sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f3fb081c5cb80d134b07b349dfe8c52a835674f9132cf0b592c5d5a4479b4a5e | Shell | 2,173 | 61 | #!/bin/bash -e
if [ $# -lt 5 ] || [ $# -gt 6 ]; then
echo "usage v1: lrna_index_rsem.sh <ref_fasta_gz> <spike_in_fasta_gz> <annotation_gtf_gz> <annotation_version> <genome> [<gender>]"
echo "Creates RSEM index of reference genome, annotation and spike-ins for long-RNA-seq. Is independent of DX and encodeD."
... |
6ff5847c047c7226ae37ecd201f10cbcb4daeee534b1f032fede7bb7aa11f318 | Shell | 2,174 | 64 | #!/bin/bash
# shellcheck disable=SC2206
# THIS FILE IS GENERATED BY AUTOMATION SCRIPT! PLEASE REFER TO ORIGINAL SCRIPT!
# THIS FILE IS A TEMPLATE AND IT SHOULD NOT BE DEPLOYED TO PRODUCTION!
${PARTITION_OPTION}
#SBATCH --job-name=${JOB_NAME}
#SBATCH --output=${JOB_NAME}.log
${GIVEN_NODE}
### This script works for any n... |
3b624642e42027b27b7abf297a98c5d756ee5b7ece17513fc3ec1c7a2c7b8cbc | Shell | 2,178 | 47 | #!/bin/bash
# In this script we are annotating the genes to the MeRIP sites
module load bedtools/2.29.2
# Peak files of each replicate
merip_rep1=$1
merip_rep2=$2
merip_rep3=$3
# Replicate intersection bed file
yth_merip=$4
# GTF file
gtf=/GPFS/Magda_lab_permanent/maitenat/mm39.ncbiRefSeq.gtf
# Annotate the gene sy... |
3cbf2d1ad6a061510a8f21e8cf41eef0ab3fe1197774b5fa93021c32147e06a8 | Shell | 2,181 | 84 | #!/bin/bash
input="TS72.txt"
toolname=$1
rm Score.csv
while IFS= read -r line
do
PDBID=$line
#====================================================
nativepath="../Data/Natives"
native="Native/"$PDBID"_native.pdb"
path=""
prediction="Prediction/"$PDBID"_$toolname.pdb"
if [ "$to... |
7c6e8988d8a2f2188df7329feae9aab1942865cb439ae75e00a056043af0f771 | Shell | 2,182 | 80 | #!/bin/sh
#
# Estimate factors in two random splits independently
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
output_dir=$1
data_dir=${CBIG_REPDATA_DIR}/stable_projects/disorder_subtypes/Tang2020_ASDFactors/results/splitHalf
corpus_set1=${data_dir}/... |
fdafee18e76db1bf5475b103f93cf7fee2b919566cf2218985d447a1800166ab | Shell | 2,197 | 46 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-00:30 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=8000 # Memory pool for all cores (see also ... |
92122131d474535b4c18ccab39453f5ba53fe06e0a5f6eb190f0960abf312cbc | Shell | 2,205 | 48 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 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 p... |
8e80ba9d5e91f13dfbb6ec04ddfb8cef3e6eb279a1d89c8ea3e4ad9171081799 | Shell | 2,206 | 81 | #!/bin/bash
ctx_wt=.5
lik_softmax_beta=0.33
# gen_grad=.5
# pe_tracker_size=32
# match_tracker_size=4
# n_pe_std=3
for lr in 1e-3
do
for update_freq in 4
do
for dim_context in 128
do
for dim_hidden in 16 32
do
for stickiness in 4
do
for concentration in 1 2
... |
b10aa6a054aad202a1ccabb50a3bb581ae80f971e1ba5bd053fda86ed0d06e19 | Shell | 2,209 | 58 | data_path="chembl"
task_name="chembl"
n_gpu=8
save_dir="pretrain_save"
tmp_save_dir="tmp_save"
task_num=1
loss_func="pretrain_mlm"
dict_name="dict.txt"
charge_dict_name="dict_charge.txt"
only_polar=-1
conf_size=11
split_mode="predefine"
MASTER_PORT=10090
# train params
local_batch_size=16
batch_size=16
lr=1e-4
epoch=1... |
f9b32504c0b66a6286546decbad13e9cae2b8559acf36a6db0ada6a93265d774 | Shell | 2,215 | 77 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -s <scriptDir> -p <spmDir>... |
fd8e9bdd9d88d7797f31397ebe217f136457c89fced8d30a99728fd46d6fd2ab | Shell | 2,217 | 67 | #!/bin/bash
set -euo pipefail
# TODO(aslonnie): refactor this test to be hermetic.
PYTHON_VERSION=3.10
echo "--- Build image"
bazel run //ci/ray_ci:build_in_docker -- docker \
--python-version "$PYTHON_VERSION" \
--platform cpu --canonical-tag kuberay-test
docker tag rayproject/ray:kuberay-test ray-ci:kuber... |
35afcde79c183871411f197b9df7dbabafddda2e9b6a6ba0e41459f243c9df69 | Shell | 2,231 | 41 | ############### ToRORd ##############################
MODEL_FILE_CPU="ToRORd_fkatp_endo.c"
MODEL_FILE_GPU="ToRORd_fkatp_endo.cu"
COMMON_HEADERS="ToRORd_fkatp_endo.h"
#
COMPILE_MODEL_LIB "ToRORd_fkatp_endo" "$MODEL_FILE_CPU" "$MODEL_FILE_GPU" "$COMMON_HEADERS"
############## ToRORd fkatp Mixed ENDO_MID_EPI ############... |
664a1c0b1b136d4235f7a6c0f05d9674d4548f7eb0455555151099fcfc96135c | Shell | 2,234 | 49 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
e655db9c6abb250c66703e883eec40c48b666ca579c4aab6834178d7ad9e43ef | Shell | 2,234 | 65 | #!/usr/bin/env bash
set -euxo pipefail
LLVM_VERSION="9.0.0" # This is not necessarily guaranteed (e.g. we might use the system compiler)
install_clang() {
local cc="clang++" osversion="" url="" urlbase="https://releases.llvm.org" targetdir="/usr/local"
case "${OSTYPE}" in
msys)
osversion=win
if ... |
fcad9f3118dd42fbaf8c0d099d6228d2ee4c79526b3d04021aad953368988bbb | Shell | 2,235 | 36 | #!/usr/bin/env bash
echo start `date`
outdir="./output_stage2"
train_list="./data/stage2/epoch_train_samples_1483/" # training samples lists for SPIRED-Fitness
fitness_list="./data/stage2/fitness_samples.xls" # protein list indicating the fitness samples
valid_list="./data/stage2/CAMEO_L50-700_fitness_samples.xls" # v... |
580ceb83740fad988f8c7b3a51767b7bfd97ba998432925686eca98ba3362829 | Shell | 2,239 | 58 | #! /bin/sh
#
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
# Save LD_LIBRARY_PATH to restore it later. This variable defines shared libraries used
# by matlab to open GUI/compute/etc.
# clear_fs_env.csh removes it when clearing old freesu... |
ed70b21155f5c166fb17ed7249cc07c4957107fcb81e42af278b409b56d9292e | Shell | 2,239 | 64 | #!/bin/bash
#
# Run the doc example tests that a pull request's changed doc files feed
# directly. Used by the "docs-example-test" opt-in step in
# .buildkite/others.rayci.yml.
#
# Usage: run_doc_example_tests.sh [test_in_docker flags...]
#
# Selects targets with //ci/ray_ci/doc:cmd_doc_example_targets, which never
# f... |
7f586322c9cab1b49c79cc9a68adb9b6b0e953f4e3ff5be333484d9d80254169 | Shell | 2,241 | 43 | #!/usr/bin/env bash
cd "$(dirname "$0")"
# We can't have `set -eu` since `diff-pdf` returns a non-zero output code for differing PDFs
set -eu -o pipefail
SHOWCASE_PDF="${1}/article.pdf"
OUTPUT_PATH="../../outputs"
DATA_PATH="../data"
PODMAN_LAST_REEXECUTIONS=($(ls ${OUTPUT_PATH}/podman_*/article.pdf | tail -4))
SI... |
771a36e6877a1d0c58415d8226ad2f8240bfccd3b009b7c1618a1621f5ad18f7 | Shell | 2,244 | 59 | #!/bin/bash
set -exuo pipefail
PYTHON="$1"
TRAVIS_COMMIT="${TRAVIS_COMMIT:-$BUILDKITE_COMMIT}"
export RAY_BUILD_ENV="manylinux_py${PYTHON}"
mkdir -p .whl
cd python
# Pinned here and then actually used, because the wheel builds below pass
# --no-build-isolation. Without that flag pip ignores these and builds in an
# ... |
2f95625ed9b0a5ddc5afbb5e618390840d4619bdeac0296a795fba96112ecafa | Shell | 2,247 | 16 | python draw_masks.py --img 'examples/row01_sec13_right_cam0_frm0296_1_1.jpg' --output ./ignored/visualize --weight './ignored/ignored/newnet_resnet18_64_newHead_m2_a1/04022022_164257/best_model_epoch4470.pth' --net DeepLabv3_modified_addBN --backbone 'resnet18' --feature_channel 64 --feature_map_size_layer 2 --feature_... |
9512d6268fed8a9a8613261993e1df11ef491848be3afe25f21186dc791a39af | Shell | 2,248 | 92 | #!/bin/bash
# Cleans fam file to only include samples present in an input list
set -e
###USAGE
usage(){
cat <<EOF
usage: cleanFamFile.sh [-h] SAMPLES FAMFILE OUTFILE
Clean a fam file to only include samples present in an input list
Positional arguments:
SAMPLES List of samples used during filtering of f... |
63db61bcb5a2bd83b3cb0c0f913ca6e78e547f7ece0250084785180ed1e839d2 | Shell | 2,260 | 56 | #!/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"
mkdir ${Pheno}
echo ${Pheno}
cd /${Pheno}/
mkdir STEP1
mkdir STEP2
for i in {1..22};do
Rscript step1_fitNULLGLMM.R \
--sparseGRMFile=UKB_GRM_relatednessCutoff_0.05... |
c52b0c6d6359bd3cf9c89c9c74d66c55d608722c28572da970d37d800a69400f | Shell | 2,271 | 37 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=5:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
4debd2fe6bfb252d595af68e472d00cc0a549b07ab35a39644ba418dd2edb623 | Shell | 2,280 | 63 | #!/bin/bash -e
if [ $# -lt 5 ] || [ $# -gt 6 ]; then
echo "usage v1: lrna_index_star.sh <ref_fasta_gz> <spike_in_fasta_gz> <annotation_gtf_gz> <annotation_version> <genome> [<gender>]"
echo "Creates STAR index of reference genome, annotation and spike-ins for long-RNA-seq. Is independent of DX and encodeD."
... |
4f4124595be83dfc3a14fb80d883cd513d66ad91c776db74c31081e5df916619 | Shell | 2,280 | 50 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=20:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
f48645b7a7835ee901165d90c945636810cc984ab6b66b27257d36163d471c72 | Shell | 2,287 | 37 |
# Looking at promoter-only models:
Rscript ./summarizeFitResults.R --featureSelection Binary_PromOnly_Motif_Counts --summarizationPolicy alpha0.5_max --predictionFraming regression --paramFile VaryPromoters
Rscript ./summarizeFitResults.R --featureSelection Binary_PromOnly_Motif_Counts --summarizationPolicy alpha0.... |
2d96b9227d1764ab75e6d1b67edecef965fe90d4a728a5cbbaf0080e819932f4 | Shell | 2,291 | 51 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
a397d1ae1d98025f17cf47c85545afef460b48c2a00e2264720408fb5bc3c688 | Shell | 2,292 | 57 | #!/bin/bash
# bam-to-bigwig-stranded.sh
main() {
# Now in resources/usr/bin
#echo "* Download and install STAR..."
#git clone https://github.com/alexdobin/STAR
#(cd STAR; git checkout tags/STAR_2.4.0k)
#(cd STAR; make)
#wget https://github.com/ENCODE-DCC/kentUtils/archive/v302.1.0.tar.gz
#... |
9379004ff7c0eb8b9a62774c15767f7b2e89a7869e5d832a1ebd88a7e0c4e7c8 | Shell | 2,294 | 56 | #!/bin/bash -e
if [ $# -lt 3 ] || [ $# -gt 4 ]; then
echo "usage v1: rampage_signal.sh <bam_file> <chrom_sizes> <signal_root_name> [<stranded:T/F>]"
echo "Converts BAMs from rampage alignments to signal files: *._rampage_5p.bw. Is independent of DX and encodeD."
exit -1;
fi
bam_file=$1 # Bam file.
c... |
0227f9774018386b20f9621ab6beb5cb43c734e753b03bf5d8fb1e61f08a0199 | Shell | 2,295 | 51 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 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 p... |
4cc039aa159eb976e2fcf930f51abd96e71436d1b0ed09895407922d9198daa9 | Shell | 2,326 | 52 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=20:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
e4d2dd92fa43ac6b73a04dc7b3a7a8ee6a555ed5efdd698f2aa3659af5613920 | Shell | 2,345 | 98 | #!/bin/bash
## This will fit the tensor to the aligned dwi data using FSL dtifit(https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#DTIFIT).
# parse inputs
dwi=`jq -r '.dwi' config.json`;
bvals=`jq -r '.bvals' config.json`;
bvecs=`jq -r '.bvecs' config.json`;
mask=`jq -r '.mask' config.json`;
shell=`jq -r '.shell' ... |
400886989b7bb99c0dfb25cfc719a7902e1b878c777bb53da33930172b860434 | Shell | 2,352 | 43 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=144:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1... |
e32549b8d58f7128f950e4e0e5e49386a4679889073996d8bbb44ed6acac0fbe | Shell | 2,361 | 34 | ECHO=
MODEL_FILES=
TENSORS="/mnt/disks/annotated-cardiac-tensors-45k-2021-03-25/2020-09-21/"
TENSOR_MAPS="ecg.ecg_rest_median_raw_10 mri.lax_4ch_heart_center "
#array=( "drop_fuse_unsupervised_train_64.csv" "drop_fuse_unsupervised_train_128.csv" "drop_fuse_unsupervised_train_256.csv" "drop_fuse_unsupervised_train_512.c... |
6428f49c3483a504a727d6f279574fa0457c669dec946e47e0fdd7dd46e8ab48 | Shell | 2,365 | 60 | #!/bin/bash
function usage() {
printf "Usage: \n \
%s -d <REPO_BASE_DIR> \n \
<REPO_BASE_DIR> \t path to gatk-sv base directory" "$1"
}
if [[ "$#" == 0 ]]; then
usage "$0"; exit 0;
fi
#################################################
# Parsing arguments
#################################################
w... |
d491ae92fd9308d8b5e1e6d3b576e6dbccf525ac7866454c53615f889ee93ce6 | Shell | 2,366 | 80 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
547d0bfd1858e84b30da3bb88a392db9699baf97816e6938b3d86db97bdb2b10 | Shell | 2,377 | 61 | #!/bin/bash
############################### Nuissance Regressors & High Pass Filter ###################################
# Purpose: This script calculates the nuisance regressors (wm and csf), removes those from the data, and then highpass filters the data
# Create a list of subjects to use in this analysis and cou... |
f41d5c1b8df121794def61882c4a6bbcd4b691fbfaa418c109fc21328b4692e1 | Shell | 2,385 | 46 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-10:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=36000 # Memory pool for all cores (see also... |
4097e38d638d9b0f8bacdf52b6c94c5f15261668f861d9e895ffe8af74a3cb1e | Shell | 2,387 | 83 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
8c52cdc062117435f115d49721bdf54526ded74a1aabacdaef68a110b508ffcd | Shell | 2,391 | 51 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=5:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
49d8ee1f4fd321c30d73ccdde8f77768379997244c4a2a863203233511c67e32 | Shell | 2,393 | 79 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
5a64ebe2a996c47335e09706c58a37a5801dd1cb71510449b238258f19624dbc | Shell | 2,416 | 61 | #!/bin/bash -e
if [ $# -ne 5 ]; then
echo "usage v1: lrna_align_star_se.sh <star_index.tgz> <reads.fq.gz> <library_id> <ncpus> <bam_root>"
echo "Align single-end reads with STAR. Is independent of DX and encodeD."
exit -1;
fi
star_index_tgz=$1 # STAR Index archive.
reads_fq_gz=$2 # gzipped fastq of ... |
ea6717793d6087ba916e81518f2f9e749ce460597663bf53d0e939bc8f9d6008 | Shell | 2,424 | 83 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
06b4ed537b957eb625b7ea459a6aea3271fc4fc6c2c3079ae10593fc786b9ced | Shell | 2,426 | 57 | #!/bin/bash
# quant-rsem.sh
main() {
# Now in resources/usr/bin
# echo "* Dowload and install RSEM..."
# git clone https://github.com/bli25wisc/RSEM.git
#wget https://github.com/deweylab/RSEM/archive/v1.2.23.tar.gz -O rsem.tgz >> install.log 2>&1
#mkdir rsem
#tar -xzf rsem.tgz -C rsem --st... |
34aa06868520c0045c3e6f422556dd50b5302d5b62010363e323da606d0d9fd0 | Shell | 2,426 | 51 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2020, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
04011a7b05ced738a748f0f7ce6d0ee91be8cf786845e1aec81247f73026ca99 | Shell | 2,430 | 81 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -s <scriptDir>... |
f3e97ade1a2a548519ea8b38ae287d432ffffa623476197c8b22a65098cced1b | Shell | 2,439 | 53 | #!/bin/bash
#SBATCH -n 1 # 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 shared # Partition to submit to
#SBATCH --mem=16000 # Memory pool for all cores (see also... |
b6989ecf4cee475bbfa059b2c3d72c00c3d7aaf69ee189ce1e426628a4c6aa14 | Shell | 2,444 | 56 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=3:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
168e07e5ac8bd796e4c7ec2233affd007a797167e59b9348410ed64ed01961a6 | Shell | 2,465 | 50 | #!/bin/bash
#######################################################################################
#RNA QuantSeq Analysis: https://www.lexogen.com/quantseq-data-analysis/
#######################################################################################
#intall packages if don't have them:
#install qualimap
#a... |
47ab51e2347b8661e014e3d618d45329211d2e17150bcd0124ff49ea789ea8bd | Shell | 2,469 | 52 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
2b17554b33504c51f6e471c8c7f8836b176ab0c7ea085271f06a8fafec0f90e6 | Shell | 2,474 | 52 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=1:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 #... |
84c71215f99a8b1848bfdb42aed3e6f4948165db25a2905e053bb10bf350458f | Shell | 2,486 | 94 | #!/bin/bash
## HiC-Pro
## Copyright (c) 2015 Institut Curie
## Author(s): Nicolas Servant, Eric Viara
## Contact: nicolas.servant@curie.fr
## This software is distributed without any guarantee under the terms of the BSD-3 licence.
## See the LICENCE file for details
##
## Mapping statis... |
678187958a1e38877fe5b3da4ed2a563589aa350d7e398eb0e05d9ef2a3d29d0 | Shell | 2,487 | 52 | #!/bin/bash
#SBATCH -n 1 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-00:30 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=8000 # Memory pool for all cores (see also ... |
1182da0184d8bb5c65d71ebd54fcfd156ac5336df4b6c6d05170aac72c9d6bbd | Shell | 2,497 | 51 | #!/bin/bash
#SBATCH -n 4 # 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=16000 # Memory pool for all cores (see also... |
8c37a798de2acafff02d378dd7c6ad72b2be104b07ea5804b1ce6a5c3650bb2b | Shell | 2,507 | 94 | #!/usr/bin/env bash
# Log installation
exec > >(tee install.log) 2>&1
# Allow user to specify install path
# or default to current directory
INSTALL_PATH="$PWD/miniconda"
if [ ! -z "$1" ]
then
INSTALL_PATH="$1"
INSTALL_PATH="$(cd $(dirname "$1") && pwd)/$1"
fi
# Fail if any command fails
set -e
set -v
# We ... |
b48b1cf6e9a14cc56ce846dafb72a7e88b73e6596f24119c50e6dcf55c880110 | Shell | 2,517 | 92 | #!/bin/bash
#################################################
#################################################
# Validates all WDL JSON input files
#################################################
#################################################
set -e
#################################################
# Utility f... |
649b94668b368a9ee3377278b5b045fbaf97beaceff6607179ee6d84f6ef0ed9 | Shell | 2,524 | 44 | # Get fetal-specific peaks and shared fetal-adult peaks
bedtools intersect -wa -a ../../../data/reads/2018_12_21_bdrl_batch1_batch2_novaseq/nobackup/analysis/call_peaks/merged_peaks.bed -b /net/shendure/vol10/projects/scATAC/nobackup/human_atlas/Roadmap_Epi_Data/fetalorigin_onetoone_nobrain_combined_merged.bed > fetal_... |
d45c13af24a2d260f7ee50bd5de4882b017f4c6244ed165f9887a25fc8df74e0 | Shell | 2,527 | 80 | #!/bin/sh
# 06_b_pnm_thermnoise.sh
# What shall be done
prepInput=1
runpnm=1
# 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
project_d... |
daa66712c8794536bdbb3435ff154d9425a00e6200f91afc4666ddae7177f389 | Shell | 2,534 | 53 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
e382deda32877dd3815ad06fd983d9f5e396d0c473a45e73629451e79c213e97 | Shell | 2,541 | 62 | #!/bin/bash
# rampage-signals.sh
main() {
# Now in resources/usr/bin
#echo "* Download and install STAR..."
#git clone https://github.com/alexdobin/STAR
#(cd STAR; git checkout tags/STAR_2.4.0k)
#(cd STAR; make)
#wget https://github.com/ENCODE-DCC/kentUtils/archive/v302.1.0.tar.gz
# If ava... |
72a268ca1ceadb10c1512092abe991d0555d31225bce1441e513443f4a8a9bbf | Shell | 2,542 | 105 | #!/bin/bash
# Wrapper for bedtools unionbedg to create a multi-sample coverage
# matrix from the output of binCov.py
set -e
#Usage statement
usage(){
cat <<EOF
usage: makeMatrix.sh [-h] [-z] [-N] [-r RESTRICT] [-o OUTFILE] SAMPLES
Helper tool to automate creation of sorted coverage matrices from
binCov.py output b... |
14ef4eb638089d50375bb492a4457a34d15b8e10c831cbafe166f8a3485331bc | Shell | 2,547 | 26 | #!/bin/tcsh -f
# Calculates the NUMBER OF voxel overlap between the Lexical Frequency clusters and the Phonological Neighborhood Clusters for each participant
# The masks are thresholded at: p <0.01, alpha of < 0.05, and cluster threshold of 77.6
# there are 12 missing participants because they had no surviving cluster... |
68151a9977005aa5840fad5868d77eefefc27c6da687c425b8c90bbe5d87b3a5 | Shell | 2,548 | 74 | #!/bin/bash
# 1_ExtractDHR.sh
# create mask that
# What shall be done
prep_mask=1
extract_timeseries=1
#common directories
atlas_dir=/data/u_dabbagh_software/sct_5.5/data/PAM50/atlas #insert here your path to the SCT PAM50 atlas
project_dir=/data/pt_02306/main/data/pain-reliability-spinalcord
mask_dir=$project_dir/de... |
6b1ee593bea4e8641c353f48cddeeccc8f4195325f8f9b19a6058f14313b0755 | Shell | 2,559 | 52 | #!/bin/bash
#SBATCH -n 1 # 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 shared # Partition to submit to
#SBATCH --mem=16000 # Memory pool for all cores (see also... |
421556eb0bc65805f52b726e70976718e0530aa702111e9a802e7d9f4d94a138 | Shell | 2,575 | 86 | #!/bin/bash
# Build an environment for building ray wheels for the manylinux2014 platform.
set -exuo pipefail
BAZELISK_VERSION="v1.26.0"
ARCH="$(uname -m)"
case "$ARCH" in
x86_64|amd64)
ARCH="x86_64"
;;
aarch64|arm64)
ARCH="aarch64"
;;
*)
echo "Unsupported arch: $ARCH" >&2
exit 1
;... |
caf595cb4fe55b71d219f6f2ad981130c1c1e6e517906ceb13166e868c61770e | Shell | 2,592 | 65 | #!/bin/bash -e
if [ $# -ne 7 ]; then
echo "usage v1: lrna_align_star_pe.sh <star_index.tgz> <read1.fq.gz> <read2.fq.gz> <library_id> <ncpus> <ram_GB> <bam_root>"
echo "Align paired-end reads with STAR. Is independent of DX and encodeD."
exit -1;
fi
star_index_tgz=$1 # STAR Index archive.
read1_fq_gz=$2 ... |
c9f4407b473b758b78b740ca91e2076e43ed99135ed8162513bb37a2e0c5f910 | Shell | 2,594 | 60 | #!/bin/bash
#SBATCH --export=ALL # export all environment variables to the batch job
#SBATCH -D . # set working directory to .
#SBATCH -p mrcq # submit to the parallel queue
#SBATCH --time=10:00:00 # maximum walltime for the job
#SBATCH -A Research_Project-MRC148213 # research project to submit under
#SBATCH --nodes=1 ... |
6c78a1228df6d4a7bfc70ef6c8297032008bb15392939f50332e6f7f7e23479d | Shell | 2,598 | 79 | python3 /project/run_transformer.py run \
--training_subjects='/path/to/training_samples.csv' \
--validation_subjects='/path/to/validation_samples.csv' \
--conditioning_path='/path/to/conditioning.tsv' \
--conditionings='(\"age\", \"PTGENDER\", \"pathology\")' \
--project_directory='/results/' \
--experimen... |
feb362c86b9f43e7537da93ea9416e9b9ceb02a2e3541238e6e2e18fa621453c | Shell | 2,619 | 81 | #!/bin/bash
## Nicolas Servant - 07/09/15
##
dir=$(dirname $0)
while [ $# -gt 0 ]
do
case "$1" in
(-c) conf_file=$2; shift;;
(--) shift; break;;
(-*) echo "$0: error - unrecognized option $1" 1>&2; exit 1;;
(*) break;;
esac
shift
done
##read_config $ncrna_conf
CONF=$conf_file . $dir/hic.inc.sh
## D... |
8f33342f3afb1955b8a34717ae8a0eeedefabc4f80175ce36d20aaf3eed8e1e6 | Shell | 2,634 | 88 | #!/bin/bash
#
# IntegrateGQ_depthonly.sh
#
set -euo pipefail
vcf=$1
RD_melted_genotypes=$2
RD_melted_variants_genotypes=$3
#Final Output for individual genotype file VID IID RD-Geno, RD-GQ, PE-Geno, PE-GQ, SR-Geno, SR-GQ, Combined-Geno, Combined-GQ#
##Final Output for variant genotype file VID PE-GQ,SR-GQ,Combin... |
1272fc5a1af5d4f7a2755f0be1123fb1ffffafdc04a4dc49a620436a8fffacd7 | Shell | 2,642 | 85 | #!/bin/bash
ctx_wt=.5
lik_softmax_beta=0.33
# gen_grad=.5
# pe_tracker_size=32
# match_tracker_size=4
# n_pe_std=3
gen_grad=0.0
pe_tracker_size=0
match_tracker_size=0
n_pe_std=0.0
for subj_id in {0..11}
do
for lr in 1e-3
do
for update_freq in 4
do
for dim_context in 128
do
for dim_hidd... |
db704e56d1525a257980bf29cc95b748942ab60c346666724e7d0403b84369e6 | Shell | 2,645 | 85 | #!/bin/sh
# 04_PNMCombined.sh
# What shall be done
prepInput=1
runpnm=1
# 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
project_dir=/d... |
4a2b048c66bb08cc46775a2c6123370e8068f52c3875316a2e6f0386a105b6a4 | Shell | 2,649 | 53 | #This is to re-analyze the fp-map using the new asite file. 220102.
geneList="fp_transcript_all_gene.txt"
geneID=( $(cut -d ',' -f1 ${geneList} ) )
genotype="R57C10_In_1"
mkdir "190919_Neuro_Glia/all_transcript_new_${genotype}"
for id in ${geneID[@]}
do
echo "fp-transcript -o 190919_Neuro_Glia/all_transcript_new_${g... |
438601e6d3a339d9f9b1d7136fb9173bc111a1bd33571f15909a86c57336042c | Shell | 2,650 | 93 | #!/usr/bin/env bash
set -e
set -o pipefail
# Prerequisites: mamba, git, Perl with DBI, Bioperl, DBD::mysql modules
REPO_DIR="$(cd "$(echo "$1")"; pwd)"
TO_INSTALL="$2" # valid values: ensembl-vep absplice kipoi-veff2 faatpipe vep-plugins
VEP_PLUGINDIR=$REPO_DIR/ensembl-vep/Plugins
VEP_CACHEDIR=$REPO_DIR/ensembl-vep/... |
7dc03d498e7ed157c3d02e1ed82a2984e60c1722000237eb8c7303a0ff1d59de | Shell | 2,655 | 29 | #!/usr/bin/env bash
/home/exacloud/lustre1/fnl_lab/code/external/GUIs/MATLAB/R2018a/mcc -v -m -R -singleCompThread \
-o GUI_environments GUI_environments.m \
-a /home/exacloud/lustre1/fnl_lab/code/internal/GUIs/BIDS_conn_matrix_maker/GUI_environments.fig \
-a /home/exacloud/lustre1/fnl_lab/code/internal/GUIs/... |
af89cae9b7b4ce1eec83352f9a76e08505a33845fb740fee5e1fc7aa70e1f42d | Shell | 2,657 | 65 | #!/bin/bash
set -ex
export CI="true"
export PYTHON="3.10"
export RAY_BUILD_ENV="macos-py${PYTHON}"
export RAY_USE_RANDOM_PORTS="1"
export RAY_DEFAULT_BUILD="1"
export LC_ALL="en_US.UTF-8"
export LANG="en_US.UTF-8"
export BUILD="1"
export DL="1"
export TORCH_VERSION=2.3.0
export TORCHVISION_VERSION=0.18.0
build() {
... |
6e8edea3a08a70d5e88e3ecef3c3259486b4de53a783803de4102f38ed8b21e0 | Shell | 2,658 | 61 | #1)fastqc was used to evaluate the rowdata
cd /mnt/home/quanjian/quan/BS/runfile/
while read line
do
sample=$(echo $line | cut -d " " -f 1)
r1=$(echo $line | cut -d " " -f 2)
r2=$(echo $line | cut -d " " -f 3)
sbatch --export=sample="$sample",r1="$r1",r2="$r2" --output=/mnt/home/quanjian/quan/BS/log/fastqcCheck/... |
d2dffef5cf092d914cd1143ac96aad66e63df5e14fb28c70df72f546bfc98bfa | Shell | 2,663 | 51 | #!/bin/bash
#SBATCH -n 4 # Number of cores (-n)
#SBATCH -N 1 # Ensure that all cores are on one Node (-N)
#SBATCH -t 0-4:00 # Runtime in D-HH:MM, minimum of 10 minutes
#SBATCH -p shared # Partition to submit to
#SBATCH --mem=32000 # Memory pool for all cores (see also ... |
27253fc2dc199df4ce781f1589e590d4fe9d617429a6bda5d52be9dab5edab6d | Shell | 2,666 | 56 | #!/usr/bin/env bash
# Set FSL Variable
OLD_FSLOUTPUTTYPE=$FSLOUTPUTTYPE
FSLOUTPUTTYPE=NIFTI
# Download Upstream Template
wget http://imaging.org.au/uploads/AMBMC/ambmc-c57bl6-model-symmet_v0.8-nii.tar.gz
tar xvzf ambmc-c57bl6-model-symmet_v0.8-nii.tar.gz
cp ambmc-c57bl6-model-symmet_v0.8-nii/ambmc-c57bl6-model-symmet... |
a86071a326931c68e72e214c9cefeece0c9fc8619fd33fd7a0c7bbe4edf6f835 | Shell | 2,687 | 66 | #!/bin/bash
#
# Run nnUNetv2_plan_and_preprocess, nnUNetv2_train, and nnUNetv2_predict on the dataset
#
# Example usage:
# bash run_training.sh <GPU> <dataset_id> <dataset_name> <config> <trainer>
# bash run_training.sh 1 301 Dataset301_LumbarRootlets 3d_fullres nnUNetTrainer
#
# Authors: Naga Karthik, Jan Valo... |
debb0b44902d2b455ff48084e6eb9ffa53300780a7943c829333760325f2bec3 | Shell | 2,694 | 61 | #!/bin/sh
#Resize to same size as dsurqec atlases
ResampleImage 3 abi_10micron_average.nii abi_15micron_average.nii 0.015x0.015x0.015 size=1 spacing=0 4
fslorient -copyqform2sform abi_15micron_average.nii
ResampleImage 3 abi_10micron_average.nii abi_40micron_average.nii 0.04x0.04x0.04 size=1 spacing=0 4
fslorient -cop... |
00a82950963f8351c02f6a3cf908d9d094976a8c41fbc4656cb7757d82807358 | Shell | 2,695 | 82 | python3 /project/run_transformer.py run \
--training_subjects='/path/to/training_samples.csv' \
--validation_subjects='/path/to/validation_samples.csv' \
--conditioning_path='/path/to/conditioning.tsv' \
--conditionings='(\"25004-2.0\", \"31-0.0\", \"21003-2.0\", \"25009-2.0\")' \
--project_directory='/result... |
8a6479a3567ee2a3da21d498b67b2f742e3849887a272049837622c9cd2bc195 | Shell | 2,698 | 92 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2:-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
c790ae45be67d4eca15521a925e22e46c40d31e2dd8e51c50ff88f8acd29c20a | Shell | 2,700 | 64 | #!/bin/bash
########################################################################################################
QCsumstat=MetS_noUKB_F1_GWAS.csv
inDelimiter=comma
SelectedColumns='SNP A1 A2 est SE Pval_Estimate'
RenamedColumns='MarkerName A1 A2 Beta SE P'
outDelimiter=tab
Suffix=.REFORMAT4PRS.GWAS
outExtension=tx... |
44a08fbe689cc2c495daa4268199283b3351636ee247949d2c8525ef25febc3d | Shell | 2,709 | 90 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -t <newTemp> -... |
4f318fb8a578c396adf80a9312a49e7d0fbbb17bc275f2c8d13de5389beef147 | Shell | 2,710 | 55 | #!/bin/bash
#######################################################################################
#RNA QuantSeq Analysis: https://www.lexogen.com/quantseq-data-analysis/
#######################################################################################
#From Lexogen: The programs umi2index and collapse_UMI_ba... |
5d03063fef5a00878a3bcd9c4b42b2f9b3eab12b792acf32a78da54a5b4cc23e | Shell | 2,720 | 115 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO_ROOT="$(cd "${SCRIPT_DIR}/.." && pwd)"
cd "${REPO_ROOT}"
MODE="all"
SCILENCE_ARGS=()
for arg in "$@"; do
case "${arg}" in
stage1|stage2|all)
MODE="${arg}"
;;
--scilence)
SCILENCE_ARGS+=(-... |
6dea5032ca866a47edf8b8cb97dba053e07f5c1a6aa7246eaa8197f9935397f5 | Shell | 2,724 | 68 | #!/bin/bash -e
if [ $# -lt 5 ] || [ $# -gt 6 ]; then
echo "usage v1: srna_align.sh <star_index.tgz> <reads.fq.gz> <library_id> <ncpus> <bam_root> [<clipping_model>]"
echo "Align single-end short-RNA-seq reads with STAR. Is independent of DX and encodeD."
exit -1;
fi
star_index_tgz=$1 # STAR Index archi... |
5c703f6c48090179372b9084cbcdc59722c1c467b4cd70a4963f0506aaf5086f | Shell | 2,730 | 76 | #!/usr/bin/env bash
SCRIPT_PATH="$( cd -- "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )"
PIPELINE_DIR="$SCRIPT_PATH/../pipelines"
CONFIG_DIR="$PIPELINE_DIR/config"
WORK_DIR="$SCRIPT_PATH/../example"
STATIC_DIR="$SCRIPT_PATH/_static"
if ! command -v "snakemake" &> /dev/null; then
echo "Please install snakemake (di... |
805049811c59dc9e5576cdf6b8ed6970b6257420d2b1c040419c44bd69949ba9 | Shell | 2,740 | 81 | Phenotypes=('BMI'
'WC'
'T2D'
'FG'
'HTN'
'TG'
'HDL')
Cleaned_sumstat=('CLEANED.BMI_GIANT2018.txt'
'CLEANED.WC_UKB.txt'
'CLEANED.T2D_meta_FinngenR7_Mahajan2022_MVP.txt'
'CLEANED.FG_MAGIC.txt'
'CLEANED.HTN_meta_FinngenR7_UKB.txt'
'CLEANED.TG_GLGC_UKB.txt'
'CLEANED.HDL_GLGC_UKB.tx... |
76a3edab951bb872da99a0a2713a53ec927afa69f8834077d70016a32f4130b7 | Shell | 2,745 | 81 | #!/usr/bin/env bash
apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends openjdk-8-jdk net-tools curl netcat-openbsd gnupg libsnappy-dev && rm -rf /var/lib/apt/lists/*
export JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/
curl -O https://dist.apache.org/repos/dist/release/hadoop/... |
f4f0dd9a96c6fb7a59b4e7e6d4f48b2f4b3dd38d4dd0c19b079705d1ece26792 | Shell | 2,765 | 79 | #!/bin/bash -e
if [ $# -ne 7 ]; then
echo "usage v1: rampage_peaks.sh <rampage_bam> <control_bam> <annotation_gtf_gz> <chrom_sizes> <'rampage'|'cage'> <ncpus> <peaks_root_name>"
echo "Generages Rampage Peaks from marked bam, producing files: *.bed.gz/.bb/.gtf.gz/.tsv. Is independent of DX and encodeD."
exi... |
5082a0da125477b70cef4c89243598b8b064f2d13d96720d9720a60b3348f89c | Shell | 2,772 | 64 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
e211c55cd6683f56e0d2ea5cacce8a7a2a67f9c82cb7f87284752c4b6b3dac17 | Shell | 2,772 | 61 |
# Looking at promoter-only models:
Rscript ./summarizeFitResults.R --featureSelection Binary_PromOnly_Motif_Counts --summarizationPolicy alpha0.5_max --predictionFraming regression --paramFile VaryPromoters
Rscript ./summarizeFitResults.R --featureSelection Binary_PromOnly_Motif_Counts --summarizationPolicy alpha0.... |
10704c09cdec6b9e343266352057a9e4b21f27b9e216e4bf93466f5b7c58e355 | Shell | 2,780 | 46 | ##Generate m6A-peak bed files
#all the m6A-peaks in the lung
cat ~/Database/Lung_m6A-QTL_all/* |cut -f 1 |sort -u |\
sed 's/_/\t/g' |awk -v OFS='\t' '{print $1,$2,$3,$1"_"$2"_"$3}' |sort -k 1,1V -k 2,2n > ~/Downstream_analysis/Regulators/Lung.m6A_background.bed
#significant m6A-peaks in the lung
sed '1d' ~/2SMR/Resul... |
0a7bd12cd2494bf9c23faf5370dc307a350474c7b21a4d10045f308686e8ef5a | Shell | 2,783 | 61 | #!/usr/bin/env bash
####################################################################################################
# Copyright (c) 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This p... |
5b59bf71a92dfbe3723eb1fa3f0ac5be6b9c2128cb4db1396f0c02d89781beda | Shell | 2,790 | 79 | #!/bin/bash
set -Exeuo pipefail
# -------------------------------------------------------
# ==================== Input & Setup ====================
# -------------------------------------------------------
input_json=${1}
output_json_filename=${2-""}
output_dir=${3:-""}
input_json="$(realpath ${input_json})"
if [... |
c5de33379a0708fce3f75d7ed5b9165fe83adab5b0bfbdeae85aa88b17bacbff | Shell | 2,790 | 83 | #!/bin/bash
# This script is a bash implementation of the following workflow/task in WDL:
# Filename: wdl/Manta.wdl
# Workflow: Manta
set -Exeuo pipefail
if [ -z "${SV_SHELL_CLEAN_UP_WORKING_DIR:-}" ]; then
SV_SHELL_CLEAN_UP_WORKING_DIR=true
fi
sample_id=$1
bam_or_cram_file=$2
bam_or_cram_index=$3
reference_fasta... |
953dbcd14881e18971fcf325fa3fa51f775bf6beb1b58c4159cee4098e26c2f2 | Shell | 2,794 | 89 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -i <inDir> -d <idList> -r <reorientSa... |
6c300d9c8f92da7c5eeb3951a6593604cb3a763918e9d00d18ff08c8eacd32a7 | Shell | 2,795 | 72 | #!/bin/bash -e
if [ $# -lt 6 ] || [ $# -gt 7 ]; then
echo "usage v1: rampage_align_star.sh <star_index.tgz> <read1.fq.gz> [<read2.fq.gz>] <library_id> <ncpus> <ram_GB> <bam_root>"
echo "Align paired-end reads with STAR for Rampage. Is independent of DX and encodeD."
exit -1;
fi
star_index_tgz=$1 # STAR I... |
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