sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
586da65ac7ae19ce2d3712df5fbd848818b21a92f7f38a4f60ff6982ee1a0933 | Shell | 1,173 | 41 | source /home/fs0/jdf650/scratch/miniconda3/bin/activate fsl_sub
cd /home/fs0/jdf650/scratch/DPhil-Human-fMRI/DPhil-Human-fMRI-BrainModelling
# run_create_design=false
# run_fit=true
# # Create design files for all subjects and sessions
# if $run_create_design; then
# for subject in {1..20}; do
# for sess... |
547d4c378bd013a0444682a28d8028f1d39af41c9a2bbd87c475a002a2a4d236 | Shell | 1,174 | 25 | SUBJECTS_DIR="PATH/TO/DATA"
MGH_RLT_DIR="PATH/TO/RESULT"
export FREESURFER_HOME="PATH/TO/FREESURFER"
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=$SUBJECTS_DIR
export FSLDIR="PATH/TO/FSL"
export FS_LICENSE="FREESURFER/license.txt"
source $FSLDIR/etc/fslconf/fsl.sh
for id in $MGH_RLT_DIR/*.mgh; do
... |
a2017866b1a5c2380d050fff53c40e71206126e475334a44ee8b32a9d03fdd2a | Shell | 1,177 | 36 | #!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
set -x
ExtractDir=$CBIG_CODE_DIR/data/templates/surface/
SubjectDir=$1
SubjList=$2
ResamplingMethod='BARYCENTRIC -largest'
for Subject in $SubjList
do
for Hemisphere in L R
do
MetricIn=$Subje... |
5b15e93b8cce55dd2a57abe8e391af2c79c16880187412c1abe155c0d9aafae2 | Shell | 1,178 | 32 | #!/bin/bash
# validate a vcf file against genome in a bottle calls for NA12878
# $1 - variants.vcf.gz
# #2 - giab file, i.e. bcbio/genomes/Hsapiens/GRCh37/validation/giab-NA12878/truth_small_variants.vcf.gz
# $3 - regions.bed
# $4 - rtg sdf reference, i.e. bcbio/genomes/Hsapiens/GRCh37/rtg/GRCh37.sdf
# rtg manual
# ht... |
2ccbcbc854ef10a510d02b59428ed068e24cbfd68aeb470460c7f4c3acc985dc | Shell | 1,179 | 22 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh # Change the path to your conda.sh file
conda deactivate
conda activate XGBoost
# Define the path to your script and log directory
script_path='/data/project/sleep_ENIGMA_Cognition/Codes/ENIGMA_Sleep_Cognitive/Code/Out-of-sample_validation/preprocessor_m... |
1fff74be14652f579950c17236aae8d273586fddd6935fb5b5d79c07977f2b3b | Shell | 1,180 | 41 | #!/bin/bash
#PBS -q gpu
#PBS -l walltime=200:00:00 -l nodes=gpu03:ppn=8 -l mem=50G
#PBS -N C2C
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="cell2location"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREAD... |
aae37b2e981978c2ced96922f4edcb48ccc3e60ae814ce260c5fdd5a15bcbc30 | Shell | 1,180 | 40 | #!/bin/bash
#SBATCH -c 8
#SBATCH -t 1-12:00
#SBATCH -p medium
#SBATCH --mem=128G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_betweenness_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_betweenness_%j.err
#
# Re-run betweenness centrality on the latest BANC v888 edgelists.
# Runs v3 + v2 sequentially (each ~hours... |
338ace0ab94ed9a525cf144885e8e7dbdb1f64bc2365ad33946f93a560316d3f | Shell | 1,182 | 41 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script takes a FASTA file and reformats it such that the sequences
# themselves are all on a single line below the sequence nam... |
8ba1697dfef79c1da7861ec2b5d5700c13139252914174c9554f28055453694c | Shell | 1,182 | 32 | #!/bin/bash
#SBATCH -c 4
#SBATCH -t 0-18:00
#SBATCH -p medium
#SBATCH --mem=150G
#SBATCH -o jobs/banc_assess_synapses_plot_%j.out
#SBATCH -e jobs/banc_assess_synapses_plot_%j.err
# Regenerate EDF 1d (banc_synapse_proportion_on_cell.png) with the corrected
# Y axis (proportion 0-1 instead of percent 0-100). Just the fi... |
8c487b27440cea1223628afa08fc063ae007f95d03b1297b09174938c955c854 | Shell | 1,183 | 32 | #!/usr/bin/env bash
# Copyright (c) Meta Platforms, Inc. and affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# Propagate failures properly
set -e
mcss_path=../../habitat-sim/docs/m.css
# Regenerate the compiled CSS file (yes, in... |
0271934c6dfd7d0693b860e5b120d4e0de32c988f6cf0970bef104afa6f95a1e | Shell | 1,185 | 31 | #!/bin/bash
#
# This scripts injects a function named `DEBUG_STOREFUNCTION()` into a Igor Pro
# Procedure directly after the declaration of variables.
#
# The script can be used to count the calls to functions during code execution.
# Its result is similar to code coverage statistics for Igor Pro.
#
GIT_TOPLEVEL=$(git... |
e2d33fda8580d13bbb100c4f38776a659e10bf9e83b1e96c1b90ff63fcf22700 | Shell | 1,186 | 29 | #!/usr/bin/env bash
# Récupère les réseaux réels depuis des miroirs GitHub accessibles, puis
# construit les edgelists consommés par bench_epidemic.py.
set -e
mkdir -p data && cd data
# 1) ego-Facebook (SNAP McAuley & Leskovec, NIPS 2012) — 4039 / 88234
curl -sL -o facebook_combined.txt \
https://raw.githubuserconte... |
aae86be2f4bd8ba9eca33c0352d0b046a471f695e3e1c71a664dfa8b26621fdf | Shell | 1,188 | 45 | #!/bin/sh
#/media/StorageOne/HTS/VirusMeta/ffp/ffp_block_step1.sh /media/StorageOne/HTS/PublicData/nt_pb/virus_block_ffp_7 /media/StorageOne/HTS/PublicData/nt_pb/family 7
export path_htsa_dir=/media/StorageOne/HTS #path to HTSA analysis dir
export path_pipeline=VirusMeta
export working_dir=$1
export family_dir=$2
# e... |
ebc5137d11320dbd0f34ad52bf78c194e556837f2309d397dd0d7145ecd4fee4 | Shell | 1,190 | 45 | #!/bin/bash
# Set base directories
project_dir="/project/normative_cerebellum"
input_dir="${project_dir}/data"
output_dir="${project_dir}/segmentations"
# Subject list
subject_list="${project_dir}/hcpd_subjects.txt"
# Atlas names
atlas_names=(
"fusion"
"MDTB"
"rest"
)
# Atlas files (in same order as atlas na... |
566240a4f23a6b413e16cc580d0016be4cf88bc0aefd5028141594f293ce48be | Shell | 1,192 | 43 | #!/bin/bash
#for sub_num in {1..30}
#do
#singularity run --cleanenv -B /mnt/c/Users/qying/Desktop:/mnt \
#/home/qying/fmriprep-24.0.0.simg \
# /mnt/TN_E /mnt/TN_E_prep \
# participant \
# --skip_bids_validation --fs-license-file /mnt/license.txt --fs-no-reconall --participant-label sub-${sub_num}
#done
for ... |
433a48beda74a1a067f2aa6abf1e1de6bdd6c8c8806df4bfc3c355d192d3b83f | Shell | 1,193 | 43 | #!/bin/bash
### This script runs infercnv on each sample in the CARE oligodendroglioma 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/pa... |
540de3769712511f0cc40bc76f740f331128070751af5d3f058584b96c6ad16a | Shell | 1,195 | 28 | #!/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... |
f1f0b894866364bd7d74c9b03d52852e4cb3c27d52140794fd5cdb8b36527fca | Shell | 1,198 | 43 | #!/bin/bash
#SBATCH --job-name=brmmu04040.2vs14
#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=brmmu04040... |
4998b3b37b9ee66ec689e2336973c054e94aa2ac166119733f486def1b41da9a | Shell | 1,199 | 45 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2000
#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/fs/recon_all-%A_%a.out
#SBAT... |
635d6deeecc1a256feb1aad5b3bd234087815caf19aac9950b47ccc4437f0a16 | Shell | 1,199 | 50 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cuttlefish
#SBATCH --time=999:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=soCanu
#SBATCH --error=error_%j.txt
#SBATCH --output=output_%j.txt
# --- set draft version --- #
draft_assembly="$1"
if [ -z "$draft_assembly" ]; then
echo_error "... |
45ca213e20e733eb9ee1790748d4243f1d3637089566e616526c43b40b5148b0 | Shell | 1,200 | 28 | #!/usr/bin/env bash
set -euo pipefail
python scripts/prepare_homology.py \
--mode blast \
--sp-ref C_elegans \
--sp-que D_melanogaster \
--query-display-name Drosophila \
--ref-protein examples/homology/celegans_dmelanogaster/raw/Caenorhabditis_elegans.WBcel235.pep.all.fa \
--que-protein examples/homology/... |
68d81d3f01d3a5328edf0e5b761a9af24ebf595c5afebe011c9ca9d9b4f8a485 | Shell | 1,201 | 44 | #########################################
## To prepare step 1 file that will be used in regenie/BOLT/fastGWA/SAIGE in UKB WB samples
##
## array bed
step1file_pre=$1
## imputed bgen
step2file=$2
## list of FID/IID for UKB WB samples with covariate info
sample_keep=$3
# bed region file listing ICLD and low-complexity ... |
e96789ae9aabe88302b1825a7d4a41c972c296044eb5bf1aae001cd3716aebfa | Shell | 1,203 | 38 | #!/bin/bash
set -e -u
echo -e "\n START: SurfaceSmoothing"
Subject="$1"
ASLVariable="$2" #$StudyFolder/$SubjectID/T1w/ASL/CIFTIPrepare/<perfusion_calib or arrival>
T1DownSampleFolder="$3" #"$StudyFolder/$SubjectID/T1w/fsaverage_LR32k"
AtlasDownSampleFolder="$4" #"$StudyFolder/$SubjectID/MNINonLinear/fsaverage_LR32k" ... |
8641f62e174aca54539dc406692d0a5c7171a8ef117981d00516abc1aa85eec6 | Shell | 1,207 | 44 | #!/bin/bash
#####
# Example:
# $CBIG_CODE_DIR/stable_projects/preprocessing/CBIG2022_DiffProc/MRtrix/ \
# CBIG_DiffProc_tractography_4_del_tractograms.sh $subj_list $output_dir
#
# This script removes tractograms produced by the CBIG MRtrix pipeline to save storage space. A list of
# subjects and the output... |
aa607f806a6b253708c2630d25514c48a4765d9d1681682c018d99c05465be02 | Shell | 1,208 | 42 | #!/bin/bash
#PBS -q gpu
#PBS -l walltime=200:00:00 -l nodes=1:ppn=16 -l mem=100G
#PBS -N C2C
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="cell2location"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=... |
18477607b4dc2f65914647138e6c357077d26ce3f336762933d5405219d4c2a8 | Shell | 1,209 | 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
#Atlas information defined on Standard Template (i.e. Parcellation mask)
src=$5
#prefi... |
47f67dbb37218d2f241281b374304abff6fbb755b2a44b2b7fa6feff518dc2ab | Shell | 1,209 | 33 | #! /bin/bash
step=2
## Calculate the ROI-based sulc measure
if [[ $step -eq 1 ]]
then
sour_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/NIIDATA/T1
sublist=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/LIST/sublist_init.txt
for sub in $(cat $sublist)
do
export SUBJECTS_DIR=${sour_dir... |
770852a2abca63e6844affc05235e99a56643e466aac246b70bbd6bec8ef03e0 | Shell | 1,209 | 30 | #!/bin/bash
# Run full pipeline (injection + detection + matching + photometry + catalogue)
# with IRAF available for aperture photometry. Clusters are sampled directly from SLUG
# (no user-supplied coords). Requires IRAF to be installed.
set -e
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
cd "$ROOT"
# Defa... |
ca85e8e89fa3f54a18b4de1d572ac50c9cc0ff8a1dad92a9b2dc70534a65294a | Shell | 1,209 | 35 | #!/bin/bash
## Example bash script to align ChIP-seq reads to the reference genome using BWA. To run this script, do: qsub -t 1-n submit_bwa.sh CONFIG IDS READ_DIR 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... |
2ebffec6a4fc217879ef775adb6d4c5a492819a6eb9eb6637d62c59f27e8a77d | Shell | 1,210 | 34 | #!/bin/bash
#SBATCH -c 1 # Request cores
#SBATCH -t 0-96:00 # Runtime in D-HH:MM format
#SBATCH -p medium # Partition to run in
#SBATCH --mem-per-cpu=10G # Memory per core
#SBATCH -o jobs/banc_ngl_%j.out # File to whic... |
c63c63e2a1fdbb43764b9494895b4c994c99c828937c464315fc788dc142e14a | Shell | 1,212 | 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
# "Lic... |
5eea52ac3e89fdfd2a9755b4632bbe2a86908d2ae8b56ec654086f7c5c4d402d | Shell | 1,213 | 51 | #!/bin/bash
CONDA_EV=~/miniconda3
WORK_ROT=~/work/MeCAP
cd ${WORK_ROT} || exit
RUN_NAME=mecap_scaf_mca_layer_0
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}/data/results
SAVE_DIR=${RESL_DIR}/${RUN_NAME}
ENV_NAME=mecap
EXEC_PAT=${CONDA_EV}/envs/${ENV_NAME}/bin/python
source ${CONDA_EV}/etc... |
df80dd04facb1f1ddd2afc80b36c2ce1441d5bd2be45ab2f946a049701208254 | Shell | 1,217 | 37 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=4
#PBS -N RenameFrag
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${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}
... |
4c11329af7b2589eeea5d64d7e0196b79c0f0034fe1a0a06a135c864af96d039 | Shell | 1,218 | 37 | #!/bin/bash
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
set -x
ExtractDir=$CBIG_CODE_DIR/data/templates/surface/
SubjectDir=$1
SubjList=$2
ResamplingMethod=BARYCENTRIC
for Subject in $SubjList
do
for Hemisphere in L R
do
MetricIn=$SubjectDir/"$Subj... |
383f5ea49ddf9e35381e0826f90ebd232793dce464bb6f81e5f0c97543d96dc7 | Shell | 1,222 | 43 | #!/bin/bash
#SBATCH --job-name=deaVSMC.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=VSMC.2vs14.ou... |
7e253d1efb70e45e7c0749e4fbc468eba157424454dddadee80254c479cc8014 | Shell | 1,222 | 43 | #!/bin/bash
#SBATCH --job-name=deaVECC.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=VECC.2vs14.ou... |
a55b942e08e8da7e1176333e50e4eed958e66f442f00e85433e559c0b71faa49 | Shell | 1,222 | 43 | #!/bin/bash
#SBATCH --job-name=deaAtf3.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Atf3.2vs14.ou... |
a7c1158466c462a01cfbbc432af38f1603887dcaf06d8acd6958930f38d01b1a | Shell | 1,222 | 43 | #!/bin/bash
#SBATCH --job-name=deaNppb.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Nppb.2vs14.ou... |
82296fe7b549c3ed7458556b45ac5e2b9fa6db806d114ae83b0dd4ae3ef60834 | Shell | 1,225 | 36 | #!/usr/bin/env bash
# Copyright (c) Meta Platforms, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# Propagate failures properly
set -e
mcss_path=./m.css
# Regenerate the compiled CSS file
$mcss_path/css/postproces... |
0979c740246a8ff51394f3fc4e6e350755bd435d7e5d75a3a346467ec720fa90 | Shell | 1,227 | 43 | #!/bin/bash
#SBATCH --job-name=deaS100b.2vs14
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=19cm51@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=S100b.2vs14.... |
84958892fd3f9aa9f32bd45829e3d2fbde7307c9842ae9ab1f29ff542ab5a6a9 | Shell | 1,227 | 43 | #!/bin/bash
#SBATCH --job-name=deaCldn9.2vs14
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=19cm51@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=1
#SBATCH --mem=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Cldn9.2vs14.... |
e9a12672b29b79be73cbc642d62af54463bf77d60a5decdb0808ca2b739a756b | Shell | 1,227 | 60 | #!/bin/bash
set -e
if [ "$#" -lt 1 ]; then
echo "Usage: $0 <SERIES> <sample_list>"
exit 1
fi
SERIES=$1
SAMPLE_LIST=${2:-""}
OUTPUT_DIR="${GITHUB_WORKSPACE}/output/$SERIES"
# Create output directory and copy all scripts
mkdir -p $OUTPUT_DIR
cp ./scripts/* $OUTPUT_DIR
# Copy subset file if provided
if [[ $SAM... |
9ee44c3160a7530cdfbc07a1f12948912891a297ac4518699c1f0c00c1155b83 | Shell | 1,232 | 43 | #!/bin/bash
#SBATCH --job-name=deaMrgpra.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Mrgpra.2vs1... |
ae8b354af6e63547bd9088800c2da24665ca1be84a29ef62a680391068589042 | Shell | 1,232 | 43 | #!/bin/bash
#SBATCH --job-name=deaNeuron.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Neuron.2vs1... |
ff1a967e18b9ca4f9dd6df155643f342dd7e5541d478cd6133ebd8b86a2ea12d | Shell | 1,232 | 43 | #!/bin/bash
#SBATCH --job-name=deaMrgprd.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Mrgprd.2vs1... |
a28606bbc532b0e23ba0ddab6de36f921051f89faf6ae6408bcad2f9cac69367 | Shell | 1,234 | 32 | #!/bin/bash
#####
# Example:
# $CBIG_CODE_DIR/stable_projects/preprocessing/CBIG2022_DiffProc/ \
# TBSS/CBIG_DiffProc_TBSS_wrapper.sh path/to/tbss/dir
#
# This function runs the TBSS workflow, assuming the file directory has already been set up.
# Refer to the readme in the TBSS folder for instructions.
#
... |
6092d2a2fb5acd3ee3f94447c7469c17a7608fcd9ef97b4921b0d49932898729 | Shell | 1,237 | 43 | #!/bin/bash
#SBATCH --job-name=deaZcchc12.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Zcchc12.2v... |
29b9bda990b0a4f8c5f594709a88e04faef46e8a9324dd8310ae3ba4a5049fc6 | Shell | 1,240 | 35 | #!/bin/bash
###############################################################################
# A very quick and dirty way to get a dataset from the DTAdb MariaDB instance.#
# Not for production. #
# ... |
3028fda638dd7dce7ad16bad68c904239b0f02d71dbcdee3759459e710cb358a | Shell | 1,240 | 40 | #!/bin/bash
#read input file from command line
# Format should be iSTR-ID gSTR-ID
input=$1
istr_base=data/iSTR/white_british/all/
gstr_base=data/gSTR/white_british/white_british_varqced_2
base=data/imputation_quality
out_base=${base}/out
#Make this point to the correlate_genotypes.py script
py_base=${base}/correlat... |
0c3b8a14acbbdbd92a4c906cd5adbb51cc20d499374becf90b602d7762f0581b | Shell | 1,243 | 20 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory
wd=$pd/data/brain_dataset/processed_data/
mkdir -p $wd
cd $wd
# download count matrix and metadata for all five primate species
wget https://data.nemoarchive.org/publication_release/Great_Ape_MTG_Analysis/human_mat.RDS
wget https:... |
f36320da8905be8c6522baeccdbc983b91daa0270ab1c02a58e1ef49178d10e2 | Shell | 1,243 | 32 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=HAIL_table
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=20
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=200G
#SBATCH --chdir /data7/johnathan/
#SBATCH -o /data7/johnathan/test_logs... |
7d1634c14da7e12fc4fd3817623f4761addfb1dde4f21538f6553a8d85c386c3 | Shell | 1,246 | 43 | #!/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... |
283c01479d63a5e939b40d7760f8ba991618a64d5767b5fa4516d3b755fdd14a | Shell | 1,250 | 48 | #!/usr/bin/env bash
err_exit() {
local msg="$1"
local code=1 # Default exit code
if [[ "$2" =~ ^[0-9]+$ ]]; then
code="$2" # use it as the exit code.
elif [[ -n "$2" ]]; then ## usage text?
# This uses Bash's indirect parameter expansion. Output goes to stdout.
printf '%s\n' "${!2}"
fi
# Print ... |
42076f1b76b5ee999e09996340135fbe547e35b2772999b58d77ffa467f250b2 | Shell | 1,252 | 43 | #!/bin/bash
#SBATCH --job-name=deaFibroblast.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Fibrobl... |
58f4308ad3d86a26cd92bc551313c5d871b80b19368cbab3427380e9a1b7715b | Shell | 1,252 | 43 | #!/bin/bash
#SBATCH --job-name=deaTh_Fam19a4.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Th_Fam1... |
ee40ca20b8656dbf6903bbeba7fdd561addb566dbac184c668cb2a7e17007b72 | Shell | 1,252 | 39 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=8
#PBS -N filter_bam
#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}
... |
4d8ea67e9375cab6a7d4b06d902002813e80371bfce828e5c6398c4619f9c4d2 | Shell | 1,253 | 44 | #!/bin/bash
# Define color codes
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[0;33m'
CYAN='\033[0;36m'
NC='\033[0m' # No color
# Ensure that poetry is in PATH
export PATH="$HOME/.local/bin:$PATH"
# Install poetry if it's not installed
if ! command -v poetry &> /dev/null
then
echo -e "${YELLOW}Poetry not foun... |
f128ce6a5be841a9cedd0db43e031c30dde1caf7e83f04cdf18161792e0533fd | Shell | 1,255 | 30 | #!/bin/bash
# Restore from the backup if needed
cp LC_original.nii.gz LC.nii.gz
# 1. Try a very gentle "hard-coded" erosion approach
# This will only erode the mask where voxels have fewer than N neighbors
# First, create a connectivity map (each voxel value = number of neighbors)
fslmaths LC.nii.gz -kernel box 3x3x3... |
430a6f4fa500bd74741b65827e4b5f5ff97e95254a2633a69089b2d70f1ebfea | Shell | 1,257 | 44 | #!/bin/bash
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --cpus-per-task=16
#SBATCH --job-name=sepoffMM
#SBATCH --array=0-8
#SBATCH --error=jobmm_error_%A_%a.txt
#SBATCH --output=jobmm_output_%A_%a.txt
# set environment
path_minimap2="/gpfs/scic/software/biotools/minimap2-2.28"
path_project="/gpfs/scic/d... |
46d410235dc56148723ab497048133691238dbf196fdb1abbc65ac2334019f2a | Shell | 1,257 | 43 | #!/bin/bash
#SBATCH --job-name=deaImmune_Cell.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Immune... |
5fbd8a594ddde044c8df30f3d51b1f1a99b7ef14cabe72b730e1dd9fbbe8c3bc | Shell | 1,259 | 46 | #!/bin/bash
#SBATCH --job-name=soMPIBR
#SBATCH --partition=gpus
#SBATCH --time=300:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=500G
#SBATCH --error=joblog_error_hifiasm_%A_%a.txt
#SBATCH --output=joblog_output_hifiasm_%A_%a.txt
path_hifiasm="/gpfs/scic/software/biotools/hifiasm-0.25.0"
path_asse... |
b118bb25b8ab9b3c2c1e29a189043f990e4135e372954c7c417b240031a2da49 | Shell | 1,259 | 23 | #!/bin/bash
export path_htsa_dir=/media/StorageOne/HTS #path to HTSA analysis dir
export path_pipeline=VirusMeta
export gi_list=$1 #gi_list (HPV_TTV.txt)
export taxonomic_order=$2 #family
export taxonomic_directory=$3 #/media/StorageOne/HTS/PublicData/nt_pb/family/
export taxonomic_order_name_list=$4 #family.txt
awk... |
d66c6db2bec379e35f011e5c7e2b4d352367a988a0253f96d36a038f12bc5920 | Shell | 1,259 | 35 | # this function plots values on the cortical surface with freeview
# Written by Ruby Kong, Angela Tam & CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
data_dir=$1
id=$2
annot_dir=$data_dir/annot
fig_dir=$data_dir/figures
mkdir -p $fig_dir
cd $annot_dir
for hemi in {lh,rh}; do
fo... |
25eb8043afc6bd2d7c4bebfd520d40cf67fc19245feb9a176e11ab9c4388a301 | Shell | 1,261 | 41 | #!/bin/bash
#SBATCH --partition=octopus
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2000
#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/fs/wang_atlas_mapping-%A_%a.... |
24aaf6c09c36918e8623805f696784ecd371fbbc6886e196dd3c06e570068211 | Shell | 1,262 | 43 | #!/bin/bash
#SBATCH --job-name=deaSchwann_Cell.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Schwa... |
ce1f8a1b3710d6441056b6290e63d3ae6652139466cd49e6491fcca94109b79a | Shell | 1,263 | 27 | ## Chromosomes List
awk '{print NR "\t" $s}' chromosomes.tsv > numbered_chromosomes.tsv
sed -i 's#^1\t#index\tchromosome\n1\t#' numbered_chromosomes.tsv
## Scaffold Group List (1 group)
awk 'NR>1 {print $1}' scaffold_groups.tsv | uniq | \
awk 'BEGIN {printf("index\tsg\n")} {printf("%d\t%s\n", ++n, $1)}' > numbered_sc... |
63c3f56ecbbee264f62099090bb6ba2c0afdb51a89fd74f1455d2e19e9a27941 | Shell | 1,266 | 41 | #!/usr/bin/env bash
set -euo pipefail
# Submit 3-stage chain:
# 1) CPU pipeline PBS
# 2) GPU NN PBS (afterok CPU)
# 3) PyPI publish PBS (afterok GPU)
#
# Usage:
# bash scripts/submit_cpu_gpu_pypi.sh
# bash scripts/submit_cpu_gpu_pypi.sh scripts/run_pipeline_pbs.sh scripts/run_nn_gpu_pbs.sh scripts/run_publis... |
c737f9b70f21119c7787b4d521b4a86be58f4f001bd4846fdd21a2b493e8b766 | Shell | 1,267 | 43 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# specify the study and dataset origin
flgStudy="offlineTUS" # offlineTUS, amygdala-ACC-TUS
flgCity="Oxford" # Oxford, Paris
# specify the dataset version (denoted with a suffix), based on th... |
7401f938a371f2ac85db6a04ab00adcd3f61c6e09dbe64c28214d300f40a6dfc | Shell | 1,268 | 43 | #!/bin/bash
INPUT_FILE=$1
# TODO: Naming scheme for the study ID, comment/uncomment to change it
# The study ID is the same as the name of the folder it is in
STUDY_ID=$(basename $(dirname $INPUT_FILE))
TT=$(basename $(dirname $(dirname $INPUT_FILE)))
# other option: The study ID is the same as the name of the file
# ... |
0e9aefa73882ed49bd2630d9bb1c9215bc7e7256a6b68c497b0532f5eebb8c31 | Shell | 1,269 | 34 | #!/bin/bash
#####################################################################
# Copyright 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://www.... |
261fed088bcdfbd76ea1329ee0457352ce2d1e8f741bb1e2d6ffd8661e1219a4 | Shell | 1,272 | 43 | #!/bin/bash
#SBATCH --job-name=deaRed_blood_cell.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Red... |
fde078b169684d6eafa562276996f723ba7a3d4955fde21fbcc6f250b6025ba5 | Shell | 1,272 | 43 | #!/bin/bash
#SBATCH --job-name=deaSatellite_Cell.2vs14
#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=5GB # Job memory request
#SBATCH --time=0-5:00:00 # Day-Hours-Minutes-Seconds
#SBATCH --output=Sat... |
830d40865f7b72d26d7064c2116ccfa4d234ed70aa5079e9c0a76bd5d82a0586 | Shell | 1,274 | 34 | #!/bin/bash
### This script runs GATK/Picard's liftover on VCF files in ssm2filter results ###
# Activate the conda environment that contains GATK4.
conda activate /projects/verhaak-lab/USERS/johnsk/glass4/.snakemake/conda/e8563520
### Input arguments ###
ARRAYID="`expr $1`"
# List of barcodes for which we have VCF... |
2993b9586b5da3c0a7737dbee5eb5fad7b059cf2ea28e02759af4a9fef524530 | Shell | 1,275 | 45 | #!/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 ../..
title() {
sharps="#################################"
printf "\n%s\n%s\n%s\n" ${sharps} "$1" ${sharps}
}
infer_config=AI/infer.yaml
output_dir=${OUT... |
29cee82c3890296936b9ef1da479379e3a04b0e8fcdc3265eba256ff76f16a58 | Shell | 1,275 | 30 | #!/bin/bash
set -e ${DEBUG:+-x}
echo >&3 "=> Checking data directory permissions: $LABEL_STUDIO_BASE_DATA_DIR"
# Check if data directory is writable
if [ ! -w "$LABEL_STUDIO_BASE_DATA_DIR" ]; then
echo >&3 "ERROR: Data directory is not writable: $LABEL_STUDIO_BASE_DATA_DIR"
echo >&3 "------------------------... |
d89372e4666a7ddb83716aacc6f9e93dacc28dcc5c472d8845132d00ee6bd5c9 | Shell | 1,276 | 43 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# specify the study and dataset origin
flgStudy="amygdala-ACC-TUS" # offlineTUS, amygdala-ACC-TUS
flgCity="Oxford" # Oxford, Paris
# specify the dataset version (denoted with a suffix), based... |
e6092db3ee2bc11235adb331fccdf119306576162a71723f76fa14da63ed5f40 | Shell | 1,279 | 30 | #!/bin/bash
# Common O2 environment for bancpipeline SBATCH jobs
# sbatch runs a non-interactive, non-login shell where LMOD's `module`
# function is not defined. Source it explicitly so `module load` works
# regardless of how this script is invoked.
# On O2 the LMOD init lives at /etc/profile.d/modules.sh (sometimes
... |
3c413714b863813feaee658564885c0358eda4b3cdbe4b87d289eaaeb6d32678 | Shell | 1,280 | 51 | #!/bin/bash
#SBATCH -c 4 # number of core to be used
#SBATCH -t 0-06:00 # estimated run-time in D-HH:MM
#SBATCH -p short # p=short <6h, p=mid <2d, p=long <4d
#SBATCH --mem=10000 # Memory pool for all cores (see also --mem-per-cpu); mem=10000 # memory 10GB
# Get sample name
s... |
468b82ffa21e6e20905500f869be38f608615a86737435aee2c96d411e1dc5bd | Shell | 1,285 | 39 | #!/bin/bash
# Load the modules
module purge
module load Python/3.7.4-GCCcore-8.3.0
source /tmp/${SLURM_JOB_USER}.${SLURM_JOB_ID}/prolog.env
HOME="/trinity/home/agarcia/"
WORKDIR="${HOME}/Results/AirwaySegmentation_DLCST-LUVAR/"
export PYTHONPATH="${WORKDIR}/Code/src/:${PYTHONPATH}"
# Load python virtual environmen... |
3cb0f874e39bbf158316914621b41c2125f56d3e5e70ed8d4b8d22dcfabaa1d4 | Shell | 1,286 | 33 | #!/bin/bash
subc=$1
inp="fragments"
for sample in `cat list.86`
do
in_barcode="/geschwindlabshares/RexachGroup/Xia_Data/atac_cellrangerOut/bam/barcodes/${subc}.${sample}.barcodes.txt"
SAM_body="/geschwindlabshares/RexachGroup/Xia_Data/atac_cellrangerOut/bam/sam/body_${sample}.sam"
SAM_header="/geschwindlabshares/... |
ae1d0f41608b60c76ca8364be67b08c2646ef33093eae5ee6ac44bf41a524aff | Shell | 1,287 | 52 | #!/bin/sh
########################################
##idba
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export idba_work_dir=$3
export diginorm_work_dir=$4
cd $project_work_dir
echo "starting trinity assembly..."
if [ -d $idba_work_dir ];
then
rm -r $idba_work_dir
fi
mkd... |
1b996e5a6607000b0a66ee268d9d29c366f58996f0cc2f1671a23e0619d6e82f | Shell | 1,290 | 50 | #!/bin/bash
set -e # Exit on error
# Info: Have to run from within the resources directory otherwise paths incorrect
#
# Run first: tests/test_locally.py
#
# use nnunetv2 env
#
# Usage: ./release.sh -> will ask for new version number
# go to root of package
cd ..
echo "Reminder: First run tests/test_locally.py"
e... |
9fe8360ab6856358d8e854d7abb7df323d73dfc13c3ccddc25536bb5aea7dd7e | Shell | 1,290 | 43 | #!/bin/bash
# ------------------------------------------------------------------------------
# GWAS Analysis Script using PLINK2
# Description: Performs univariate GWAS with variance standardization
# ------------------------------------------------------------------------------
# PBS 资源配置
#PBS -q new
#PBS -l nodes=1:... |
abf3a5b56a1c9340139b6e747faf303146a62682c2433f64c73dd5f0448b8325 | Shell | 1,290 | 35 | #!/bin/bash
# Define source and destination directories
SOURCE_DIR="/.../depredict/repositories/EMBARC/data/data_bids/derivatives"
DEST_DIR="/.../EMBARC/03_FSL_FEAT/Whole-data"
# Loop through all subjects
for subject in $(ls $DEST_DIR); do
if [[ $subject == "sub-"* ]]; then # Ensure it's a valid subject folder
... |
e6128ca7ae3a1f65688f48f2ca97c28e0b5b6733733a42b5416e32ee756287dd | Shell | 1,291 | 46 | #!/bin/bash
# chmod +x setup_protify.sh
# ./setup_protify.sh
# Set up error handling
set -e # Exit immediately if a command exits with a non-zero status
echo "Setting up Python virtual environment for Protify..."
# Create virtual environment
python3 -m venv ~/protify_venv
# Activate virtual environment
source ~/p... |
2ddfefec05e5f58dde1af420709325c9068efa2b1a962ade1ffa56a37f7f1bc9 | Shell | 1,292 | 31 | #!/bin/bash
# this function runs all the example multi-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=... |
dc3af22da18792ce62e9813a3b2c106de112a0e3b659196ed13d3e09e19ce51d | Shell | 1,292 | 32 | #!/bin/bash
#SBATCH -c 2
#SBATCH -t 0-01:00
#SBATCH -p short
#SBATCH --mem-per-cpu=48G # 96G total — 24G/cpu OOM'd on 39969154 (one-pass 12-col read peaked >48G)
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_v3_synapse_sample_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_v3_synapse_sample_%j.err
#SBATCH -J banc... |
14d053c35d4996b8212480b8ae1a1d3dbb5e9380f48f04ed980f9b60d4936fd5 | Shell | 1,294 | 30 | #!/bin/bash
# Define the feature combinations and targets
feature_combs=("Sleep" "Cov" "Brain" "CT" "SA" "Subcor" "Sleep_Cov"
"Sleep_Cov_Brain" "Sleep_Cov_CT" "Sleep_Cov_SA" "Sleep_Cov_Subcor"
"Sleep_Brain" "Sleep_CT" "Sleep_SA" "Sleep_Subcor"
"Cov_Brain" "Cov_CT" "Cov_SA" ... |
480dcf436539a638119615e35945ffc0af88467f3e68a613c6b2a279d62eff10 | Shell | 1,295 | 34 | # export MODEL_DIR="stabilityai/stable-diffusion-2-1-base"
export MODEL_DIR="Manojb/stable-diffusion-2-1-base"
export OUTPUT_DIR="/workspace/results/DeDistortNet"
export TRAIN_JSON_FILE="/workspace/data/preprocessed/PROSTATEx_train_metadata.jsonl"
export VAL_JSON_FILE="/workspace/data/preprocessed/PROSTATEx_validation_... |
c42eb2bf0d404abf1c5a665c340b40991c0b7b2770fb1d57b03b6ecbe09a9a87 | Shell | 1,295 | 44 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=2
#PBS -N macs2_pool
#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}
... |
c50dc1e0c2a30a2af535a096c935d5b2624a615841fa152538d63612a69655f8 | Shell | 1,295 | 44 | #!/bin/bash
#SBATCH --job-name=soSanger
#SBATCH --partition=gpus
#SBATCH --time=300:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=700G
#SBATCH --error=joblog_error_pacbioclean_%A_%a.txt
#SBATCH --output=joblog_output_pacbioclean_%A_%a.txt
#SBATCH --nodelist=lnx-cm-21008
path_hifiasm="/gpfs/scic/so... |
38534293201af415975e131dd14cc09152f983b01e1a88e6a67eca159c952916 | Shell | 1,296 | 37 | #!/bin/bash
# Converts pairwise IDR peak overlap output to narrowPeak
if [[ "$#" -lt 1 ]]
then
echo 'Converts pairwise IDR peak overlap output to narrowPeak' 1>&2
echo "USAGE: $(basename $0) [idrOverlapFile] [oDir]" 1>&2
echo '[idrOverlapFile]: overlap output file from pairwise IDR analysis' 1>&2
e... |
a9730ecfe8dd72338f586c5a1e9434d41db40da55d162da04c0843f89c664b2b | Shell | 1,300 | 31 | #!/bin/bash
# get MM2 home
MM2_HOME=$1
EMU_VERSION="1.1"
if ! [ -d "$MM2_HOME" ]; then
echo "[$MM2_HOME] is not a directory."
else
# tests if mvn is installed
command -v mvn >/dev/null 2>&1 || { echo >&2 "Failed to call mvn, are you sure Maven is installed?";}
# tests if the Micro-Manager jars are present and... |
bb3a87430d4b17cd451d88faa7e06d085f439f90287b8de2f2d0d0b6b2de3554 | Shell | 1,301 | 34 | #!/usr/bin/env bash
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$ROOT"
python train.py \
--gpu 0 \
--dataset_dir 'data/Example_train/' \
--save_dir 'data/Example_train/results/' \
--dataset_name 'custom' \
--cl_idname 'depmap_id' \
--drug_idname 'name' \
--label 'auc' \
--init_seed 42 ... |
2f0800d08e1bc2a3dafa820399a1568fa95851c6c605468928382ed112bda559 | Shell | 1,302 | 53 | #!/bin/bash -x
### get script directory
BIN=$(dirname "${BASH_SOURCE[0]}")
pushd $BIN > /dev/null
BASEDIR=`pwd`
popd > /dev/null
mkdir $BASEDIR/AF_data/
pushd $BASEDIR/AF_data/ > /dev/null
### download AF2 parameters
mkdir params
pushd params > /dev/null
wget https://storage.googleapis.com/alphafold/alphafold_params... |
cc14be1ed6d6750a64e8a7b5fe32efc83bce8e523061d10202411b5d358b100d | Shell | 1,305 | 39 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=2
#PBS -N split_bed
#PBS -j oe
#PBS -o /home/whe/qsub_opt/${PBS_JOBID}.${PBS_JOBNAME}.log
# activate env
conda_env="py38_bio"
_CONDA_ROOT="${HOME}/Programs/miniconda3"
source ${_CONDA_ROOT}/bin/activate ${conda_env}
export OMP_NUM_THREADS=${PBS_NP}
e... |
bdc867db2f66cf21feda72bbe42aa5c7ee5e06b28cff208622943ed5bf27cad0 | Shell | 1,306 | 42 | #!/bin/bash
#SBATCH -c 4
#SBATCH -t 0-01:00
#SBATCH -p short
#SBATCH --mem=64G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_spectral_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_spectral_%j.err
#
# Re-run spectral clustering on the latest BANC v888 + SeaTable inclusions.
# Runs v3 + v2 in parallel via backgrou... |
cb93fbc8d6008b3027da2134c68bafb07cae064f3366f3e8e55e9c5d84c4e721 | Shell | 1,308 | 44 | #!/bin/bash
#PBS -q batch
#PBS -l walltime=72:00:00 -l nodes=1:ppn=8
#PBS -N MergePeak
#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}
exp... |
9ef21eb140a8f0d8add4d626b3baa2532f37d0a5c1f6fd33f73ec293af8d9f2c | Shell | 1,309 | 35 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
input_dir=$pd/data/validations/ATAC_seq_FASTQ
output_dir=$pd/data/validations/ATAC_seq_FASTQ_trimmed
mkdir -p $output_dir
for i in `ls ${input_dir}/*r1.fastq.gz| xargs -n1 basename`;
do
sample_name=`cut -d _ -f 1-3 <<< $i`
... |
a36ccd7b71d5d8fe87a53524d2b907e6c23745a989c1b4792e8c31848e60f9ce | Shell | 1,310 | 32 | #!/bin/sh
# /media/StorageOne/HTS/VirusMeta/ffp/ffp_block_step1.sh /media/StorageOne/HTS/PublicData/nt_pb/family /media/StorageOne/HTS/PublicData/nt_pb/virus_block_ffp_7 /media/StorageOne/HTS/PublicData/nt_pb/virus_genomes_ffp_7 7 /media/StorageOne/HTS/PublicData/nt_pb/ffp_7_final /media/StorageOne/HTS/PublicData/nt_... |
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