sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
10cd773fd72437d9e95106c84d041104361da333aab29be4cc2c8dc9fb7918c7 | Shell | 1,075 | 33 | #!/usr/bin/env bash
# Simple command to run tests using installed bcbio_nextgen python/nose
# Can pass an optional argument with the type of tests to run
# ./run_tests.sh rnaseq
# ./run_tests.sh speed=1
# ./run_tests.sh devel
# ./run_tests.sh docker
# ./run_tests.sh docker_ipython
# Portable resolution of symlinks htt... |
7683bd287a51afc9587fee53b6b5422a488d111b35d3431d04f6e61af7604491 | Shell | 1,075 | 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... |
04ea44ec1f1c3a10faa892bbaa47fab40cb5809d0ba65da6688b4af21cb947c0 | Shell | 1,076 | 33 | #!/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... |
0b7aea55e76594ca02516f019a7700cf28092624377f2d53bfa508c0e9d867ae | Shell | 1,076 | 33 | #!/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... |
3c4bc84f033dffc40128b60df6649963a31e76889bc185bdddf19ff2b52badcc | Shell | 1,076 | 33 | #!/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... |
5d16773f8cecceaaf1889252ca779575cb1c484b176f8ffa75525bcb7b861186 | Shell | 1,076 | 39 | #!/bin/bash
# =============================================================================
# bsub.sh — LSF job submission helper
# =============================================================================
# Wraps any starsolo command in an LSF bsub job.
#
# Usage: bsub.sh <starsolo_command_and_args…>
#
# Example:
... |
76a598a2249d71e3c608a6b1ab7f25fe7d38365779d45b1b0df8791d1d7b2fab | Shell | 1,076 | 33 | #!/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... |
bc02953c6a132a910e4c3c7adcb8dc81cef2a217ac8e412f2ffb659aa24e5e1b | Shell | 1,076 | 33 | #!/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... |
ee795b71268fc1afcbe30abeac1e7e0860f4a121d1d846618fbaed384dbfd16a | Shell | 1,076 | 33 | #!/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... |
91545609d16eb01c62eeb2d3a0eb26a18df6a3d44cdb3a44f744c5411147f652 | Shell | 1,078 | 36 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --nodes=1
#SBATCH --cpus-per-task=2
#SBATCH --mem-per-cpu=30000
#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/visual_responsiveness/slurm... |
eb94592938979cd844e9457c0ae9cf6ac41e82a7d934d00bbeba88867088f1c3 | Shell | 1,079 | 51 | #!/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" >> $outputScript;
echo "#PBS -l nodes=$nodenumbe... |
1596536cff8693a3852c508ad0fdbc618582ca819bcc312acbdb8726cc4eccf6 | Shell | 1,082 | 27 | #!/bin/bash
#nohup /media/StorageOne/HTS/viralmeta_bioifo/blast_module/nr_blast.sh /media/StorageOne/HTS /media/StorageOne/HTS/PublicData/nt_pb/pfamseq /media/StorageOne/HTS/PublicData/nt_pb/VIRUS_unique_taxa_1000.fasta blastx pfamseq
export path_htsa_dir=$1
export work_dir=$2
export work_fasta=$3 #if program is bla... |
228817dba9b0ad3b6c3c60a6cf816fd2b1909cc4d2213fd48ec431c2e4c9f621 | Shell | 1,082 | 33 | #!/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... |
35a6040d6d8adee7879a9f0a88055223f97e4a33660a5c779c7b1916691f0f6a | Shell | 1,082 | 45 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=sepoffGB
#SBATCH --array=0-1
#SBATCH --error=joblog_error_%A_%a.txt
#SBATCH --output=joblog_output_%A_%a.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
# data sour... |
391257ac5cea38b79cd8d5852a85daeadf0de570ff8b8738bed07259592f05ec | Shell | 1,082 | 33 | #!/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... |
53235666f375f7c9457d154e7d48b1bc1906bf71bc6880757f20695a99b89808 | Shell | 1,082 | 33 | #!/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... |
5ddb82b6b4ae7cf0c110f987deb3863973d6c1bc6beee5166d92420abcbdac2c | Shell | 1,082 | 33 | #!/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... |
bf2ba912da721e69f5f5898386896fd942958fc90e15c1ab64479de5c6f460c5 | Shell | 1,082 | 33 | #!/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... |
c4fc2d4eddc46c749ac09bd338b98f89e17edad0accff15d50d3e4983d4d2e77 | Shell | 1,082 | 33 | #!/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... |
e2537660c6e6f06797215e25ddedc8b7a06ec46be53e687f82bb709503ebac0c | Shell | 1,083 | 31 | #!/usr/bin/env bash
command -v jq >/dev/null || exit 0
input=$(cat)
cwd=$(echo "$input" | jq -r '.workspace.current_dir')
dir=$(basename "$cwd")
model=$(echo "$input" | jq -r '.model.display_name // empty')
model=${model% (1M context)}
cd "$cwd" 2>/dev/null || cd /
branch=$(git rev-parse --abbrev-ref HEAD 2>/dev/nu... |
16220aa4945e44884695ccd922f76b4c7c31ab2eab70e3ac4346f76701fc001d | Shell | 1,084 | 35 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --nodes=1
#SBATCH --cpus-per-task=64
#SBATCH --mem-per-cpu=5000
#SBATCH --mail-type=BEGIN,END
#SBATCH --mail-user=alex.lepauvre@ae.mpg.de
#SBATCH --time 200:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/activation_analysis/slurm-... |
cae8e0be94bff9f0082b0e18bd6182df851376e134c17a0163bf6f668347e2b1 | Shell | 1,084 | 35 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --nodes=1
#SBATCH --cpus-per-task=64
#SBATCH --mem-per-cpu=5000
#SBATCH --mail-type=BEGIN,END
#SBATCH --mail-user=alex.lepauvre@ae.mpg.de
#SBATCH --time 200:00:00
#SBATCH --output=/mnt/beegfs/XNAT/COGITATE/ECoG/phase_2/processed/bids/derivatives/activation_analysis/slurm-... |
0c94d969fa579eed7f9ca441d95404734c80dea44747b5dbd0fdbfa8185d8e7b | Shell | 1,086 | 22 | #!/bin/bash
# Download the marmoset genome
wget http://hgdownload.soe.ucsc.edu/goldenPath/calJac3/bigZips/calJac3.fa.gz
# Subset the small chromosomes to test if the tool works
cd /home2/gkonop/workdir/PROGRAMS
git clone https://github.com/lh3/seqtk.git;
cd seqtk; make
seqtk subseq test.fa test.txt > hg38_chr21_22.f... |
0c59751e28d8f332da241119714accc8e8681a59b802b2d752fedc94c69fa77f | Shell | 1,087 | 39 | #!/usr/bin/env bash
# Build the NISE Apptainer/Singularity container.
#
# Usage:
# bash build_container.sh # -> ./nise.sif (rootless --fakeroot)
# bash build_container.sh my_nise.sif # custom output name
# SUDO_BUILD=1 bash build_container.sh # use `sudo` instead of --fakeroot
set -... |
c0566f02a3349c0b754aaed276e4ef3e3c2ddace5e6185db197cf5e793920668 | Shell | 1,087 | 42 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
ENV_NAME=esnuelML
EXEC_PAT=${CONDA_EV}/envs/${ENV_NAME}/bin/python
source ${CONDA_EV}/etc/profile.d/conda... |
2c9fb48492a1cc1121fe4cb077057d2ad51ad8333b05898341352f8863efb02d | Shell | 1,090 | 25 | #!/bin/bash
#
# Prepare a run directory for structural variant evaluations for NA12878 against
# Genome in a Bottle truth sets of deletions and insertions.
#
# https://bcbio-nextgen.readthedocs.org/en/latest/contents/testing.html#example-pipelines
#
set -eu -o pipefail
mkdir -p config
cd config
wget -c https://raw.g... |
70be92ea7d524467b708173063a30b8064407efbd5895685a00a493635fdb034 | Shell | 1,091 | 43 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_ref_maa_gth_predict_by_rmsd_layer_${LAYER}
SRCP_DIR=src
RUN_MODE=predict
BASE_DIR=... |
617ae90b5626fdd7902d903db7f9b5a268087fa3b5f36df8b09cdf7d200af8fc | Shell | 1,092 | 27 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory
wd=$pd/data/neural_differentiation_dataset/network_inference
mkdir -p $wd/output
# run GRNBoost2 per replicate (10 times each with 10 different seeds)
for filepath in $wd/input/count_matrices/*
do
for i in 1 2 3 4 5 6 7 8 9 10
... |
f8437a4b5e1c6b025572f51531c59e4f23ce7f836ce7c0568f9f7be5cb02cb5f | Shell | 1,092 | 29 | #!/bin/bash
# Download and process the dbSNP ALFA VCF
# TODO: Add traps etc
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
body() {
IFS= read -r header
printf '%s\n' "$header"
"$@"
}
# for the moment, we supply the download and assembly regions, in future I might
# get the... |
f343a7e6122115665b2e1527d9a662a2272e24023945da0adf4d837f74caa3f2 | Shell | 1,095 | 43 | #!/bin/bash
set -x
set -e
cat <<EOF >compile.m
addpath(genpath('GroupICAT/icatb'));
app_file = fullfile(which('gica_cmd'));
compiler.build.standaloneApplication(app_file);
exit;
EOF
host_id=$(sed --quiet --regexp-extended "s/.*HOSTID=MATLAB_HOSTID=(.{12}):.*/\1/p" "${HOME}/license.lic" |
sort | uniq)
# shellch... |
0375dc4c6a74f63ee37d69b8cf67222e7fadc4ae3d805cca21cb4cea7206106d | Shell | 1,098 | 29 | #directory with registration files from Individual to Age-Specific Template
ASTregdir=$1
#Path of Age-Specific Template
AST=$2
#directory with registration files from AST to standard Template
STregdir=$3
#Standard Template Path
ST=$4
#Individual image (brain image or tissue images)
src=$5
#prefix (individual ID or pref... |
9794692cffaffdc1be6426039c254eee15d363031ec38c1dd1805bdfe4a40aec | Shell | 1,098 | 35 | #!/bin/bash
# Path to binary for wb_command
WB_COMMAND=$1
# Path to directory containing HCP cifti timeseries
HCP_DIR=$2
# Path to HCP subject IDs
SUBJLIST=$3
OUTPUT_DIR=$4
while read -r SUBJECT;
do
echo $SUBJECT
for SESSION in rfMRI_REST1_LR rfMRI_REST1_RL rfMRI_REST2_LR rfMRI_REST2_RL;
do
SUB... |
32de868550499e0f939405e854d2b8056ca3cfe7f742216f189f4937034c1bd6 | Shell | 1,099 | 30 | #!/bin/bash
DATAPATH=${1?}
# The input template - generated by hand, not satisfying constraints
CMR_TEMPLATE=$DATAPATH/placenta_template_anterioralign3_bcmrep.vtk
# The target - generated by applying an ANTS transformation to the template
CMR_TARGET=$DATAPATH/placenta_template_def_to_target.vtk
# Fit the template t... |
85642a4bc9216831fab0e623af4b5e8ba21a8295e1714e52ffae198e7818330f | Shell | 1,102 | 48 | #!/bin/bash
set -e # Stop on any error
export LIBnn=lib
echo "Configuring..." # Configure with verbose output
./configure \
--prefix="${PREFIX}" \
--enable-lto=yes \
--enable-R-profiling=no \
--enable-byte-compiled-packages=no \
--enable-java=no \
--enable-nls=no \
--enable-openmp=no \
... |
d37fa2c8b2418e7255a22364a6a4a94f022c3af9366c8d65609efe07e1913b76 | Shell | 1,102 | 28 | #!/bin/bash
#SBATCH -c 4
#SBATCH -t 0-04:00
#SBATCH -p priority
#SBATCH --mem=64G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_aggregate_influence_priority_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_aggregate_influence_priority_%j.err
##########################################################################... |
ac063aa051bebf0708f0b71e5e856130b18bd115dbf9f3ee4b983dd8f3fad069 | Shell | 1,104 | 33 | #!/bin/bash
# A simple bash script to extract the positional data and the VEP annotations
# from the Ensembl DB SNP mapping files, into a counts files.
# requires simple_progress to be installed
infile="$1"
outfile="$2"
clinvar="$3"
tmpdir="${4:-/tmp}"
if [[ ! -r "$infile" ]]; then
echo "[error] $infile not readab... |
e5a58c57e918ac28e8dec003f398a4030c304e81d67228fb451fe9fcc727ac22 | Shell | 1,106 | 38 | #!/bin/bash
echo "Enter the patient folder location: "
read patient
if [ ! -d "$patient" ]; then
echo "Error: Patient folder '$patient' does not exist."
exit 1
fi
echo "Enter the patient group's preprocessed scan subfolder: "
read patient_subfolder
patient_dir="${patient}/${patient_subfolder}"
if [ ! -d "$pa... |
fb17a9e006b42abdd20cfa7c60d98cb07d2d4d2b09e6a932b6fdb0ef4956f57c | Shell | 1,106 | 31 | #!/bin/bash
set -xe
echo "Activating test environment:"
conda activate testenv
if [[ $PYTHON_VERSION == free-threaded* ]]; then
# This is needed because for now some C extensions have not declared their
# thread-safety with free-threaded Python, for example numpy and coverage.tracer
export PYTHON_GIL=0
... |
247fb20e0270345a05d7cdce68022f483dddf43a6ab96b637448184fce307e4d | Shell | 1,107 | 22 | #conda create -y --name ont-fast5-api python=3.6
conda activate ont-fast5-api
#get single F5
multi_to_single_fast5 -i ~/data/ONT/F5_data/mouse/fast5_pass -s ~/data/ONT/F5_data/mouse/fast5_pass/single/ -t 60
#Correction by NGS
gunzip -c ~/data/BGI/mouse/mouse_?.fq.gz | awk "NR % 4 == 2" | sort -T ./temp | tr NT TN | r... |
259261f868ba5d2d62997f5af29fc867c8e773a94196b55454cec4788f05f210 | Shell | 1,108 | 23 | #!/usr/bin/env bash
# Install from master:
# curl -LsSf https://raw.githubusercontent.com/mlflow/mlflow/HEAD/dev/install-skinny.sh | sh
#
# Install from a specific branch:
# curl -LsSf https://raw.githubusercontent.com/mlflow/mlflow/HEAD/dev/install-skinny.sh | sh -s <branch>
#
# Install from a specific PR:
# curl -LsS... |
e8af9e44c67e5fb3687e62e53debfc86ea1c7e17103dc066708fb794916376bf | Shell | 1,109 | 31 | #!/usr/bin/env bash
INPUT_DIR=$1
WILDCARD=${2}
OUTPUT_FILE=${3:-"files.txt"}
PORT=${4:-8081}
echo "Usage: sh serve_local_files.sh INPUT_DIR WILDCARD OUTPUT_FILE PORT"
echo "This script scans INPUT_DIR directory with WILDCARD filter [all files by default],"
echo "generates OUTPUT_FILE [files.txt by default] with a file... |
582467c4791929e41ff78b4cd33387eff73d3070eb416d5c28bc26bf846706fc | Shell | 1,110 | 44 | #!/bin/bash
#SBATCH --job-name=downloadReads
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=19cm51@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=2GB # Job memory request
#SBATCH --time=0-1:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=downloadReads... |
fa3eff2cf8c2f5f25836d9bc3afe7fc0baf0cfca2fc16800eae674e1cb05c3eb | Shell | 1,111 | 25 | #!/bin/bash
# this function runs all the example single kernel regression
#
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# set cluster; change it to cluster="none" if you don't have a cluster
cluster=CBIG_cluster
# set other input variables
outdir... |
58071511d9c7e4e182c9a5952051d66016f61671796106d9b59a4b21a72e909e | Shell | 1,112 | 43 | #!/bin/bash
#SBATCH --cpus-per-task=16
#SBATCH --mem 128G
#SBATCH --ntasks-per-node=2
genome=$1
lane=$2
path=/data/share/htp/perturb-seq/TF94_combined/mapping/
if [[ $genome == "hg38" ]]; then
gg="/data/share/htp/perturb-seq/genome_data/GRCh38_withdCas9"
elif [[ $genome == "macFas6" ]]; then
gg="/data/share/... |
8f5f94fc74021ba62b737ee8285020b01094571eb000b6c6e01336e568ce6510 | Shell | 1,112 | 45 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=32
#PBS -N Intg-spe-INT
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${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}... |
b2611de50bea1387acdde4f8e6aaf8d20c2bb7f3faaeda54b152e4e88d44a476 | Shell | 1,113 | 42 | #!/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.
prefix=$8
RESULT_DIR="$2/output_phe_$1/${prefix}_$1_k_$5_rng_num_100"
FILE=$RESULT_DIR/final_result.mat
if [ -f "$FILE" ]; then
echo "$FILE exis... |
0074389a1722d3c97508f0e6c219a65d80db20988ebc81c713b6b4fa62e5a235 | Shell | 1,114 | 47 | function validate_generic {
local query="$1"
local message="$2"
local opt="$3"
if [ ! ${opt} "$query" ]; then
echo "$message"
exit 1
fi
}
function validate_file {
local query="$1"
local message="$2"
validate_generic "$query" "$message" -f
}
function validate_path {
... |
c0d8c10b3840f0d45ddd867712e01f17382d1d63d21e7fa92253006e2ee70596 | Shell | 1,114 | 45 | #!/bin/bash
#PBS -q fat
#PBS -l walltime=72:00:00 -l nodes=1:ppn=16
#PBS -N Intg-spe-EXC
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${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}
e... |
ba551ddd26801af10bd1d2cfed6bc0332502891643e1fc547427cf8e9732f735 | Shell | 1,115 | 61 | #!/bin/bash
# install stuff needed for the `script` phase
# Where rustup gets installed.
export PATH="$PATH:$HOME/.cargo/bin"
set -ex
. "$(dirname $0)/utils.sh"
install_rustup() {
curl https://sh.rustup.rs -sSf \
| sh -s -- -y --default-toolchain="$TRAVIS_RUST_VERSION"
rustc -V
cargo -V
}
instal... |
df6296f3c77e051ec7247bfe3817f685a04c11985b7d5cbf2f818381a758c96c | Shell | 1,116 | 37 | #!/usr/bin/env bash
set -euo pipefail
# Build and deploy the ComptoxAI static site (Sphinx docs + React app) to S3.
# Usage: ./infra/deploy-site.sh [--invalidate]
#
# Requires: AWS CLI configured, S3_BUCKET env var set.
# Optional: CLOUDFRONT_DIST_ID env var for cache invalidation.
REPO_ROOT="$(cd "$(dirname "$0")/..... |
f2d633a4c92416c2bd2b455275021ab6cc6540f8cb9c440bf126dd68bfa3acbe | Shell | 1,119 | 34 | #@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... |
f0188f0e41222f5614d54e293577ad56f49e29ad2f6317a8bfb14ab26391286e | Shell | 1,121 | 30 | #!/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 "Licens... |
31b5b514da08b4293c6a12402592c182f077b33cc7b8aa1d89e0035e47a42584 | Shell | 1,122 | 44 | #!/bin/sh
# this script creates the app bundles so the Finder will allow
# drag and drop, double clicking of apps, and double clicking of
# hoc files.
if test "$1" = "" ; then
echo "launch_inst needs 3 arguments"
exit
else
cpu=$1
IDIR="$2/.."
srcdir="$3"
objdir=`pwd`
fi
bindir="$2/${cpu}/bin"
# Note: .icns fil... |
de350391ff417374c8cf02d4e22daa8aab940e172d10fddafb234bd3f055d322 | Shell | 1,122 | 48 | #!/usr/bin/env bash
set -euo pipefail
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
EVROOT="${maindir}/derivatives/fsl/EVFiles-FIR"
[[ -d "$EVROOT" ]] || { echo "ERROR: EV root no... |
e152995fb87370595a7bdc361680d2574898c2b95d3346a8f8aef9031dadcd49 | Shell | 1,124 | 36 | #!/bin/bash
#SBATCH --time=00-06:00:00
#SBATCH --mem=20G
#SBATCH --cpus-per-task=1
module load bedtools
module load gatk
module load bcftools
# read the input vcf
invcf=$1
# read the reference genome
ref=$2
# read bed file with repetitive and low complexity regions
maskbed=$3
# declare the output vcf from the input ... |
04b2ac38221150f09f4ee77e3f2d205c00cd7469e8659e3c356439e5492a86d2 | Shell | 1,126 | 31 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script is specific to CBIG HPC cluster.
# Initialize directory
input_dir="$CBIG_REPDATA_DIR/stable_projects/predict_phenotypes/Chen2024_MMM"
base_dir="$CBIG_CODE_DIR/stable_projects/predi... |
2076609c6aa24a6ca45bf94f210fcb5541074ad3db8f26d946e61eb1c6a78829 | Shell | 1,126 | 19 | #!/usr/bin/env bash
set -eu -o pipefail
# order is important, "REPLACEME" -> "workflow"
cat \
| sed 's/github.com.argoproj.argo_workflows.v4.pkg.apis.workflow.v1alpha1./io.argoproj.REPLACEME.v1alpha1./' \
| sed 's/github.com.argoproj.argo_events.pkg.apis.common./io.argoproj.events.v1alpha1./' \
| sed 's/gi... |
658401cf03378d83102be3a98534c47457c810d2e2693503282c59dc67e950a2 | Shell | 1,128 | 48 | #!/bin/sh
# check if script is running on Github
if [ -f "$GITHUB_PATH" ]; then
# setup github runner
case $OS in
Windows*)
cat <<EOF >> $GITHUB_PATH
/usr/local/bin
/usr/bin
/bin
EOF
;;
*)
;;
esac
fi
# setup git
git config --local filter.compress.clean ... |
b8584b7242f38eaccd6a6109e424d8d80b022284017ddfb66adbd0ed18835e0e | Shell | 1,128 | 48 | #!/usr/bin/env bash
set -euo pipefail
export PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True
X_NPY=""
META_NPZ=""
OUT_ROOT="/mnt/d/eeg_v64_storage/runs/V13_MOTOR_POOL_5x5_EMA_$(date +%Y%m%d_%H%M%S)"
mkdir -p "$OUT_ROOT"
echo "[OK] OUT_ROOT=$OUT_ROOT"
# Core hyperparams (NPJ: keep fixed)
EPOCHS=120
BATCH=256
LR=3e-... |
51bab3fa90376d5fdf320917dda8039a31befb01b0a5bd19ace40e9d83bc7532 | Shell | 1,130 | 30 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=VEP_annotation
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=20
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=200G
#SBATCH --chdir /data7/WGS_processing/src # TODO: set dir to cache ... |
2429fbd21181942e4b4ff5f45f2525486583e23c7422267e3edc34603c71e9b9 | Shell | 1,131 | 40 | #!/bin/bash
# This is a script shell for deploying a pymeshlab-portable folder.
# Requires a properly built PyMeshLab (see 1_build.sh).
#
# This script can be run only in the oldest supported linux distro
# due to linuxdeployqt tool choice (see https://github.com/probonopd/linuxdeployqt/issues/340).
#
# Without given a... |
004269edcf488118f4ce6448dbf66ea5db15d3a7026dc208167edbba0dbd7e8a | Shell | 1,132 | 46 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Mouse_IndexPath_35_A}
DataPath=${FastpPath_A}
FASTQ1=${FASTP1_A} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPath... |
393b5189abe4f2445f84cf610381e166737b61e3bef17c196eb1edf036f58a6a | Shell | 1,132 | 46 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Mouse_IndexPath_50_A}
DataPath=${FastpPath_A}
FASTQ1=${FASTP1_A} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPath... |
24cd7b234482b8dc0cf4d1dff6900383a436db7899ac772593fb43c7b6f8c7e4 | Shell | 1,133 | 48 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
RUN_NAME=optimizing
SRCP_DIR=src
RUN_MODE=optimize_conf
BASE_DIR=${WORK_ROT}/data/references/benchmark
RE... |
9c78cadee9fcb4ad4aa311acc87903014f098b7834c1bfe9afcba22a4011017c | Shell | 1,133 | 46 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Rat_IndexPath_75_A}
DataPath=${FastpPath_A}
FASTQ1=${FASTP1_A} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPath_A... |
58692357b2c0bd688de58970fbb2921a272799a5aacb1db85784e03becc1042f | Shell | 1,134 | 27 | #!/bin/bash
########################################################################
# #
# This pipeline is only for processing the multicenter diffusion data. #
# From Qiqi Tong, CBIST, Zhejiang University. #
# ... |
b0d939299f1ca749fb9a901654f4a69555ee6342e2ef2f431bfd2c624745ba07 | Shell | 1,134 | 46 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Mouse_IndexPath_125_A}
DataPath=${FastpPath_A}
FASTQ1=${FASTP1_A} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPat... |
b8d4e97a5e9a2942bb0c83c39a90c4b8754f1ca98c1956c36cd092db3813e2b3 | Shell | 1,134 | 46 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Mouse_IndexPath_100_A}
DataPath=${FastpPath_A}
FASTQ1=${FASTP1_A} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPat... |
d8e58a6a41ab5eae0763491af40d4091aaf7f2de3c5b1d4699e723af5e8b6df3 | Shell | 1,134 | 46 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Mouse_IndexPath_150_A}
DataPath=${FastpPath_A}
FASTQ1=${FASTP1_A} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPat... |
07426778974d5f099649f4e19bd9819c0ff184ceaf7234eef11bd8b1c8174299 | Shell | 1,135 | 46 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Rat_IndexPath_150_A}
DataPath=${FastpPath_A}
FASTQ1=${FASTP1_A} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPath_... |
ce7d5167c10737f2eb864cf01ea6d440211514fbb8d6db413f49f7f5f1815580 | Shell | 1,135 | 46 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ID=$1
ConfigFile=$2
source ${ConfigFile}
#####
IndexPath=${Rat_IndexPath_125_A}
DataPath=${FastpPath_A}
FASTQ1=${FASTP1_A} # this script is for FASTQ filtered by FASTP
FASTQ2=${FASTP2_A} # this script is for FASTQ filtered by FASTP
OutPath=${AlignPath_A}
AllOutPath=${AlignAllPath_... |
764851f7895d026e35b4ec71a9f5dc028cab07bce5523eeb6538cfe48405e705 | Shell | 1,137 | 26 | #!/bin/bash
set -eu
if [[ "$#" -lt 6 ]]; then
echo -e "Please provide:"
echo -e " [1] local directory of GATK build (required)"
echo -e " [2] cluster name (required)"
echo -e " [3] absolute path to the output directory on the cluster (HDFS,required)"
echo -e " [4] absolute path to the BAM on t... |
82f09a01b458491e8883567c907c6ac2ef67e327457a0731c145b9f13f35732b | Shell | 1,137 | 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 accross many subvolumes.
# Illustration of how the current volume decomposition and handling
# of cues "in the eye of the behold... |
eb09e947fa96d1f3d1fab53d89f31661ec5901b636646a8430653016c966b1d4 | Shell | 1,137 | 22 | #############################################################################################
# 超参数设置
# GPU_ID: '0','1','2','3','4','5','6','7'
# DATASET: 'CIFARFS','CUB_Croped','Aircraft','CUB','FC100','StanfordDog','StanfordCar','MiniImagenet','TieredImagenet'
########################################################... |
411780ab6152db65d9ee39f67e717e46cf08c6fee924723809e2ccf42979841c | Shell | 1,138 | 37 | echo "The Heart modelling code is under ${HEART_MODELLING_CODE}"
echo "The Data is under ${PAPER3_DATA}"
python ${HEART_MODELLING_CODE}/auxiliar/conductionSystem/projectSubendo_5.py \
--data_path ${PAPER3_DATA}/Models/invivo/he/sample2 \
--cs_name lva_up_lvs \
--out_name cs_subendo_i... |
793ea70534cef67bf90a48b1763422e50b7f1a1de50e9af05cb3e7e55f0b5a47 | Shell | 1,139 | 29 | #!/usr/bin/env bash
# Downloads the Claude Code binary from the official distribution URL and verifies it against the
# checksum published in the per-version manifest, avoiding `curl | bash` which
# pipes an unverified script with access to CI secrets.
# Ref: https://github.com/dagster-io/erk/blob/61ecee08754717959bb2f... |
50902b67d46750a27d1d1a5df0de002353b14427e6617f3bcd8e83e4426c7f4d | Shell | 1,140 | 32 | #!/bin/bash -e
echo "Installing dependencies"
python -m pip install --upgrade pip build wheel
python -m pip install --upgrade -r requirements.txt
if [ -n "${OPTIONAL_DEPENDS}" ]; then
for DEP in ${OPTIONAL_DEPENDS}; do
if [ ${DEP} == "mayavi" ]; then
python -m pip install numpy vtk==9.0.1
... |
515687e7efd5f708f638befbdde62f24b0be9e0945dd706a1f8988b2ba232adb | Shell | 1,140 | 36 | #!/usr/bin/env bash
# Setup pre-commit hooks for the byteff2 repository.
# Works with both venv (pip) and uv environments.
set -euo pipefail
REPO_ROOT="$(cd "$(dirname "$0")" && pwd)"
cd "$REPO_ROOT"
# -- ensure we are inside a git repository -----------------------------------
if ! git rev-parse --git-dir >/dev/null... |
632c118430725d5ec1c260ab902fa74af414b715bb8fee9a13413efc8ce581d8 | Shell | 1,140 | 41 | #!/bin/bash
## Check if xtb is installed
#if ! command -v xtb &> /dev/null
#then
# echo "xtb could not be found. Please install xtb to use this script."
# exit
#fi
### generate molden.input
# Loop through all molecule_*.xyz files in the current directory
for file in DPI_xyz/*
do
echo "file is: $file"
fo... |
c105b5abfa9cfa07667078e8948dd1906e08bdb54901687e1cd8889fd28642d2 | Shell | 1,140 | 42 | #!/bin/bash
REF_POP_FILE="$HOME"/ref_pop_map.txt
SIMPLE_PRS_PATH="$HOME"/code/merit/scripts/simple_prs.py
# OUTDIR="/scratch/simple_prs_out"
# GWAS_FILES=("/scratch/bgen_test/UKBB.GWAS1KG.EXOME.CAD.SOFT.META.PublicRelease.300517.txt.gz")
OUTDIR="/data/simple_prs_out"
GWAS_FILES=("/data/bgen_test/UKBB.GWAS1KG.EXOME.CAD.... |
77707de95edc50de9c9370888185c36d55bf1aa215d901a00abd2d83b33ce7c3 | Shell | 1,142 | 54 | #!/bin/bash
copy_with_suffix() {
src="$1"
dest_dir="$2"
base=$(basename "$src")
name="${base%.*}"
ext="${base##*.}"
[[ "$name" == "$ext" ]] && ext="" || ext=".$ext"
target="$dest_dir/$name$ext"
i=1
while [ -e "$target" ]; do
target="$dest_dir/${name}_$i$ext"
((i++... |
a29260d5caffe481a7651b3764b8800cb729cdd217be40c8e40888e87ed165fe | Shell | 1,145 | 36 | ####Benchmark4####
FASTADIR=./dockground/fasta/
META=./dockground/dockground.csv
MODE='bench4'
OUTDIR=./dockground/fasta/merged/
#python3 ./merge_fasta.py --fastadir $FASTADIR --meta $META --mode $MODE --outdir $OUTDIR
#####Marks#######
#Positive set
FASTADIR=./marks/fasta/
META=./marks/final_ids_lens.csv
MODE='marks'... |
7fc9dacfb11d94dfeb884da7a48cd480a87e82fbd122a2c2d3c87225525c4da6 | Shell | 1,146 | 22 | #! /bin/bash
step=1
## Parcellate individual surface using Schaefer300 Atlas
if [[ $step -eq 1 ]]
then
sour_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/NIIDATA/T1
atlas_dir=/Data/sharehome/huyang/MyAtlases/Schaefer
sublist=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/LIST/sublist_init.txt
... |
f45d808382b888b0875d568b43e76ddf35ea6ab68f3c20a047be99946cef82b8 | Shell | 1,146 | 29 | #!/bin/bash
# this function runs all the example linear ridge regression
#
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# set cluster; change it to cluster="none" if you don't have a cluster
cluster=CBIG_cluster
# set other input variables
outdir=... |
952895da7a3092c4ed484ba4447fee7675371fdec8890a9fa30b6028c3628ba8 | Shell | 1,148 | 56 | #!/bin/sh
# from "cvs update" to file in ftp site versions/alpha directory
NSRC=$HOME/neuron/nrn
cd $NSRC
oldver=""
if test -f oldver ; then
oldver="`cat oldver`"
fi
cvs update -d
newver="`sh nrnversion.sh commit`"
if test "$oldver" = "$newver" ; then
exit
fi
./build.sh
os="`sh config.guess|sed 's/^\([^-]*\)-\([^... |
3dd6fec0985a3489b30c9071b180b0f10433d9b168cf28a0d2c3da41e2f52a80 | Shell | 1,149 | 20 | #!/bin/bash -l
#SBATCH --job-name=modelbuild
#SBATCH --time=1:00:00
#SBATCH --account=proj83
#SBATCH --partition=prod
#SBATCH --mem=0
#SBATCH --exclusive
#SBATCH --constraint=cpu
source /gpfs/bbp.cscs.ch/home/pokorny/ToposampleKernel/bin/activate
python -u ../../library/modelling.py /gpfs/bbp.cscs.ch/project/proj102/... |
d2c33f971c67d5f0329a906166d3ea06d9454e7928ddbff9602106f63d714662 | Shell | 1,149 | 46 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=soffSTRT
#SBATCH --error=joblog_error_%j.txt
#SBATCH --output=joblog_output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
function getSampleName {
local fi... |
d8eb21580ab4fe8d85fcd880aa0271e29f25171c0ace3ec5d177634904ca6567 | Shell | 1,150 | 61 | #!/bin/bash
#Author: Yang Li <yal054@ucsd.edu>
#File: igv.createXML.sh
#Create Date: 2019-10-04
usage() {
cat <<EOF
Usage: igv.createXML.sh [-h] [-p <path>] [-u <URL>] [-g <genome>] [-o <output>]" 1>&2
Description:
Options:
-h, --help Print help and exit
-p, --path local path
-u... |
a42be24aa8fb2ad05912ac0f65c5195c73c98f303083a7922bf2219a2b020f12 | Shell | 1,151 | 42 | #!/bin/bash
## Example bash script to call peaks using MACS2 on merged replicates. To run this script, do: qsub -t 1-n submit_macs2.sh CONFIG IDS BAM_DIR
## CONFIG is the path to the file scripts/config.sh which contains environment variables set to commonly used paths and files in the script.
## IDS is a list of samp... |
e4501145285d5d2b03d46b1a2ae7652ec713271d2d9eb33d5ef20fb468c1a04d | Shell | 1,152 | 42 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=32
#PBS -N MetaUS-spe-INT
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${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_N... |
7317e39f06bee887fee2ec7c95452d2f31979d8e0ddcb2cf1d743bb52e92e06c | Shell | 1,153 | 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 "Lice... |
4d209c61c7eb512b101aaeeb9f03fee955479803b047b917d507826dd93d2219 | Shell | 1,155 | 41 | #!/bin/bash
### This script runs infercnv on each sample in the CARE astrocytoma dataset ###
# Activate the conda environment for running inferCNV, if not currently active.
module load miniconda
conda activate infercnv_env
### Input arguments ###
ARRAYID="`expr $1`"
# Sample ID list.
SAMPLE_ID_FILE="/vast/palmer/pi... |
8fe8f2cbaa9de9a472103766957baba2a9b5c68713c6f9c7e89d81fcdecb3b27 | Shell | 1,156 | 41 | #!/bin/sh
#can save cellbuild session after
host=hines@10.10.0.2
#host=hines@128.178.97.80
# needs to be executed in nrnwinobj
m=/c/marshalnrn64/nrn/bin
mx=$host:mxe/usr/x86_64-w64-mingw32.shared
mxt=$host:mxe/tmp-neuron-x86_64-w64-mingw32.shared
scp $mx/x86_64/bin/libIVhines-3.dll $m
scp $mxt/nrn-7.5/src/modlunit... |
3db78c495a2786d7887897b9e908b96ce28018c05593bc920fe715fcbb14457b | Shell | 1,160 | 32 | #! /bin/bash
/home/tolhs/fslcompiled/fsl/bin/flirt \
-in /data/BCBToolKit/Tools/extraFiles/Priors/brainWithSkullTemplate.nii.gz \
-ref /home/tolhs/fslcompiled/fsl/data/standard/MNI152 \
-out /data/Chris/ants_NKI_priors_mni \
-omat /data/Chris/ants_NKI_priors_mni.mat \
-bins 256 -cost corratio -searchrx -90 9... |
8329cf90e4d4cf27eed9ee9705cb9b153fbac8ca5e5a2a0218d1fe35ab818ff1 | Shell | 1,161 | 26 | #!/bin/bash
# define project directory
pd=/your/project/directory/
mkdir -p $pd/data/neural_differentiation_dataset/genomes/
cd $pd/data/neural_differentiation_dataset/genomes/
# get hg38 genome sequence and annotation
wget https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-GRCh38-2020-A-2.0.0.tar.gz
tar... |
5d472df8a30bc560503a28634f87a981ac9d0c917e227ecf4fde1d4d015bb12c | Shell | 1,164 | 38 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=12
#PBS -N Intg-ssv4
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${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}
ex... |
a8c359f41b911eff4b7cb2cf0327c44a3613aad89ee41e5ce0f19b82f65c8497 | Shell | 1,167 | 41 | #!/bin/bash
# change to the dir of the script
cd $( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
# change to the dir to the project
cd ../..
function title() {
sharps="#################################"
printf "\n%s\n%s\n%s\n" ${sharps} "$1" ${sharps}
}
hpo_config="AI/hpo.yaml"
output_di... |
84010f66ec6ae7a9e396c6ee77ab1c715c192714b7eb06c604a7347414bef0db | Shell | 1,168 | 43 | #!/bin/bash
# Run CellBender
module load python/3.8.x-anaconda
module load gcc/12.2.0
source activate cellbender
source ~/load_modules.sh
# input dir
INPUT_DIR="/home2/gkonop/project/02_MATRIX_FOR_CELLBENDER/KRIENEN_FERRET"
### cellbender
# Directory where cellbender results will be stored
DIR="/home2/gkonop/project... |
b7586a9e3534555d558e890ca719fcfa0b944e4f3f9619de4a5faeb4e2814910 | Shell | 1,171 | 43 | #!/bin/bash
#PBS -q fat
#PBS -l walltime=72:00:00 -l nodes=1:ppn=32
#PBS -N MetaUS-spe-EXC
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${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}... |
e05107911a72f02b1dddce46e113daed8c786f3c7bdf966316e55508adae8c2a | Shell | 1,172 | 53 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ConfigFile="/home/joonho345/1_Epilepsy_RNA/script/Scratch_settings.sh"
source ${ConfigFile}
#ConfigFile=$1
#source ${ConfigFile}
#####
OutPath_50=${IndexPath_50}
OutPath_100=${IndexPath_100}
OutPath_125=${IndexPath_125}
OutPath_150=${IndexPath_150}
#####
STAR \
--runThreadN 10 \
... |
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