sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c312f89ab13c77af7fd3a7cfc7f92fb5576a4a07c8f309f666d83a6f1ef05e6e | Shell | 924 | 24 | #!/bin/bash
# 5_TSNRExtractQuality.sh
# Loop across sessions for data preparation
for subject in {1..40}; do
for session in {1..2}; do
printf -v sub "%02d" $subject
printf -v ses "%02d" $session
echo "subject: " $sub "session: " $ses
#Directories
github_folder=/data/pt_02306/main/code/github/pai... |
cec141ce35ec9dc9a2e1140b65a3a644ee00ca866d9dfffd29092327018b5743 | Shell | 924 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=F3
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/QC.MetS12_F3_GWAS.withQsnp.csv
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas1-snplist ... |
d2b6a4eac2a9ce78e4fb08d8a4cb034cd246b9846f4f128c4a4b7cd21519b5f3 | Shell | 924 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=Qsnp
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/QC.MetS12_GWAS_MetS.withQsnp.csv
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas1-snpl... |
e4d060d4250259ddca6467b3da36dd1c22527dab8ddf96bde4f1cb1f18472f10 | Shell | 924 | 11 | #!/bin/sh
#$ -S /bin/sh
echo Start Time :
date
#../../bin/LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -InGWAS gwas.pvalue -InGFF In.gff -Region chr11:24100000:24200000 -OutPng -SeleVar 1
../../bin/LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -InGWAS gwas.pvalue -InGFF In.gff... |
75f959e49f43087c6c4c2015386183f64eeaf906d07ff1c3a0a68f5e92e6b4a6 | Shell | 925 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=FG
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/cojo_out_jma.FG.snplist.chr_pos
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas1-snplist... |
ed271c14cdb52764b3ece718f4fc59ff3785a3a7954d231e6fc5fc0894ce74a6 | Shell | 927 | 16 | ### Co-registration using T1 as a reference
### Pre-installed packages: FSL6;
### The input folder is expected to contain multiple subjects after skull-stripping
INPUTDIR=/your/input/folder/
OUTPUTDIR=/your/output/folder/
mkdir $OUTPUTDIR
for file in ${INPUTDIR}*; do
mkdir $OUTPUTDIR$(basename "$file")
echo "... |
1aab9b40f4799dcc0d38255c5ad4ec97f2b07629c5ce4650d0e75d851d5cbc84 | Shell | 928 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=MetS_lind
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/UKBB_MetS_alla_Stefan.rsid.txt.gz
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas... |
bebd14ea7b641b2a2c1599bfd0c620e5e4da23389e04b3eb5a569f5325f5d808 | Shell | 928 | 25 | #!/bin/bash
#SBATCH -J tabnet
#SBATCH --output=slurm_out/linear_out.%j
#SBATCH --error=slurm_out/linear_err.%j
#SBATCH --partition=mcml-dgx-a100-40x8
#SBATCH --qos mcml
#SBATCH --gres=gpu:1
#SBATCH --time 3-00:00:00
#SBATCH --mem=90GB
#SBATCH --cpus-per-task=6
DSSFS02_HOME="/dss/dssfs02/lwp-dss-0001/pn36po/pn36po-dss... |
4e90c6ae44ba6fddf78f5f1ffadb27d9af962280796427da53c8fe53d20c3d4a | Shell | 929 | 25 | #!/bin/bash
#SBATCH -J tabnet
#SBATCH --output=slurm_out/tabnet_out.%j
#SBATCH --error=slurm_out/tabnet_err.%j
#SBATCH --partition=mcml-dgx-a100-40x8
#SBATCH --qos mcml
#SBATCH --gres=gpu:1
#SBATCH --time 3-00:00:00
#SBATCH --mem=90GB
#SBATCH --cpus-per-task=6
DSSFS02_HOME="/dss/dssfs02/lwp-dss-0001/pn36po/pn36po-dss... |
3e753cf14c6d518afc22b2b17d712085351432440ae93e1eaca44f07c8bfa2b6 | Shell | 930 | 26 | #!/bin/bash
folder_name=${1%/}
#read the last line of the log, get job IX
log_name=$folder_name/status.csv
last_line=$(tac $log_name |egrep -m 1 .)
IFS=',' read -ra ADDR <<< "$last_line"
job_ID=${ADDR[4]}
UpdateLog.sh $folder_name unzip_data $job_ID START Unzipping_Data
#decompress using ffmpeg
if test -f $folder_na... |
6504fca9f57e0271e74eb556d236a21f34c54dcbc9bf22e62edbe9251281fdb5 | Shell | 930 | 10 | #!/bin/sh
#$ -S /bin/sh
echo Start Time :
date
../../bin/LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -InGWAS ../Example3/gwas.pvalue -InGFF ../Example3/In.gff -Region chr11:24100000:24200000 -OutPng -SeleVar 4 -TopSite
# [-SeleVar 3]: GWAS with RR ,heatmap with D'. [-SeleVar 4]: GWAS with D' ... |
40ae92745dcce914ea9ef839c7e48123219cddc3b465f6c190341e9e587c1afc | Shell | 931 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=T2D
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/CLEANED.T2D_meta_FinngenR7_Mahajan2022_MVP.txt
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
... |
d91bccd4b4ce7ef0089b0db422294723049d2c45ccd4ed81c05ef27418b39e2d | Shell | 935 | 27 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-01:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p serial_requeue # Partition to submit to
#SBATCH --mem=30000 # Memory pool for all cores (... |
ca5d6365f77950fbf29012ac3aeb5c2b6b50c296bbab0ab59f68e13db7a7f2be | Shell | 936 | 10 | julia --project=. -e 'cd("notebooks"); using NBInclude; @nbinclude("Fig2.ipynb"); exit();'
julia --project=. -e 'cd("notebooks"); using NBInclude; @nbinclude("Fig3A.ipynb"); exit();'
julia --project=. -e 'cd("notebooks"); using NBInclude; @nbinclude("Fig3B.ipynb"); exit();'
julia --project=. -e 'cd("notebooks"); usi... |
75fc3c2c406acbe7e9bfbe68df0e26448fe59973dd8a54ea4071b80e36c94ed0 | Shell | 938 | 29 | #!/bin/bash
# usage: run-bertrbp.sh <positive.fa> <negative.fa> <test.fa> <outdir>
set -eu
function realpath { echo $(cd $(dirname $1); pwd)/$(basename $1); }
P_fa=`realpath $1`
N_fa=`realpath $2`
T_fa=`realpath $3`
OUTDIR=`realpath $4`
CWD="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
mkdir -p... |
a87a649f6e55acd4edaf4b74aeed818bda570f2f854d1ac3ceb579775fafa4af | Shell | 947 | 32 | #!/bin/bash
rscript=/snp_independence.R
trait1=MetS
trait2=MetS_walree
gwas1_snplist=../COJO/extract_cojo/cojo_out_jma.MetS.snplist.chr_pos
gwas2=../COJO/cojo_input/CF_MetS_results_adapt.txt.gz
r2_thres=0.01
p_thres=5e-8
window=500
n_thread=30
/home/sanghyeon/.conda/envs/R4_HPC/bin/Rscript ${rscript} \
--gwas1-s... |
90972afc3087ad854e93d928719dd91f8c090d8958ca5ef2257b67a2405eb7e8 | Shell | 948 | 36 | #!/bin/bash
#################################################################
## create nested directories for raw data and input data files ##
#################################################################
proj_dir="/path/to/main_project_folder/" # edit this line
EXPERIMENT_LIST=$(cat "LIST_EXPERIMENTS.txt")
VAR... |
511f915e9e40ef35af4fc53a7b2875786a1e2fa21c78ccea4ea7d048d42ab82b | Shell | 958 | 29 | #!/bin/bash
echo "Test environment information"
echo "----------------------------"
echo "Python version: $(python --version 2>/dev/null || echo 'Python not installed')"
echo "Ray version: $(ray --version 2>/dev/null || echo 'Ray not installed')"
echo "Installed pip packages:"
python -m pip freeze 2>/dev/null || echo ... |
1deece5281d2e597695fbc801a11e2510645f226abc15f3b5d5b78b632c75cf2 | Shell | 961 | 26 | #!/bin/bash
source 00_global_variables.sh
cts_Cahoy=./Cahoy.ldcts
cts_Multi_tissue_gene_expr=./Multi_tissue_gene_expr.ldcts
cts_Multi_tissue_chromatin=./Multi_tissue_chromatin.ldcts
cts_GTEx_brain=./GTEx_brain.ldcts
cts_ImmGen=./ImmGen.ldcts
cts_Corces_ATAC=./Corces_ATAC.ldcts
LDSCSEG_weights=./weights_hm3_no_hla/wei... |
e09a71ad258eb0360c614f21d71caeca75d342c885940922a1eea5e009623fd2 | Shell | 962 | 30 | #!/bin/bash
#
# mantatloc_check.sh
#
# Script to check raw manta calls##
#
##standardized manta vcf##
std_vcf=$1
discfile=$2
id=$3
meibed=$4
cytobands=$5
set -e
##format manta vcf to work with svtk resolve##
cat <(zcat $std_vcf|egrep ^##) \
<(echo "##FORMAT=<ID=manta,Number=1,Type=Integer,Description=\"manta genot... |
f9ffeacf3f62d8f84d89bea4632727baaf4b5942964b9eec5031b406163e53ce | Shell | 967 | 44 | #!/bin/bash
#SBATCH -J St3_P100
#SBATCH --mem-per-cpu=8G
#SBATCH --cpus-per-task=2
#SBATCH --partition=pi_anticevic
#SBATCH --time=1-00:00:00
#SBATCH --output="/CAP_Time_Analytics/cap_codes/slurm_output/St3_P100-%A_%a.out"
#SBATCH --array=1-1000
module load miniconda
source activate /gpfs/gibbs/pi/n3/software/env/pyca... |
0b1505c342bef8b75cdd35af3b06529cdeec05615f3232c9d0928d148bb77285 | Shell | 968 | 8 | !/bin/csh -f
# Maps the cluster overlaps between the Lexical Frequency AmpMod Cluster 1 (832 voxels; left cerebellum VII/Crus II) and the Phonological Neighborhood Density Cluster 2 (64 voxels; left cerebellum crus II)
# The masks are thresholded at: p <0.001, alpha of < 0.01, and cluster threshold of 31.5
# This is fr... |
f89d53271b002c4298e5fc5bf05d9b36efae05e429cc3249b196dffde7f3a89d | Shell | 969 | 26 | while getopts "a:o:h" opt; do
case $opt in
a) alignfile=$OPTARG;;
o) outp=$OPTARG;;
h) printf "$helpmessage"
exit;;
?) printf "$helpmessage"
exit;;
esac
done
if [ $OPTIND -eq 1 ]; then
printf "$helpmessage"
exit
fi
outprefix=${outp}
outname=$outprefix"_vf_k"$kfilt"_I"$I"_X"$L"_filt... |
e82e84db338402cacc6d4a7faba2de786870697e449d42aa2a6127d175ef3a1e | Shell | 973 | 34 | #!/bin/bash
###################### Calculate Brain Volume ########################
# Purpose: This script calculates total brain volume and saves it to a csv file.
# Specify the template brain
T_brain=${FSL_DIR}/data/standard/MNI152_T1_1mm_brain
# Create your subject list
SUBJECTS_DIR=/nfs/turbo/lsa-csmonk/FF_Dat... |
8cc8e1d72c15f73d72782e17a630d496b07645fdee026059bca5290f62982896 | Shell | 979 | 8 | !/bin/csh -f
# Maps the cluster overlaps between the Lexical Frequency AmpMod Cluster 2 (606 voxels; RIGHT cerebellum VII/Crus II) and the Phonological Neighborhood Density Cluster 1 (404 voxels; RIGHT cerebellum crus II)
# The masks are thresholded at: p <0.001, alpha of < 0.01, and cluster threshold of 31.5
# This is... |
49ac45f968926c662f392af64622eff676cb1fd4b4686055d957da986d0b33d1 | Shell | 984 | 37 | #!/bin/bash
clear
# parallel --eta --ungroup python3 run_ppo.py -c cfg/ant/cbp.yml -s {1} ::: $(seq 0 19) &
# parallel --eta --ungroup python3 run_ppo.py -c cfg/ant/l2.yml -s {1} ::: $(seq 0 19) &
# parallel --eta --ungroup python3 run_ppo.py -c cfg/ant/ns.yml -s {1} ::: $(seq 0 19) &
# parallel --eta --ungroup python3... |
c17f8d34b912717a15c226e066332ea076403c49e0e45ba22f35866f95edb966 | Shell | 985 | 19 | #data_path=/media/leo/Data/row013_auto
data_path=/media/leo/5d7aa88a-dacb-4f50-90ec-6af3274316c5/row003_auto
#data_path=/media/leo/5d7aa88a-dacb-4f50-90ec-6af3274316c5//Resnet_Segmentation/data/ #for trainval data
#output_path=${data_path}_out
output_path="/media/leo/dddd21c6-acd6-45cc-a4bf-d796523767ed/row003_auto_ou... |
d68a409b5753f2ebec7764db05cef451dfd60b95f8944fc61abef20db8ce063d | Shell | 986 | 48 | #!/bin/bash
#SBATCH -J mast_res
#SBATCH -N 1
#SBATCH -n 16
#SBATCH -p kellis
#SBATCH --time=12:00:00
#SBATCH --mem=20G
#SBATCH --output=/home/cboix/data/DEVTRAJ/db/out/mast_res_%j.log
#SBATCH --export=ALL
#SBATCH --requeue
# OLD version of analysis
# Arguments:
file=$1
ind=$2
chunksize=$3
path=$4
start=`date ... |
658815aabfd065a69697b9c803556b71544ec1386ca1fe80ddb498ab70f45c5b | Shell | 989 | 36 | #!/usr/bin/env bash
NAME=${1:-sam-p4}
shift 1
INSTANCE_TYPE=${1:-n1-standard-4}
shift 1
DISK_SIZE=${1:-100GB}
shift 1
ACCEL=${1:-nvidia-tesla-t4}
shift 1
echo "Creating GPU instance ${NAME} from family dl-image of type ${INSTANCE_TYPE} with GPU ${ACCEL}..."
echo "$@"
gcloud compute instances create ${NAME} \
--proj... |
79364006daa5c49202b2aadcae8ae6a97a14092ff39c34b5735b99ec3a4c6bf3 | Shell | 991 | 9 | mkdir /Users/chaokuan-hao/Documents/Projects/PR_SPLAM/results/polyA_STAR/
for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895; do
mkdir /Users/chaokuan-hao/Documents/Projects/PR_SPLAM/results/polyA_STAR/$sample/
echo scp -r s3:/ccb/salz3/kh.chao/SPLAM/results/polyA_STAR/${sample}... |
a7f287db1385b94966bb7d33d28a4e79a691aab86e316df292fb968da0edf6ef | Shell | 992 | 34 | #!/bin/bash
# Run all datasets
# requires downloading all graph datasets and placing them in ../data/graphs
outdir=../data/predictions
for dataset in ../data/graphs/*.jsonl;
do
name=$(basename $dataset)
outfile="$outdir/${name%.*}.csv"
if [[ -e $outfile ]]; then
echo "Prediction file exist: $outf... |
0bf8351517a06b86e5d9722acee7c553c954a28e0c24b6e8b8e5a858e62b5c91 | Shell | 1,014 | 31 | #!/bin/bash -e
if [ $# -ne 2 ]; then
echo "usage v1: lrna_bam_to_unstranded_signals.sh <bam_file> <chrom_sizes>"
echo "Converts BAMs from alignments from unstranded libraries to bigwig format. Is independent of DX and encodeD."
exit -1;
fi
bam_file=$1 # Bam file.
chrom_sizes=$2 # chrom_sizes file t... |
88d3af6125949d691e3b1284f78babdcdeaaebadcb1dc79aa4885ea380207467 | Shell | 1,014 | 36 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
eef7cf5777edd218020d9a4cffbfc8a5e3f44ce6974d1d532e80c05147ae320d | Shell | 1,014 | 19 | # for threshold in {2..100}
# do
# SEQ_LEN=800
# project_root=/ccb/cybertron/khchao/splam-analysis-results/
# output_dir=${project_root}train/results/Negs/Neg_${threshold}/Select_junctions/${SEQ_LEN}bp/${threshold}_juncs/
# bedtools getfasta -s -fi ${project_root}Dataset/hg38_p12_ucsc.no_alts.no_fixs.f... |
f41e90a1d516b0cd5051c01652cd8f4acd933326d078682c7659616126835de6 | Shell | 1,014 | 38 | #!/usr/bin/env bash
set -o errexit
set -o pipefail
set -o nounset
#RAW DATA LOCATOINS
#beta version of ICD10 (WHO) -> phecodes mapping
#https://phewascatalog.org/phecodes_icd10
#There is an ICD10CM (US) version as well
#Phecode definition map is here
#https://phewascatalog.org/phecodes
#SHARED_DATASET -- should alrea... |
452b003ae1eb5e4ff557f096017e3484299ea39a6c2375fb14c87a0c31e569e6 | Shell | 1,018 | 5 | python main.py --save_path experiments/model_train/DeltaSplice_rep0/ --is_train=True --train_data_path=data/train_val_test/train/data.json --valid_data_path=data/train_val_test/valid/data.json --seed=321
python main.py --save_path experiments/model_train/DeltaSplice_rep1/ --is_train=True --train_data_path=data/train_va... |
2abb5aa3ae84717ce5fe779c126b222b18fc33acda19ae6f3f7cf60477499d79 | Shell | 1,019 | 33 | #!/bin/bash
######################## QC Average FD Script ################################
# Purpose: The goal of this script is to calculate the subject-level average of a specific QC metric (e.g. FD) and write it to a txt file for review.
#Note: this errored out on subjects that had numbers in scientific notatio... |
cb4deeae35ba14dbe7ee294b485897c4fc91755b4494287677a403da26841078 | Shell | 1,024 | 12 | #! /bin/bash
qsub -l mfree=80G -l centos=7 -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_15_Greg_ATAC_Code_nobackup /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_15_Greg_ATAC_Code_nobackup/singleNB10.sh All_Cells ArchR 50
qsub -l mfree=80G -l centos=7 -wd /net/trapnell/vol1/... |
f9524c39efaabf50d56893581ba2d0a491b2393d5723d417d953137ae723aa89 | Shell | 1,026 | 36 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
8c8ada1c59d68a1e37f7e8ccde37123fbc10a73f424b20bd2fd20fccff085308 | Shell | 1,028 | 42 | #!/bin/bash
set -exuo pipefail
PYTHON="$1"
if [[ ! "${OSTYPE}" =~ ^linux ]]; then
echo "ERROR: This wheel test script is only for Linux platforms." >/dev/stderr
exit 1
fi
PYTHON_VERSION="${PYTHON//./}"
which python
which pip
RAY_PLACEHOLDER_VERSION="100.0.0-dev"
MINIFORGE_BIN_PATH="/opt/miniforge/bin"
PYTHON_... |
d616083188e6211d7bd12094ec306f9c7546096cfcd05569c1416662086ce871 | Shell | 1,030 | 35 | #! /bin/bash
# FIMO needs a few things. It needs motifs in MEME format (already pulled from JASPAR)
# MOTIF_FILE=./fileOutputs/JASPAR_2020_CORE_Vertebrates_non-redundant_meme.txt
MOTIF_FILE=./fileOutputs/JASPAR2018_CORE_vertebrates_non-redundant_pfms_meme.txt
inputSeqFile=$1
# cds_p_allHeartATAC_peakSeqsAsFasta.fa
#... |
104e900e58370e13087f857c726ef09ed4b18025cce1f2a493f082a9bbe8155e | Shell | 1,031 | 36 | #!/bin/sh
# script for execution of deployed applications
#
# Sets up the MATLAB Runtime environment for the current $ARCH and executes
# the specified command.
#
exe_name=$0
exe_dir=`dirname "$0"`
echo "------------------------------------------"
if [ "x$1" = "x" ]; then
echo Usage:
echo $0 \<deployedMCRroot\>... |
1dab1ec2e06a554f4a8cb2b22763d83188be472210fd8d04622bb9336ad495fe | Shell | 1,033 | 43 | #!/bin/bash
# creatation: 1-25-2022
# Author: Ruitu Lyu (lvruitu@gmail.com)
# Stop on error
set -e
###
### setup.sh - This script is used to setup the 'KAS-Analyzer' pipeline.
###
### Usage: ./setup.sh
###
### -h or --help Print the help.
###
# Help message for shell scripts
help() {
sed -rn 's/^### ?//;T;p' "... |
b7b482785f539f21f89aec6970aec6bb48ff52d769ae63c5d1bcf2bdea8972e6 | Shell | 1,033 | 19 | #! /bin/bash
# Rscript /net/trapnell/vol1/home/readdf/trapLabDir/fibrosis/results/2020_12_29_SymSim_Power_Work/runSimulations.R 3
# Rscript /net/trapnell/vol1/home/readdf/trapLabDir/fibrosis/results/2020_12_29_SymSim_Power_Work/runSimulations.R 5
# Rscript /net/trapnell/vol1/home/readdf/trapLabDir/fibrosis/results/202... |
44508faba6de6f3d89621c702e343c7e0abd084b71dd089bd58424b28a31af1a | Shell | 1,034 | 35 | #!/bin/bash
#$ -S /bin/bash
#$ -N remVar
#$ -cwd
#$ -o /mnt/analysis-psp/users/timchang/v3/pc/2211/data/vcfs/bm/eur/hwe/remVar.$TASK_ID.log
#$ -j y
#$ -m bea
#$ -l h_data=2G,h_rt=48:00:00
#$ -hold_jid hwe
#$ -t 1:22
#remove Variants from list
chr=($(seq 1 1 22) X Y M)
echo ${chr[${SGE_TASK_ID}-1]}
indir=/mnt/analys... |
c95eacaed6b7120adc22b46682972a1ce8e03ff3f612ec5cf3b7f87a94d34086 | Shell | 1,034 | 23 |
echo start `date`
outdir="./output_stage2"
train_list="./stage2_sample_lists/all_length400_resolution3_before2020_5.xls"
valid_list="./stage2_sample_lists/CAMEO_2020_2021.xls"
# users can use ./data/PDB_coord_seq.sh make hdf5 files for training and validation
coords_seq_hdf5="./data/xyz_tokens_label8_psi_phi_before202... |
0e6446d2b5b9455157ffea178e358aa1968eda03e0cdd9ac536cd808b8373b77 | Shell | 1,035 | 9 | mkdir /Users/chaokuan-hao/Documents/Projects/PR_SPLAM/results/ribozero_STAR/
for sample in R12258 R12260 R12263 R12265 R12266 R12277 R12278 R12280 R12285 R12287; do
mkdir /Users/chaokuan-hao/Documents/Projects/PR_SPLAM/results/ribozero_STAR/$sample/
echo scp -r s3:/ccb/salz3/kh.chao/SPLAM/results/ribo... |
27569a7080ce56515c5ca600a92f6f80a306b34fada674da3963f2f7f8b10f3a | Shell | 1,036 | 10 | #!/bin/csh -f
# Maps the cluster overlaps between individual cluster masks for lexical frequency and phonological neighborhood density
# The masks are thresholded at an individual level of: p <0.01, alpha of < 0.05, and cluster threshold of 77.6
set top_dir = top_dir/
3dcalc -a /Volumes/Research/MyersLab/SPLATScast/... |
6e22b4b7c90700e9525833ac713f700ae7b068f8e38f247e3eab8fff7301cd83 | Shell | 1,043 | 28 | #!/bin/bash
# build-wheel.sh - Build Ray manylinux wheels locally
#
# This is a thin wrapper that delegates to ci/build/build_wheel.py via uv.
# Run with --help for usage information.
set -euo pipefail
# Check for uv
if ! command -v uv &>/dev/null; then
echo "Error: uv is required. Install from: https://docs.astr... |
85193bee3db1388961906798d6ff829e9b0f71082805a15479a04c73dd57a1a0 | Shell | 1,051 | 35 | #!/bin/bash
#$ -S /bin/bash
#$ -N hwe
#$ -cwd
#$ -o /mnt/analysis-psp/users/timchang/v3/pc/2211/data/vcfs/bm/eur/hwe.$TASK_ID.log
#$ -j y
#$ -m bea
#$ -l h_data=7G,h_rt=48:00:00
#$ -hold_jid keep
#$ -t 1:22
#find hwe less than 1E-7
chr=($(seq 1 1 22) X Y M)
echo ${chr[${SGE_TASK_ID}-1]}
indir=/mnt/analysis-psp/user... |
76cc6dc7d3e0530281ca510a3d8bdc5eb56748171b0b75fcf017eeb389f65ac6 | Shell | 1,052 | 33 | #!/bin/bash
#$ -S /bin/bash
#$ -N bcf_mult
#$ -cwd
#$ -o /mnt/analysis-psp/users/timchang/v3/pc/2211/data/vcfs/multi/samp/multi.$TASK_ID.log
#$ -j y
#$ -m bea
#$ -l h_data=6G,h_rt=48:00:00
#$ -tc 16
#$ -t 1;22
#psp con samples
#remove monomorphic
chr=($(seq 1 1 22) X Y M)
echo ${chr[${SGE_TASK_ID}-1]}
indir=/mnt/an... |
dde11e4395b198c51e21f176a330cddf45391eb373a11eb3d47966212de38639 | Shell | 1,057 | 24 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-02:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=16G # Memory pool for all cores (see also -... |
061820e2f74fd202b60dc1ed761c4acd7de9b9e6f6c4586c2f4efa3efa9bcf55 | Shell | 1,058 | 18 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
31098b533dc22f9192394df35236f4c6fdee84900124e6509129e34a7fc008d4 | Shell | 1,061 | 22 | #!/usr/bin/bash
vamb \
--outdir /home/projects/cpr_10006/projects/vamb/almeida_vaevaeout_vamb \
--fasta /home/projects/cpr_10006/projects/vamb/analysis/almeida/data/almeida.fna \
--rpkm /home/projects/cpr_10006/projects/vamb/analysis/almeida/data/almeida.jgi.depth.npz \
-l 32 \
-e 300 \
-q 25 7... |
775c624e516f87b4592938c9c4ec1e5b60d0896e1d82977c5dca7c36e193de66 | Shell | 1,066 | 22 | #!/usr/bin/bash
# vamb \
# --outdir /home/projects/cpr_10006/people/svekut/cami2_almeida10_vamb_20102023 \
# --fasta /home/projects/cpr_10006/people/paupie/vaevae/almeida_10_samples/03_abundances/abundances/contigs.flt.fna.gz \
# --rpkm /home/projects/cpr_10006/people/paupie/vaevae/abundances_compositions/... |
4213154c159240c0c20756ed6fb072306b256547ae1b6109ce52212982704408 | Shell | 1,068 | 25 | # You need load the required modules, in this case the intel
# compilers and intel mpi.
module load intel/2.144
module load impi/5.0.0.028
# It is very important putting number of the OMP variables
# on the correspondent system variable. In this case the value
# have to be equal to 1 (only one thread per MPI ... |
75ec8902523c2588c86234dc9ecf2bfdfa4a3638f9f8d1e5ec3ee005b57bb195 | Shell | 1,069 | 24 | # prepare genomes for STAR and RSEM
# run from the directory intended to be STAR genome directory
# input parameters:
fastaGenome=$1 #fasta file(s), e.g. "male.hg19.fa"
gtf=$2 #all-inclusive gtf file "gencode.v19.annotation.gtf"
# example
# ./STAR_RSEM_prep.sh male.hg19.fa gencode.v19.annotation_tRNA_spi... |
5f7d93f5d7b10cc9831ced9e1f80f03606e273ef3026385453db56ab262b6969 | Shell | 1,071 | 49 | #!/bin/bash
#SBATCH -J St2_P100
#SBATCH --mem-per-cpu=8G
#SBATCH --cpus-per-task=12
#SBATCH --partition=pi_anticevic
#SBATCH --time=1-00:00:00
#SBATCH --output="/CAP_Time_Analytics/cap_codes/slurm_output/St2_P100-%A_%a.out"
#SBATCH --array=901-1000
module load miniconda
source activate /gpfs/gibbs/pi/n3/software/env/p... |
cc25a60800b22c21c7efd3a45d7572ddbfc74887dcdd5f0eb53c7c2fe163b8ac | Shell | 1,072 | 48 | #!/bin/bash
# usage: run-cmfinder.sh <positive.fa> <negative.fa> <test.fa> <outdir>
# note: it does not use negative.fa
function realpath { echo $(cd $(dirname $1); pwd)/$(basename $1); }
P_fa=`realpath $1`
N_fa=`realpath $2`
T_fa=`realpath $3`
OUTDIR=`realpath $4`
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /de... |
04fc38f3890922b5ebd2bb29d49879007d112dd7d9fd0d9eb6c8cf9b7bf1a70d | Shell | 1,073 | 31 | #!/bin/bash
set -eu
# Optionally accept the first argument as an execution descriptor
INFRASTRUCTURE=${1}
[[ ! -z "$INFRASTRUCTURE" ]] && INFRASTRUCTURE+="_"
MYDATE=$(date +%Y%m%d%H%M%S)
OUTDIR="../outputs/${INFRASTRUCTURE}${MYDATE}"
# To ensure that we have all environment variables from neuroscience packages load... |
20698701abaf4141e0228ce067d9003c12316417f5f10573b30bf99bb1e7c15f | Shell | 1,076 | 31 |
splitNum=10
# for eachType in Endothelium Fibroblast Lymphocyte Myeloid Perivascular Ventricular_Cardiomyocytes Neuron Adipocytes
# for eachType in Adipocytes
for eachType in Endothelium Fibroblast Lymphocyte Myeloid Perivascular Ventricular_Cardiomyocytes Neuron Adipocytes
do
# Loop through and submit a job for eac... |
e42f257ace4274f709d820376fa545dd5bad1febbddbee525d9186479bb2e4db | Shell | 1,077 | 48 | #!/bin/bash
# Request 4 nodes using 128 cores per node for 128 MPI tasks per node.
#SBATCH --job-name=cp2kdev
#SBATCH --nodes=8
#SBATCH --tasks-per-node=1
#SBATCH --cpus-per-task=128
#SBATCH --time=00:08:00
# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=e05-surfin-blu
#... |
1fda482242cd4035604eaffaf1b61e69fca98b27f9f6ca8360e29e2ff9ee5ef4 | Shell | 1,079 | 44 | #!/bin/bash
############################################################
## Converts raw CMIP6 data files to a 128x64 lonxlat grid ##
## -- saves regridded file with suffix "_r128x64.nc" #######
############################################################
proj_dir="/path/to/main_project_folder/" # edit this line
raw_... |
20135d773bcc3506c915436ebba428b4a848cc026fbc744551513978ecb4962a | Shell | 1,081 | 46 | #!/bin/sh
#
# Downloads the sequence for a strain of e. coli from NCBI and builds a
# Bowtie index for it
#
GENOMES_MIRROR=ftp://ftp.ncbi.nlm.nih.gov/genomes
BOWTIE_BUILD_EXE=./bowtie2-build
if [ ! -x "$BOWTIE_BUILD_EXE" ] ; then
if ! which bowtie2-build ; then
echo "Could not find bowtie2-build in current direct... |
e2e7322ee87ce80e925972a1aecfa959ef39e0cce8878060fcc38844c79ad321 | Shell | 1,081 | 30 | #!/usr/bin/env bash
set -euo pipefail
if [[ ! -f /usr/local/bin/kind ]]; then
echo "--- Installing kind"
curl -sfL "https://github.com/kubernetes-sigs/kind/releases/download/v0.22.0/kind-linux-amd64" -o /usr/local/bin/kind
chmod +x /usr/local/bin/kind
kind --help
fi
if [[ ! -f /usr/local/bin/kubectl ... |
6b756d85f14c43d0cbb9361194d5a1aa379686a3d8e4d76391e32d511b4a5a96 | Shell | 1,082 | 28 | #!/bin/bash
# build-image.sh - Build Ray Docker images locally
#
# This is a thin wrapper that delegates to ci/build/build_image.py via uv.
# Run with --help for usage information.
set -euo pipefail
# Check for uv
if ! command -v uv &>/dev/null; then
echo "Error: uv is required. Install from: https://docs.astral.... |
c24e97300bc7633bded25f9d97c504e22dc4a6cdc546277b74a9c09c1df15f8e | Shell | 1,083 | 19 | #!/bin/bash
# Note: Running this file requires that openssl is installed on the target system.
rm *.pem
# 1. Generate Certificate Authorities' private key and self-signed certificate
openssl req -x509 -newkey rsa:4096 -days 365 -nodes -keyout ca-key.pem -out ca-cert.pem -subj "/C=US/ST=CA/L=LosAngeles/O=ISI/OU=Resear... |
91d33cf9f4b7a778a21b910f9cbe0f1829a4ff1f0163e9b1cbfcff387e735c80 | Shell | 1,084 | 34 | #!/usr/bin/env bash
# Cause the script to exit if a single command fails.
set -ex
BAZEL_LOG_DIR=${1:-"/tmp/bazel_event_logs"}
readonly PIPELINE_POSTMERGE="0189e759-8c96-4302-b6b5-b4274406bf89"
readonly PIPELINE_POSTMERGE_MACOS="018e0f94-ccb6-45c2-b072-1e624fe9a404"
readonly PIPELINE_CIV1_BRANCH="0183465b-c6fb-479b-8... |
360352a597caef18a2dd9df4223e148fd00e5ec3eb6d184a74925bf3706b3916 | Shell | 1,086 | 34 | #!/bin/bash
set -e
#local absolute path to where you want to download the dataset
LOCAL_DIR="your/path/to/BOLDMomentsDataset"
#create directory paths that mimic the openneuro dataset structure
mkdir -p "${LOCAL_DIR}/derivatives/stimuli_metadata"
#download the files
dataset_files=(
"README.txt"
"annotations.js... |
08b5f4f009c910091f269f3fc3b9e7a6861923125ae8d6e5ba5252cc70f05ecf | Shell | 1,090 | 29 | #!/bin/bash
####################################################
## create nested directories for input data files ##
####################################################
proj_dir="/path/to/main_project_folder/" # edit this line
regions=('southcentral_north_america' 'southern_europe' 'western_russia' 'western_india'... |
e0a2b3ddd5aa579c0379a5604ea55645591ee8d393fba304238e8df31513f520 | Shell | 1,095 | 25 |
echo start `date`
outdir="./output_stage3"
train_list="./stage3_sample_lists/PDB_till2022_3_CATH_24183.xls"
valid_list="./stage3_sample_lists/PDB_2022_05-2023-05.xls"
# users can use ./data/PDB_coord_seq.sh make hdf5 files for training and validation
coords_seq_hdf5="./data/PDB_till2022-03_xyz_tokens_phi_psi.h5"
CATH_... |
fbec6f57456259965fe14b2932ac5503f62257f8ea3e42c53e74f53ba27871a4 | Shell | 1,095 | 23 | # polyA
for sample in R2826 R2835 R2839 R2845 R2855 R2857 R2869 R2874 R2894 R2895 ; do
echo mkdir ../results/polyA/$sample/assembly
mkdir ../results/polyA/$sample/assembly
echo mkdir ../results/polyA/$sample/assembly/BEFORE/
mkdir ../results/polyA/$sample/assembly/BEFORE/
echo stringtie -o... |
8e54436f5077575b47efa5cb2b3704316b4de95d4c13c8293f402fc8465ff3a8 | Shell | 1,099 | 25 |
echo start `date`
outdir="./output_stage4"
train_list="./stage3_sample_lists/PDB_till2022_3_CATH_24183.xls"
valid_list="./stage3_sample_lists/PDB_2022_05-2023-05.xls"
# users can use ./data/PDB_coord_seq.sh make hdf5 files for training and validation
coords_seq_hdf5="./data/PDB_till2022-03_xyz_tokens_phi_psi.h5"
CATH_... |
99bfd04bcd2386da4bef480532230442cb4657c665201afc10681da24d414b35 | Shell | 1,106 | 15 | #!/usr/bin/env bash
python tune_cauchy.py --mode forward -N 4 --filename tuning_result_fwd_N_4.json
python tune_cauchy.py --mode forward -N 8 --filename tuning_result_fwd_N_8.json
python tune_cauchy.py --mode forward -N 16 --filename tuning_result_fwd_N_16.json
python tune_cauchy.py --mode forward -N 32 --filename tuni... |
4c371b2352c378726e24a0b440539d22ff3824958a323f0bdc7dd6ee54abd17e | Shell | 1,107 | 40 | #!/bin/bash
####################################################
## Unzip all ERA5 Land .zip files to netcdf files ##
####################################################
proj_dir="/path/to/main_project_folder/" # edit this line
regions=('southcentral_north_america' 'southern_europe' 'western_russia' 'western_india'... |
dfbc9a30e99f629ecc144d603ce1742c5ea8cca47ce08cb7bd27ac175b493044 | Shell | 1,113 | 36 | #!/bin/bash
sam=$1
pre=$(echo $sam | cut -d "/" -f 9)
tis=$(echo $pre | cut -d "_" -f 1)
tf=$(echo $pre | cut -d "_" -f 2)
rep=$(echo $pre | cut -d "_" -f 3)
EXP=${tis}_${tf}_${rep}
if [ $rep == "1224" ]; then
ID="5397-JL-0001"
else
ID="5397-JL-0002"
fi
cat HEADER.tmp $sam > /cluster/home/aanderson/allele_bias/... |
00b7851fd342a018bba4af7b023f6ca82562b7732b02bb8cb5b54d03a299a765 | Shell | 1,114 | 24 | #!/usr/bin/bash
vamb \
--model vaevae \
--outdir /home/projects/cpr_10006/projects/semi_vamb/data/human_longread/vaevaeout \
--fasta /home/projects/cpr_10006/projects/semi_vamb/data/human_longread/contigs_2kbp.fna \
--rpkm /home/projects/cpr_10006/projects/semi_vamb/data/human_longread/vambout/abundanc... |
0cef23b00394b281b271a04d89027cbd8b3aac53f050cbe70e47a7192999d002 | Shell | 1,115 | 36 | #!/bin/bash
#$ -S /bin/bash
#$ -N bcf_norm
#$ -cwd
#$ -o /mnt/analysis-psp/users/timchang/v3/pc/2211/data/vcfs/multi/norm/multi.$TASK_ID.log
#$ -j y
#$ -m bea
#$ -l h_data=6G,h_rt=48:00:00
#$ -tc 16
#$ -hold_jid bcf_multi
#$ -t 1;22
#norm left align
#remove spanning deletion
#annotate ID's
chr=($(seq 1 1 22) X Y M)
... |
b05320d0b9db63d022e39f0455ea5f5462dbb7757376d3488c452e6118393dcd | Shell | 1,117 | 20 | #! /bin/bash
qsub -P trapnelllab -l mfree=80G -wd /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_23_Run_FIMO_on_peakSeqs_nobackup /net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2021_07_23_Run_FIMO_on_peakSeqs_nobackup/runFIMO.sh cds_p_allHeartATACFRIP=0.2_FRIT=0.05UMI=1000DL=0.5_peakSeqsA... |
4c65f3f3254b47038e6a75c3aee09a4275ee926052b74ecd6764adb3c8cd9399 | Shell | 1,119 | 38 | module load R
echo ${1}
## Split by HPO ID in to separate files
echo "Splitting files by HPO ID..."
hpo_i_out=`echo ${1} | awk '{ gsub(":", "-") ; print $0 }'`
awk -v pat=${1} '$2==pat {print $0}' /path/to/hpo_perm/* > /path/to/hpo_perm_split/collect_sig_${hpo_i_out}.txt
## Compute empirical pvalue
echo "Calculat... |
4e9853a410948e434432aee8cd0261e614c1ff6c8bed635e781f8624a5e06c96 | Shell | 1,123 | 45 | #!/bin/bash
# TODO fill in the path to your plink2 install, if not in global path
# alias plink2=/path/to/plink2
# TODO fill in space-separate file with columns FID and IID, no header
INDIV=/path/to/indiv.txt
# very soft filtering parameters:
# minor allele frequency
MAF=0.001
# Hardy-Weinberg p-value
HWE_PVAL=0.... |
16c45f2a2163ff074b1abff2629a3ba2b477f96bda315154e70181dec3e42798 | Shell | 1,130 | 11 | conda activate tobias
TOBIAS ATACorrect --bam /home/tobias/CN7-10-5/CN7-e10-5_merged.bam --genome /home/arthur/tobias/GRCm38.p4.genome.fa --peaks /home/tobias/CN7-10-5/CN7_e10-5_mergedPeaks.bed --blacklist /home/tobias/mm10-blacklist.v2.bed --outdir --cores 60
TOBIAS ATACorrect --bam /home/tobias/CN7-11-5/CN7-e11-5_... |
37193d7563994ce7810f5bfb567ba68168432af24d0c82124d001856c3b74fd3 | Shell | 1,133 | 32 | #!/bin/bash
############################### ICA-AROMA loop script ###################################
# Purpose: This script runs the ICA AROMA in a loop for resting state data.
# Create a list of subjects to use in this analysis and count how many there are.
subject_dir=/nfs/turbo/lsa-csmonk/FF_Data/Working_File... |
c394645d2d84ec9920958c84c685ba8a7033f7b5b08762dca9ff7f8be8cfd890 | Shell | 1,133 | 31 | #!/bin/bash
#BATCH -p DCU
#SBATCH -N 1
#SBATCH -n 9
#SBATCH --ntasks-per-node=9
#SBATCH -o %j.out
#SBATCH -e %j.err
conda activate RSAIGE
Pheno="pheno"
echo ${Pheno}
cd /${Pheno}/
for i in {4,5,6,12,13,14,15};do
Rscript /step2_SPAtests.R \
--bedFile=/ukb_wes_chr${i}_sample_qc_final_unrelated.bed \
--bimFile=/ukb_we... |
87815b8c1b21961b8e3eb81df6569e677642ef5dfe5996fb790e629a30b02a7a | Shell | 1,136 | 46 | #!/bin/bash
# Fail if anything fails
set -e
# ngs_mapper dir
THIS=$(cd $(dirname $0) && pwd)
if [ ! -d Projects ]
then
echo "No Projects directory"
exit 1
fi
# Ya, pretty ugly
CPUS=$(grep '^processor' /proc/cpuinfo | wc -l)
if [ -z "$CPUS" ]
then
CPUS=1
fi
echo "Using $CPUS cpus"
for p in Projects/*
do... |
0782cdb9c7b2b7304a19687003a2e885afe3bee53cafdf75a85684fbcfcd47c6 | Shell | 1,138 | 41 | set -e
MAINDIR=$(pwd)
display_usage() {
echo "$(basename $0) [atlas file] [dir_of_atlas_rois] name"
# echo "This script uses MRtrix to divide the atlas file into individual files each one with a single ROI. It requires 3 arguments:
# 1) Atlas file
# 2) directory to store the individual ROI files
# 3) Name of a... |
7d21b9b7b2384963063f9acf5b17138da68a92affb910b380ac3a9557b34f14e | Shell | 1,138 | 18 | #!/bin/bash
### CIFAR-10
CUDA_VISIBLE_DEVICES=0 python train.py -name EXP -dataset cifar10 -model spiking_resnet18 -amp -T_max 1024 -epochs 1024 -interval 20 -weight_decay 5e-5 -drop_rate 0.1 -T 2 &
CUDA_VISIBLE_DEVICES=1 python train.py -name EXP -dataset cifar10 -model spiking_resnet18 -amp -T_max 1024 -epochs 1024... |
9ed39bd0e9d5970ad7fc77a4751828480824919d884c83dd502666da5633e219 | Shell | 1,138 | 30 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-01:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p serial_requeue # Partition to submit to
#SBATCH --mem=40000 # Memory pool for all cores (... |
f47d2e4c34f071a0e3545805530f6e333015dee07d886c74e4f6e54cf9b356f7 | Shell | 1,138 | 31 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-05:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p serial_requeue # Partition to submit to
#SBATCH --mem=60000 # Memory pool for all cores (... |
4b88d38d0da0f9f7e875de3b5a1c1d15e72bf30028f6ff8e880de52b040c4815 | Shell | 1,140 | 38 | #!/usr/bin/env bash
set -e
# Check if a version number is provided and validate that it is an integer
if [ -z "$1" ]; then
echo "Usage: $0 <version number>"
exit 1
fi
version="$1"
if ! [[ "$version" =~ ^[0-9]+$ ]]; then
echo "Error: Version must be an integer."
exit 1
fi
set -x
# Get the directory where th... |
c4c0a13deb984b759c287ce8f129a32a8ff00798e1b88144a9987a90678cd68d | Shell | 1,140 | 51 | #!/bin/bash
# usage: run-ideeps.sh <positive.fa> <negative.fa> <test.fa> <outdir>
set -eu
function realpath { echo $(cd $(dirname $1); pwd)/$(basename $1); }
P_fa=`realpath $1`
N_fa=`realpath $2`
T_fa=`realpath $3`
OUTDIR=`realpath $4`
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
mkdir -p ... |
0878207d234c61d5e394f18314863fc1ed7655c59d5c8831c047adfd19255dbb | Shell | 1,142 | 23 | #!/bin/bash
MAX_ATTEMPTS=120
DELAY_SECONDS=10
RAY_PROM_METRICS_FILE_PATH="/tmp/ray/prom_metrics_service_discovery.json"
CLUSTER_NAME=$1
while [ $MAX_ATTEMPTS -gt 0 ]; do
if [ -f $RAY_PROM_METRICS_FILE_PATH ]; then
echo "Ray Prometheus metrics service discovery file found at: $RAY_PROM_METRICS_FILE_PATH."
ech... |
05eb0a29f2bff2298767d1ab529e3020cdcf7d5a8416c7d0b15d7466f50ee184 | Shell | 1,149 | 39 | #!/usr/bin/env bash
#$ -S /bin/sh
echo Start Time :
date
echo Detection system platform is
if [ "$(uname)" == "Darwin" ];then
echo MacOS
cp plink_mac ../bin/plink
which "gzcat" >/dev/null 2>&1
if [ $? -eq 0 ];
then
echo check gzcat done
sed 's/ zcat/ gzcat/g' ./FileDeal.h > ./FileDeal.h.tmp
mv ./Fil... |
655cc17e6c903c5b3576b8f177e034278405592196a4d881f94cb8aa0533d2f5 | Shell | 1,152 | 43 | #!/bin/bash
#
# Path to the Nextflow processing run configuration file.
#
WORKING_DIR="/net/trapnell/vol1/home/readdf/trapLabDir/hubmap/results/2022_01_11_Dana_and_HM11_nobackup"
CONFIG_FILE="$WORKING_DIR/experiment.config"
#
# Nextflow executable and pipeline script locations.
#
NEXTFLOW="/net/trapnell/vol1/home/re... |
f2ec1b9820c3f40cb1c8c411d41625a748e75475315a895bd9763f0ed4178410 | Shell | 1,154 | 31 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-03:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p serial_requeue # Partition to submit to
#SBATCH --mem=60000 # Memory pool for all cores (... |
ac439cdda395631c5ca29aba78bd519c41f22ad1c3c7325e64867c202d1e7bb4 | Shell | 1,158 | 17 | #!/bin/bash
##-------------------------------------------------------------------------
# source config file and function script
module load Miniconda2/4.3.21
FICLE_ROOT=/gpfs/mrc0/projects/Research_Project-MRC148213/sl693/scripts/FICLE/
LOGEN_ROOT=/gpfs/mrc0/projects/Research_Project-MRC148213/sl693/scripts/LOGen
OU... |
5c8a3510d5808e010146be80a0b84a1270858e163058f484797e6495d39e646a | Shell | 1,162 | 46 | #!/bin/bash
# usage: run-rnapromo.sh <positive.fa> <negative.fa> <test.fa> <outdir>
function realpath { echo $(cd $(dirname $1); pwd)/$(basename $1); }
P_fa=`realpath $1`
N_fa=`realpath $2`
T_fa=`realpath $3`
OUTDIR=`realpath $4`
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
set -eu
mkdir -p ... |
4f1a553e8c3cef5af6ce1858a9c9a7ab2be8ea5e48b14f5e78b8fa7dd9892bc4 | Shell | 1,163 | 35 | #!/bin/bash
#$ -S /bin/bash
#$ -N keep
#$ -cwd
#$ -o /mnt/analysis-psp/users/timchang/v3/pc/2211/data/vcfs/bm/eur/keep.$TASK_ID.log
#$ -j y
#$ -m bea
#$ -l h_data=8G,h_rt=48:00:00
#$ -t 1:22
#keep sample
#keep <10% missing variants
#rmove monomorphic
#reannotate INFO
chr=($(seq 1 1 22) X Y M)
echo ${chr[${SGE_TASK_... |
2d5fb51eb8652d5286be249858479cde8986c18574fd3e79981de1cedfb3c3fd | Shell | 1,164 | 31 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-05:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p serial_requeue # Partition to submit to
#SBATCH --mem=80000 # Memory pool for all cores (... |
c56614254d776f1d55d2d3ce56c329e8d1a346654db0536110699d05b44605ff | Shell | 1,165 | 43 | #!/bin/bash
#
# Path to the Nextflow processing run configuration file.
#
WORKING_DIR="/net/trapnell/vol1/home/readdf/trapLabDir/fibrosis/results/2021_03_29_HM10_Human15_ResetPlates_nobackup"
CONFIG_FILE="$WORKING_DIR/experiment.config"
#
# Nextflow executable and pipeline script locations.
#
NEXTFLOW="/net/trapnell... |
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