdbd5f5b074db99a94f9be410119f31dcf960cde8a1bdac | Shell | 1,030 | 35 | #!/bin/bash
#SBATCH --account=def-pbellec
#SBATCH --time=24:00:00
#SBATCH --job-name=shi_sesslevel
#SBATCH --output=logs/slurm/%x/%x_%j.out
#SBATCH --error=logs/slurm/%x/%x_%j.err
#SBATCH --mem=128G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
# Get repository root - use SLURM_SUBMIT_DIR (directory where sbatch was c... |
105f380b0a475b65e8498ed62d17b8b9827051e73b5bc299c81b782f68ad6da6 | Shell | 1,034 | 27 | #!/usr/bin/env bash
# Assert RSEM honored a --<aligner>-path flag instead of falling back to PATH.
# Gold diffs cannot detect this: pointing the flag at a directory resolving the
# same binary PATH would have found produces identical output.
#
# Usage: assert_path_flag_honored.sh <probe-log> <probe-dir> <tool> <flag>
s... |
6d1926a3f136bd57f0e04eaf328be7ab5d32bc771c09becd27f03faf8300365f | Shell | 1,034 | 16 | #!/bin/bash
cd /global/project/projectdirs/m2043/BigNeuron/Data/taiwan16k/img_nopreproprcessing/
var=0;
for filename in `ls -d *`
do
echo $filename
echo $var
i=25;
# mkdir /global/project/projectdirs/m2043/BigNeuron/Data/taiwan16k/reconstructions_for_img_nopreproprcessing/$filename
... |
cd980941da3615da7bdcfa5f586e756b765aebc4047889881643f068763a1cc2 | Shell | 1,035 | 31 | #!/bin/bash
#
# A script that builds the GATK base image using Google Cloud Build, and pushes it to
# a staging location at us.gcr.io/broad-dsde-methods/gatk-base-image-staging-area
#
# Usage: build_docker_base_cloud.sh <docker_image_version>
#
# After staging the image, you should test it with GATK before actually rel... |
22a53cd705c61f56c5668dfad0140d62b55f3e59a7fefe1502b00cef95be9471 | Shell | 1,037 | 26 | #!/bin/bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); y... |
d9b1168d6f51905efd3c4d71288cb66c87e45aee52333edaa069a2a48a5297b9 | Shell | 1,039 | 23 | #!/bin/bash
#SBATCH -c 14 # number of core to be used
#SBATCH -t 0-01:00 # estimated run-time in D-HH:MM
#SBATCH -p ultrashort # p=short <6h, p=mid <2d, p=long <4d
#SBATCH --mem=100000 # Memory pool for all cores (see also --mem-per-cpu); mem=10000 # memory 10GB
# Get sample name
... |
0758c01a1c12ef7cfb65919b744b85749d5de264c188db137b9e38e47ec13709 | Shell | 1,040 | 24 | set -euo pipefail
conda activate dnabert_aug_2025
export CUDA_VISIBLE_DEVICES=5,6,7
export TOKENIZERS_PARALLELISM=false
base_model_nm="TSp_vs_genNullseqs"
subset="muscle_genNullseqs"
lr_dir="lr3e-5_ep10"
model_path="/data/projects/dna/pallavi/DNABERT_runs/DATA_RUN/dnabert2_FineTune_Zhihan_attention_extracted/july_202... |
8485a2c64bdc23865211d65a76b84f7f3d2b18e7d92c76830998a535dd4053e3 | Shell | 1,040 | 31 | #!/bin/bash -x
#SBATCH --account=inm7
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=128
#SBATCH --time=24:00:00
#SBATCH --partition=dc-cpu
#SBATCH --job-name=${ARG1}_${ARG2}
# Handle dynamic log paths inside the script
out_log="logs/outputs/${ARG2}_${ARG1}_%j.out"
err_log="logs/errors/${ARG2}_$... |
ca2c21893187662569853fdc5bbbe735399d95fa72a4b5c69a83985fecbad196 | Shell | 1,041 | 48 | #!/bin/bash
#
#This is a shell program to batch reconstruct images using 21 different methods.
#
function write_psb_script {
outputScript=$1;
inputfolder=$2;
exefilename=$3;
jobnumbers=$4;
nodenumbers=$5;
jobpernode=$6
echo "#PBS -l walltime=1:00:00" >> $outputScript;
echo "#PBS -l nodes=$nodenumber... |
9c4a760f8f5e1da6d80e8ed03a25ee4a03d29943fb0fe13f4a16633126edfdbd | Shell | 1,042 | 37 | #!/usr/bin/env bash
# Download STAR 2.7.6a (Bioconda build) into tests/tools/star-2.7.6a/bin/STAR
set -euo pipefail
ROOT="$(cd "$(dirname "$0")/.." && pwd)"
DIR="$ROOT/tests/tools/star-2.7.6a"
PKG="$DIR/star-2.7.6a-0.tar.bz2"
mkdir -p "$DIR"
if [[ -x "$DIR/bin/STAR" ]]; then
echo "STAR 2.7.6a already present at $DIR... |
571d4d6f9b56476fa579d2445e3d56d01039500c24d8a1a0f62a584242bfb706 | Shell | 1,043 | 40 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=16
#PBS -N cci
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="r4_bio"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
export M... |
6d7d9ed35e365879d5000e2fda19965ece8f06e9d837a960793ba6c3517e1b85 | Shell | 1,043 | 16 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/img_nopreproprcessing/
var=0;
for filename in `ls -d *`
do
echo $filename
echo $var
mkdir /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set1_extract_single/reconstructions_for_img_nopreproprcessing/$filename
for... |
dd483c006701d24479f4b9e31dc104ab9f0685835cbab5b92f51a066c0867d03 | Shell | 1,043 | 23 | #!/bin/bash
set -eu -o pipefail
# We need about 100Gb for the input files. Confirm we have the space.
REQ_DISK_SPACE=100
df --block-size=G --output='avail' . | sed s/G//g | awk -v req_disk_space=${REQ_DISK_SPACE} '{ if ($1 !~ /Avail/ && $1 < req_disk_space ) printf("Warning: Not enough disk space.\n Warning: Require... |
519e66f7e83e34f01f005158118e01066f70041b4e8eba24d70f9d443e185fbd | Shell | 1,044 | 37 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=1
#PBS -N bam2bedpe
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="bulk-seq"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
e... |
58b0ab0f768af3859603c6f06306c31f5dcac443822ad01db300b28f5e23a28c | Shell | 1,044 | 36 | #!/bin/bash
# Define the full training set size
TOTAL_TRAIN=4000
# Define the percentages to test
PERCENTAGES=(1 5 10 20 50 100 200 300)
# PERCENTAGES=(200 300)
echo "Starting batch experiments..."
for PCT in "${PERCENTAGES[@]}"
do
# Calculate limits (using bash arithmetic)
# train_limit = 4000 * PCT / 100
... |
d5f61f6ae4eac0f48a8847d5c5c3724994bcde8c8e2b2d8285c438be7f232b76 | Shell | 1,044 | 33 | #!/bin/bash
# Define the base directory
DATA_DIR="/.../EMBARC/03_FSL_FEAT/Whole-data"
# Loop through all subjects
for subject in $(ls $DATA_DIR); do
if [[ $subject == "sub-"* ]]; then # Ensure it's a valid subject folder
for session in $(ls $DATA_DIR/$subject); do
if [[ $session == "ses-"* ]... |
015fafe437758ba460e7390eb94750763221e2d7ce4b53d2611ba745097033a3 | Shell | 1,045 | 36 | #!/bin/bash
# Define the full training set size
TOTAL_TRAIN=4000
# Define the percentages to test
PERCENTAGES=(1 5 10 20 50 100 200 300)
# PERCENTAGES=(200 300)
echo "Starting batch experiments..."
for PCT in "${PERCENTAGES[@]}"
do
# Calculate limits (using bash arithmetic)
# train_limit = 4000 * PCT / 100
... |
0df142280e63dfefcac851362b3c167b61b1b95e4b3260dcffec14ce28b28961 | Shell | 1,045 | 23 | #!/bin/bash
cd /global/project/projectdirs/m2043/BigNeuron/bigneuron_annotation_consolidated_20150715/gold166/
for foldername in `ls -d checked*`
do
echo $foldername
cd $foldername
# mkdir /global/project/projectdirs/m2043/BigNeuron/bigneuron_annotation_consolidated_20150715/gold166_LBNL/$foldername
for subfolder i... |
36b93791f7ea625fd8d5707fb88aca044b60320abf399894e373da62c8f9453e | Shell | 1,045 | 30 |
#First run the a3m_parser for all your a3m files to obtain a list of
#organism identifiers and an array of the MSA
#Parse a3m
A3MDIR=#Path to a3m files
OUTDIR=./
#python3 ./a3m_parser.py --a3mdir $A3MDIR --outdir $OUTDIR
#Match OX (organism identifiers) and wrte statistics
OXDIR=../data/hhblits/
META=../data/full_se... |
ab56a73dc1b8fbebcf7c243aaafe1788bf66c4d6089275abd77d0cd963a4d48c | Shell | 1,045 | 31 | #!/bin/sh
# Written by Jingwei Li, Shaoshi Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
output_dir=$1
fmrinii_dir=${output_dir}/fmrinii
if [ ! -d $fmrinii_dir ]; then
mkdir -p $fmrinii_dir
else
rm -r $fmrinii_dir
mkdir $fmrinii_dir
fi
subject_list=${CBIG_C... |
fb8634dce3f4b71d78913ce835816c2f1ed1fc017f3148655367f677933b958e | Shell | 1,045 | 49 | #!/bin/sh
if [ "$#" -eq 0 ]
then
echo "Missing parameter IP_\${version}_(32|64)." 1>&2
exit 1
fi
versionString=$1
version=$(echo $versionString | cut -f 2 -d "_")
bitness=$(echo $versionString | cut -f 3 -d "_")
if [ "$CI_IGOR9_REVISION" = "" -a "$CI_IGOR10_REVISION" = "" ]
then
revision=""
else
# not using ... |
2279a401672133452b46d51287795fc60ca8514d309f4d08a7a79009bba583e8 | Shell | 1,046 | 38 | #!/bin/bash
### This script runs NMF on each sample's Undifferentiated malignant cells in the CAREmut dataset ###
# Activate the conda environment for running NMF, if not currently active.
module load miniconda
conda activate NMFenv
### Input arguments ###
ARRAYID="`expr $1`"
# Identify where the expression matric... |
7a967d35038a152eeb96b0b517e7ba555082835e3597b6e520d8e8a2bb28b6f8 | Shell | 1,046 | 16 | #!/bin/bash +x
export OMP_NUM_THREADS=1
STARTTIME=$(date +'%s')
PLUGIN_NAME=neuron_tracing/Vaa3D_Neuron2_Tuned
#/usr/bin/time -f "%U sec %M KB" ./v3d_external/bin/vaa3d -x ${PLUGIN_NAME} -f app2 -i ./myneurons/0969_seg.tif -p NULL 0 10 0
/usr/bin/time -f "%U sec %M KB" ./v3d_external/bin/vaa3d -x ${PLUGIN_NAME} -f app... |
ba16ca517a9e5b0b66fcbc64f135a54d9fedc424cbef590eb9aa24f3a4f5efef | Shell | 1,046 | 27 | f="update main folder path: main directory path pf pwm predictor"
dir=${f}/pwm_predict_folder
echo $dir;
mkdir -p $f/mosbat_input
pred_add=$dir/predictions
python3.6 create_mosbat_input_protein_bert.py -p_add ${pred_add} -c_rc_add 'update_path/'c_rc_df.csv -zf_add 'update_path/'zf_pred_df.csv -s_add ${f}/mosb... |
06e738f41145ed879b10a2cff31134ef73bbd40dcf83683e24a32a65a04b0a46 | Shell | 1,047 | 45 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Mouse_IndexPath_50_A}
DataPath=${FastpPath_A}
FASTQ0=${FASTP0_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPath_A}
Read_len=50
#####
make_dir ${OutPath}
make_dir ${AllOutPath... |
8adcfe96f5aa7669c843843176581d7ce825e29123d8a49495a3e4099b84dcbe | Shell | 1,047 | 45 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Mouse_IndexPath_75_A}
DataPath=${FastpPath_A}
FASTQ0=${FASTP0_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPath_A}
Read_len=75
#####
make_dir ${OutPath}
make_dir ${AllOutPath... |
1b9ecf08425417c596ade0e73ba38043a6709f2bbac661fdf13b07fd63737b41 | Shell | 1,048 | 45 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Rat_IndexPath_35_A}
DataPath=${FastpPath_A}
FASTQ0=${FASTP0_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPath_A}
Read_len=35
#####
make_dir ${OutPath}
make_dir ${AllOutPath}
... |
3c207beae145e92192c5c927059a586bd9e1ee71f53bd1de356268f2c0915739 | Shell | 1,048 | 16 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/img_nopreproprcessing/
var=0;
for filename in `ls -d *`
do
echo $filename
echo $var
# mkdir /lustre/atlas2/nro101/proj-shared/BigNeuron/data/Janelia/set2_accepted_single/reconstructions_for_img_nopreproprcessing/$filename
... |
78096177b8c5bfeddd7e99ea35789cba87d754e0a24feca0431603a0ff8d72fa | Shell | 1,049 | 25 | #!/usr/bin/env bash
CONFIG=${CONFIG:-example_node}
GRID=${GRID:-example}
REPEAT=${REPEAT:-3}
MAX_JOBS=${MAX_JOBS:-8}
SLEEP=${SLEEP:-1}
MAIN=${MAIN:-main}
# generate configs (after controlling computational budget)
# please remove --config_budget, if don't control computational budget
python configs_gen.py --config co... |
b1b2590e506d6b2d8303395d7bfcb0a9e4cd490c3c17c91da8b3f1f537765799 | Shell | 1,051 | 28 | #!/usr/bin/env bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Licen... |
01574f404a4c8b6d2707bd23d7ceef1a7d131e7334ead9583ecd8c18730a61de | Shell | 1,052 | 25 | #！bin/bash/
singularity run --cleanenv -B /mnt/d/data_analysis/TN:/mnt \
~/xcp_d:latest.simg \
/mnt/TN_E_prep \
/mnt/TN_E_xcp_out \
participant \
--nthreads 10 --despike -p 36P --min_coverage 0.5 --min_time 100 --lower-bpf 0.01 --upper-bpf 0.08 --bpf-order 2 -f 0.3 --head_radius 40 -w /mnt/TN_E_xcp_work --smoothing 6 ... |
0a813545e561af208302e664c3ed8ed1883a6d3d73d17e9863628e9776f4e7c0 | Shell | 1,052 | 21 | #!/bin/bash
export path_htsa_dir=/media/StorageOne/HTS
export path_pipeline=viralmeta_bioifo
export work_fasta=$1
(time /paracel/paracel/bin/pb megablast -i $work_fasta -d HG --dbpart=1 --querypart=11000 -b 10 -v 10 -e 0.0001 -m 7 -I T -o $work_fasta.HG.out 2>$work_fasta.HG.err) >& $work_fasta.HG.time
python $path... |
2230ef4a7b81921dff1ad1da0505eaa9c1f5a2d40d6cdccdf81d0f3e2b704908 | Shell | 1,053 | 28 | #!/bin/bash
#SBATCH -c 1 # Request cores
#SBATCH -t 00-600:00 # Runtime in D-HH:MM format
#SBATCH -p priority # Partition to run in
#SBATCH --mem-per-cpu=250G # Memory per core
#SBATCH -o jobs/banc_synapses_%j.out # File to whic... |
eb9f2bc042261d3a99ef1a2f79f1a0a15d80954b2a777363342aff21abde318a | Shell | 1,053 | 45 | #!/bin/bash
function help() {
echo -e "$0 <dir>\nFlatten folder structure in directory <dir>" > /dev/fd/2
exit 1
}
if [ ! $# = "1" ]; then
help
fi
dir="$1"
if [ ! -d "$dir" ]; then
echo "Directory $dir not found" > /dev/fd/2
exit 2
fi
# move files upwards
find "$dir" -mindepth 2 -type f | \
... |
319cb561d66c2d98c2e3e3bc658b1e9229b464b4a5f53048c8bf338d52811759 | Shell | 1,055 | 39 | #!/bin/bash
#PBS -q fat
#PBS -l walltime=72:00:00 -l nodes=1:ppn=16 -l mem=100G
#PBS -N RegDAP
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="py38_bio"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${P... |
7616fbe554e75874fd15eaf5c41a5fb4a5a10a94ebd7bcf7fcf7d24f503557e3 | Shell | 1,056 | 35 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --nodes=1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=5000
#SBATCH --mail-type=BEGIN,END
#SBATCH --mail-user=alex.lepauvre@ae.mpg.de
#SBATCH --time 24:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/activation_analysis/slurm-l... |
c656264a863b13d69814c6f1d4cf4a87f377b95c35031bbed79a72b9381ba362 | Shell | 1,056 | 24 | #! /bin/bash
step=1
## Project DK308 Atlas from fsaverage space to individual surface
if [[ $step -eq 1 ]]
then
sour_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/NIIDATA/T1
atlas_dir=/Data/sharehome/huyang/MyAtlases/DK308
sublist=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/LIST/sublist.txt
... |
9c2deb62195d8a831fd6e98d9461375415b550effa081722ce99ffd35dc88777 | Shell | 1,060 | 26 | ### assumes you have the $fsav subject in your exampledir, might be changed when we use freesurfer 5
#!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
workingDir=${1}
segment_name=${2}
fsav=fsaverage
export SUBJECTS_DIR=${workingDir}
# prepare subject
subjec... |
bdcd6b43d6d0f23636e376dee3371702b9c83468ff8b0e3cd24d715d1f7495e4 | Shell | 1,062 | 38 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --job-name=soffSTRT
#SBATCH --error=jobstar_error_%A_%a.txt
#SBATCH --output=jobstar_output_%A_%a.txt
#SBATCH --array=0-22
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
# data s... |
63ee373d67d918091ee2a72443343c45f325b9ab0b259b0ec969787e6a204e28 | Shell | 1,063 | 17 | #!/bin/bash
# Commands to setup a new virtual environment and install all the necessary packages
set -e
pip install --upgrade pip
python -m venv mei-env
source mei-env/bin/activate
git clone https://github.com/Stability-AI/StableCascade
pip install numpy matplotlib==3.8.2 jupyter jupyterlab_nvdashboard jupyterlab ... |
b17f6291dce3f0b78564a621674072e4bfb42ec7e9ba285c02a300f05193bf29 | Shell | 1,064 | 21 | #!/bin/bash
# Run WeightWatcher analysis on a pretrained MBBN model.
# Results (CSV + PNG) are saved to --weightwatcher_save_dir.
cd "$(dirname "$(dirname "$(dirname "$(realpath "$0")")")")"
# ── User settings ────────────────────────────────────────────────────────────
PRETRAINED_WEIGHTS="/path/to/pretrained_model.p... |
cd57a23796dbb7e8ce8a550a240e24d6a66c07a85b10f3e0c9f680b8764e8c19 | Shell | 1,065 | 39 | #!/bin/bash
#
# This bash script runs the demo_multivariate_te_mpi.py with several different settings on a SLURM batch system.
# Submit using command "sbatch demo_multivariate_te_mpi_slurm.sh".
#
#SBATCH --job-name=te_mpi
#SBATCH --output=demo_multivariate_te_mpi_res.txt
#SBATCH --time=2:00:00
#SBATCH --ntasks=4
#SBATC... |
14795196fa7b83f03b0ee2a96ce9c842ea6a97b8a929330f82a3e75e4ac69f65 | Shell | 1,066 | 34 | #!/bin/bash
#SBATCH --job-name=gcd
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=gcd.out
#SBTACH --error... |
ffe887d09a41f387e5fe2a4e423a018bc05b17a51e883ab02154d10483d951cb | Shell | 1,067 | 35 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=8000
#SBATCH --mail-type=BEGIN,END
#SBATCH --mail-user=alex.lepauvre@ae.mpg.de
#SBATCH --time 24:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/activation_analysis/slurm-on... |
89bcf19175a3ce7ee84ea9ac26f660de8770eb9e73b9eaee7cd72cbdc87502e0 | Shell | 1,068 | 48 | #!/bin/sh
N=`pwd`
if false ; then
PATH=$N/bin
cyg=yes
else
N=`cygpath -U $N`
if test -d $N/mingw ; then
PATH=$N/mingw/usr/bin:$N/mingw/mingw64/bin:$PATH
fi
PATH=$N/bin:$PATH
cyg=no
fi
export PATH
export N
#to avoid bash warning, create /tmp if it does not exist
if test $cyg = yes ; then
if test ! -e ... |
e5306d99f5c1fb63bf92bf36557d46e36044a148b22c6d7aff2d701eaf57abb3 | Shell | 1,069 | 48 | #!/usr/bin/env bash
# Entrypoint for JS commands.
#
# Usage: dev/js.sh <command> [files...]
#
# Commands:
# fmt Format files
set -euo pipefail
if [ -n "${CI:-}" ]; then
echo "Skipping dev/js.sh on CI (prettier runs in js.yml)" >&2
exit 0
fi
cmd="${1:-}"
shift || true
if [ -z "$cmd" ]; then
echo "Usage: d... |
5d2735d27d9cc5c701d11da8bef112ad2687efa42c9b07dab38af5b01b8c2a50 | Shell | 1,070 | 41 | #!/bin/bash
#SBATCH --job-name=mqall
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=mqall.out
#SBTACH --e... |
4cbc5cd1b8cc0be4f09cddf9ebee2a1efcde8aed9900d02262fb53a5934fa4a5 | Shell | 1,072 | 24 | #!/bin/bash
# command line tests of the tabix mapper
REST_URL='https://grch37.rest.ensembl.org'
REF_ASSEMBLY="/data/reference_genomes/Homo_sapiens.GRCh37.dna.toplevel.fa.gz"
INPUT_FILE="/home/rmjdcfi/analysis/CardiacMRI/gwas_hits/results/SummarLeadSNPMay2021_mapped_nearest_genes.txt"
OUTPUT_FILE="/home/rmjdcfi/analysis... |
51d12692bcc8646d243449400dbfb2a0bfcdbd2c31c9082ba9b71895a1f2190a | Shell | 1,072 | 33 | #FOXG1 site encode:ENCFF085GKB, ENCFF591AJU, ENCFF287YGM
#JUN site encode: ENCFF026KKS, ENCFF488BJY, ENCFF543DLZ, ENCFF550JRZ, ENCFF708RXW
#!/bin/bash
#SBATCH --job-name=npc_a38_cc
#SBATCH --output=final.out
#SBATCH --error=final.err
#SBATCH --time=72:00:00
#SBATCH --mem-per-cpu=20G
#SBATCH --nodes=1
#SBATCH --ntasks=... |
f168269d893d81c3efae9f136c49e39349b6bb1934fd6d12b57d34dd676f167e | Shell | 1,072 | 37 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=sepoffMM
#SBATCH --error=joblog_error_%j.txt
#SBATCH --output=joblog_output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
# data source
path_biotools="/gpfs/sc... |
9f28f1611596ddb37a4c7af80a9cb11593c0ddf95ae1d43c6b390046b98869df | Shell | 1,073 | 27 | #!/bin/bash
#####################################################################
# Copyright 2023-2024 Blue Brain Project / EPFL
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http:/... |
ec91f7bb804768a42cdb89e03aa25ed37308e879de7a8371d0b9044c6d3fc511 | Shell | 1,073 | 18 | #!/bin/sh
# Written by Yapei Xie and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
cd ~/storage
rsync -a --exclude .git CBIG/* Standalone_Xie2025_LBC
# remove useless stable projects
rm -r Standalone_Xie2025_LBC/stable_projects/brain_parcellation/Kong2022_ArealMSHBM
rm -r Standalo... |
00e2a135d63e2fd57000cdea84f617b66b2e46cd4859225641a8836df2b3ae3a | Shell | 1,074 | 36 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --nodes=1
#SBATCH --cpus-per-task=2
#SBATCH --mem-per-cpu=20000
#SBATCH --mail-type=BEGIN,END
#SBATCH --mail-user=alex.lepauvre@ae.mpg.de
#SBATCH --time 48:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/category_selectivity/slurm-... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.