sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9a757a9c6ba8c4c09f2c1d29df9e1789e41e671f6f2f35f3883f02206e3df593 | Shell | 799 | 22 | #! /bin/bash
# Add file paths to any files test should ignore between the two ENDOFLIST placeholders.
# Specify file paths relative to the root of the repository, one file path per line.
# To test locally, ensure script is run from the root repository.
read -r -d '' IGNORE_LIST <<'ENDOFLIST'
./conferences/presentations... |
582e27c7a3afe6607d301df9e64a555277ab7b71eaf39f6cf6928bdb1cb7b161 | Shell | 814 | 17 | #! /bin/bash
for dataset in ESOL FreeSolv Lipo
do
for model in RGNN NN AFP GNN ReduceNN ReduceAFP
do
for i in 100 101 102 103 104
do
python MyNet_Regression.py --dataset ${dataset} --model ${model} --cuda 3 --epochs 100 --seed ${i} --dropout 0
python MyNet_Regression.py... |
27e90873a707fc14d794126d80178b97b39cfb317633d86b50d76c3343785ca7 | Shell | 816 | 17 | #!/usr/bin/env bash
# CI runners have no GPU. The CUDA torch build pinned in poetry.lock sometimes
# segfaults while preloading its CUDA libraries on these runners, so swap in the
# CPU build of the same torch/torchvision versions after `poetry install`.
# Usage: use_cpu_torch.sh <python command>, e.g. "python" or "poe... |
c2238fefa57e376c58209678a547ebe2bda915502da034b844299f0b15a9e6fc | Shell | 816 | 33 | #!/bin/bash
#SBATCH --time=00:30:00
#SBATCH --job-name=test_cnn
#SBATCH -N 1
#SBATCH --ntasks-per-node=1
#SBATCH -C TitanX
#SBATCH --gres=gpu:1
#SBATCH --output=cnn.ASGD.Test.SBambi.LOO.%j.out
module load cuda10.1/toolkit
module load cuDNN/cuda10.1
source /home/mdo520/.bashrc
# Base directory for the experiment
cd /... |
62ba162579327a81a5d78649dc47306b1ddc33e8c50a4c00b40fa5ea551fbf26 | Shell | 819 | 28 | #!/bin/bash
#
#SBATCH --job-name=rheMac10
#SBATCH --workdir /share/lasallelab/genomes/
#SBATCH --partition=production
#SBATCH --ntasks=12
#SBATCH --mem=18000
#SBATCH --output=rheMac10.out # File to which STDOUT will be written
#SBATCH --error=rheMac10.err # File to which STDERR will be written
#SBATCH --... |
43d6f18b73e12b4013145e45ab82d4a3a713c7a4948feb15ed35b37fea2aae58 | Shell | 820 | 42 | #!/bin/bash
#$ -pe orte nengines
#$ -N jobname
#$ -cwd
#$ -V
#$ -j y
#$ -m bes
#$ -M email
#$ -S /bin/bash
set -ex
source activate conda_env
# Configure ipython profile
PWD=$(pwd)
LOGS=$PWD/logs
mkdir -p $LOGS
export IPYTHONDIR=$PWD/.ipython
export IPYTHON_PROFILE=sge.$JOB_ID
# Start ipcontroller and engines
ipco... |
1fd5c09b3037fb2a1167d821582941ec1eef01f8cb27067ac4a94ee8002a6d38 | Shell | 825 | 33 | #!/bin/bash
#SBATCH --time=20:00:00
#SBATCH --job-name=crossval_cnn
#SBATCH -N 1
#SBATCH --ntasks-per-node=1
#SBATCH -C TitanX
#SBATCH --gres=gpu:1
#SBATCH --output=cnn.ASGD.SBambi.LOO.%j.out
module load cuda10.1/toolkit
module load cuDNN/cuda10.1
source /home/mdo520/.bashrc
# Base directory for the experiment
cd /v... |
3ea662f78c5bcf765f11637f2e405cb1a3e3b1f0204229142b9afc5597e67deb | Shell | 835 | 38 | #!/bin/bash
echo Running checks
source tools/ci/env.sh
set -eu
# Required variables
echo CHECK_TYPE = $CHECK_TYPE
if [ "$CHECK_TYPE" == "workflow" ]; then
echo DATA = $DATA
echo TEST_NAME = $TEST_NAME
echo OUTPUT_DIR = $OUTPUT_DIR
echo WORK_DIR = $WORK_DIR
fi
set -x
if [ "$CHECK_TYPE" == "test" ]; then
... |
4f1231ff7a952d82b605869eb4ed9dd4ad6963ba1d69c56a0d5e10957a4caf0a | Shell | 837 | 26 | !/bin/sh
ftrait=$1
fannot=$2
foutput=$3
trait=$(basename "$ftrait")
annot=$(basename "$fannot")
echo "*** Beginning LDSC partitioned heritability..."
echo "Trait: $trait"
echo "Annot: $annot"
echo "Output: $foutput"
module load python/2.7.15
python /home/gokala/programs/ldsc/ldsc.py \
--h2 ${ftrait} \
--out ${fou... |
b624190e56e93dbd12887e477a6fe86e88b51d33bc0d7b656dbeec214612d208 | Shell | 841 | 26 | #!/bin/sh
ftrait=$1
fannot=$2
foutput=$3
trait=$(basename "$ftrait")
annot=$(basename "$fannot")
echo "*** Beginning LDSC partitioned heritability..."
echo "Trait: $trait"
echo "Annot: $annot"
echo "Output: $foutput"
module load python/2.7.15
python /home/gokala/programs/ldsc/ldsc.py \
--h2 ${ftrait} \
--out ${fo... |
1a1bb63e1acfd50d170a14ea478a87019e68eb48e418bddd7a22ea160e97355d | Shell | 858 | 22 | #!/usr/bin/env bash
set \
-o errexit \
-o nounset \
-o pipefail
if [ ! -f v4.repeats.renamed.bed ]; then
wget 'https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/4577/102/GCF_000005005.2_B73_RefGen_v4/GCF_000005005.2_B73_RefGen_v4_rm.out.gz' -O - | \
gzip -cd | \
tail -n+4 | \
tr -s ' ' ... |
f1cddac3d2d8296de45ce0c9850f13b490313a1e76d22e7b4566427a3fe4525a | Shell | 867 | 13 | #!/bin/bash
#SBATCH --ntasks 6
#SBATCH -p part0
#SBATCH --job-name feats-gen_best_mocc6
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/feats-gen_best_mocc6.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --feats_gen \
--model enetb6 \
--test_ckpt_path ".results/bsz32-lws1-r... |
b0ae4e1e0b49973f7ad42d5a3116d06fba011830e5b6e2d816e2606aca241d69 | Shell | 872 | 30 | #!/bin/bash
# Usage:
# align_symmetrize source.txt target.txt output.moses method [eflomal options]
# Where method is one of the symmetrization methods from atools (the -c
# argument).
if [ -z $4 ] ; then
echo "Error: symmetrization argument missing!"
echo "You might want to try 'grow-diag-final-and' (or 'no... |
42b51d743b77c7150b56eaf97cd57da36d7559776fa3e08e1c5655545fe2b672 | Shell | 883 | 37 | #!/bin/bash
# Upload website to gh-pages
USAGE="$0 <html_dir> <project-name> [<organization-name>]"
HTML_DIR=$1
if [ -z "$HTML_DIR" ]; then
echo $USAGE
exit 1
fi
if [ ! -e "$HTML_DIR/index.html" ]; then
echo "$HTML_DIR does not contain an index.html"
exit 1
fi
if [ -d "$HTML_DIR/.git" ]; then
echo "... |
4135e1b44f927447fa7e7ad1314cb51ecad167ca43cd01fa5b630ad232cdb6f1 | Shell | 968 | 38 | #!/bin/bash
## SGE batch file - mriqc
#$ -S /bin/bash
#$ -N mriqc
#$ -V
#$ -l mem_free=15G
#$ -pe openmp 8
#$ -j y
#$ -wd /mnt/MD1200B/egarza/public/logs/mriqc
##### END OF JOB DEFINITION #####
#module load singularityce/3.5.3
sub=`ls -d /mnt/MD1200B/egarza/public/fm_thania/data/bids/sub-*`
IMG=/mnt/MD... |
579945727cf5616d039810d4e52417e90225630e334eefc761f7fcbc220d7232 | Shell | 991 | 28 | #!/bin/bash
ftrait=$1
fannot=$2
foutput=$3
fbaseline=$4
trait=$(basename "$ftrait")
annot=$(basename "$fannot")
echo "*** Beginning LDSC partitioned heritability..."
echo "Trait: $trait"
echo "Annot: $annot"
echo "Output: $foutput"
echo "Baseline: $fbaseline"
module load python/2.7.15
python /home/gokala/programs/... |
1edd4ebdc5f9248f190a1a67865f453cc1e30dc67764c12e3a4514b817a77d74 | Shell | 998 | 28 | #!/bin/bash
ftrait=$1
fannot=$2
foutput=$3
fbaseline=$4
trait=$(basename "$ftrait")
annot=$(basename "$fannot")
echo "*** Beginning LDSC partitioned heritability..."
echo "Trait: $trait"
echo "Annot: $annot"
echo "Output: $foutput"
echo "Baseline: $fbaseline"
module load python/2.7.15
python /home/gokala/programs/... |
76df90ea1efa63beca47766ca3dd134b7e0739725bbe12e02359ecd8f61720b8 | Shell | 1,011 | 57 | #!/bin/bash
# GNU parallel for DMRichR
# Ben Laufer
DMR(){
contrast=$1
echo ${contrast}
mkdir ${contrast}
cp cytosine_reports/*.gz ${contrast}
mv sample_info_${contrast}.xlsx ${contrast}/sample_info.xlsx
cd ${contrast}
echo testCovariate is ${testCovariate}
if [[ "${contrast}" == *"GD"* ]]
then
sample... |
bec2138df67ffbd26bbfdad047173b7218cdec86f79affa946cd9a18aa32d32b | Shell | 1,015 | 51 | #!/bin/bash
#PBS -q qos
#PBS -l walltime=jobtime
#PBS -l nodes=nnodes:ppn=nprocs
#PBS -l mem=jobmem
#PBS -N jobname
#PBS -e error_stream
#PBS -o output_stream
#PBS -r n
#PBS -m bea
cd $PBS_O_WORKDIR
set -e
source activate conda_env
# Relaunch batch job if not finished
qsub -W depend=afternotok:$PBS_JOBID jobscript... |
ba1f3fd77997c701740e335f742114e46e1fab1e76b85347b2a06cc7b2507840 | Shell | 1,021 | 24 | # Copyright 2020 Google LLC.
#
# 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
f68c3e3c5c34897b99b8b10de489ddf16622d44cde403ff77a1553a49aa1ebef | Shell | 1,023 | 17 | #!/bin/bash
##############################################################################################################################################
# database: This is the name of the database to be used. Options are:
# metadata, data_all_l0, data_all_l1, data_dendro_l2, data_dendro_lm... |
b81ddca3bbb2c5f6617de7b1e9b27240870c8e83c08d8eb65c7b5a1ecd257410 | Shell | 1,037 | 32 | #!/bin/bash -x
# This script is for testing the preparation workflow to create a pdb file that is compatible for parsing by openmm
# It reads in a pdb provided in the supplementary information from 10.1021/ja512751q always of the form:
# {target}_protein.pdb and runs pdb4amber and pdbfixer to generate a new pdb file w... |
e9f0be209f18ea7a9b4b0fdc2701ebd95fbaedda201c9110ff8d0a71535ff560 | Shell | 1,072 | 52 | #!/bin/sh
# test tokenisation
# set -x
# set -e
# args are:
# string-to-parse
# expected-token
# expected-string (for string tokens)
# expected-residual
check() {
test_name="$1"
test_string="$2"
residual="$3"
token="$4"
token_string="$5"
echo -n "$test_name ..."
log=$(./test_token "$2" "$3" "$... |
5e7ffa68a51215c78eeca8219da15e492cf0c344e250967037056d0397c84817 | Shell | 1,076 | 45 | #/usr/bin/env bash
# bash completions for the "vips" command
# copy to /etc/bash_completion.d to install
_vips_compgen_f()
{
COMPREPLY=($(compgen -f -- "${COMP_WORDS[-1]}"))
if [ ${#COMPREPLY[@]} = 1 ]; then
local LASTCHAR=
if [ -d "$COMPREPLY" ]; then
LASTCHAR=/
fi
COMPREPLY=$(printf %q%... |
780f427ab3bb4527b45b9bdf852dc4351e1d99ec92db020670fc08059ef1a6d7 | Shell | 1,109 | 27 | # Copyright 2020 Google LLC.
#
# 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
f93df21bf45525c10496a29ae1fe623d951f074a45d0a7c261d95ea17fb95feb | Shell | 1,111 | 40 | #!/bin/bash
# code up the binary files in $1 as a set of name / string pairs in $2
# For example:
# $ ./wrap-profiles.sh profiles profiles.c
# we have to use arrays for the strings, since MSVC won't allow string
# literals larger than 64kb
in=$1
out=$2
echo "/* this file is generated automatically, do not edit! */"... |
075771765a36e8046b3b69d093efaaa785159dacb77c3ccec486b4abdb855ee1 | Shell | 1,116 | 31 | #!/bin/bash
#script to align Spike and RBD sequences using mafft, and infer phylogeny with RAxML
#grabnode at least 8 nodes or adjust -T option below (number of threads)
mafft --reorder --op 4.5 ./unaligned-sequences/Spikes.fasta > ./Spikes_aligned.fasta
mafft --reorder --op 4.5 ./unaligned-sequences/RBDs.fasta > ./... |
e69f7e20559c6aed189b41e7ef1e060236272c3f56c55381f173413ab1e0531d | Shell | 1,145 | 33 | #!/usr/bin/env bash
FILE="sequences.simdata.gz"
if [ ! -f "$FILE" ]
then
wget https://raw.githubusercontent.com/AvantiShri/model_storage/db919b12f750e5844402153233249bb3d24e9e9a/deeplift/genomics/sequences.simdata.gz
else
echo "File sequences.simdata.gz exists already"
fi
FILE="keras2_conv1d_record_5_model_PQ... |
f24c92cd8b21ec2f29c6f102462fec133bfe9f313dc1a474e03feee1c6387d26 | Shell | 1,150 | 54 | #!/bin/sh
# set -x
. ./variables.sh
# make a large PNG, roughly the size of Chicago.png
printf "building huge test PNG image ... "
$vips replicate $image $tmp/huge.png 30 5
echo "ok"
huge=$tmp/huge.png
printf "testing vipsthumbnail ... "
rm -f $tmp/x.png
$vipsthumbnail $huge -o $tmp/x.png
if ! $vipsheader $tmp/x.p... |
3e1d89c8332449e94200db27d930cd451490bf29c3cb13b249ead30b8dc83f41 | Shell | 1,158 | 25 | #!/usr/bin/env bash
set \
-o errexit \
-o nounset \
-o pipefail
if [ ! -f JASPAR2020_CORE_plants_non-redundant_pfms_meme.txt ]; then
wget "http://jaspar.genereg.net/download/CORE/JASPAR2020_CORE_plants_non-redundant_pfms_meme.txt"
fi
if [ ! -d JASPAR2020_CORE_plants_non-redundant_pfms_meme ]; then
wget "ht... |
e9c572c33dfd3eb25b581723b7063c90d47c589acd6ffc4b6a8d01a739c9e43a | Shell | 1,166 | 60 | #!/bin/bash
#SBATCH -p qos
#SBATCH -t jobtime
#SBATCH -n nengines
#SBATCH -C cpu|nvme
#SBATCH -A proj36
#SBATCH --mail-type=ALL
#SBATCH --mail-user=email
#SBATCH -J jobname
#SBATCH --signal=B:USR1@60
run_dependent_script() {
func="$1" ; shift
for sig ; do
trap "$func $sig" "$sig"
done
}
# trap function to relaunch t... |
7e5de6e1ff389192057d942476525379664bcbf51b6a60c242d7f988869152d3 | Shell | 1,171 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc5
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc5.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
d5e95ffdb2badae2cc5f24fa8d742f65f6adca25a12e836d459d896777a6af3c | Shell | 1,171 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc3
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc3.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
fbd1377fa51cff08e0a4d9b4b168d75a9ad62bfca6f1bda7b42b3cfed188bf1b | Shell | 1,171 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc4
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc4.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
5cbbed27493a5f350d6e04fc62fffadba28610e6b351ca61c7e5f345fdab2130 | Shell | 1,185 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc6
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc6.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
8d3af67a14cbaec171cd89f69dc3eded7d618f2689f80c2a6b72be169474421a | Shell | 1,191 | 31 | # Copyright 2025 The Magenta Authors.
#
# 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... |
292825d8cd0a7429f6b5336338e2bd50a434403aebbe140ce3f36329aee96d27 | Shell | 1,195 | 30 | #!/bin/sh
set -ex
bbp_host=anirban@bbpv1.epfl.ch
scp bbp_datapath.sh $bbp_host:~/
ssh $bbp_host "sh bbp_datapath.sh" > bbp_log
ssh $bbp_host "rm bbp_datapath.sh"
for line in $(<bbp_log);
do
bbp_path=$bbp_host:$line
CELL_ID=${bbp_path##*/}
mkdir -p $CELL_ID/config_Stage1
scp -r $b... |
fd4105c3de1b848f6a01fa26d052ae8c8eb1ac567aa62bd83f617ee672e0ca0f | Shell | 1,200 | 36 | # Copyright 2025 The Magenta Authors.
#
# 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... |
2268b56d74a894bff6343ef26e208801c9a0635c8625f31555efa25d2b020ea3 | Shell | 1,218 | 61 | #!/bin/bash
#SBATCH -q qos
#SBATCH -t jobtime
#SBATCH -N nnodes
#SBATCH -C haswell
#SBATCH -L SCRATCH
#SBATCH --mail-type=ALL
#SBATCH -J jobname
#SBATCH --signal=B:USR1@60
run_dependent_script() {
func="$1" ; shift
for sig ; do
trap "$func $sig" "$sig"
done
}
# trap function to relaunch the optimization
func_trap() ... |
41a634efcac09a736f053157d4c2abd7bc4bfdfa4cc29d2d81c6083b7858ad75 | Shell | 1,224 | 42 | #!/bin/bash
#
# Collects the pull-requests since the latest release and
# aranges them in the CHANGES.txt file.
#
# This is a script to be run before releasing a new version.
#
# Usage /bin/bash update_changes.sh 1.0.1
#
# Setting # $ help set
set -u # Treat unset variables as an error when substituting.
... |
55c0bc99be59e37d4b2f8fa3e52e2dabf13d4818918cc5d60aa2bd4e1568d0ae | Shell | 1,225 | 42 | #!/bin/bash
#
# Collects the pull-requests since the latest release and
# arranges them in the CHANGES.txt file.
#
# This is a script to be run before releasing a new version.
#
# Usage /bin/bash update_changes.sh 1.0.1
#
# Setting # $ help set
set -u # Treat unset variables as an error when substituting.... |
499272bf71aa5c4c2dc27576d68c74f219aec93dd8e06020e71c2d0e9451d21f | Shell | 1,245 | 40 | #--------------------------
#---- Clumping w/PLINK ----
#--------------------------
# Gokberk Alagoz, 2021 - last updated March 2022
# Clump sumstats before the overlap analysis.
#-----Variables-----
#TODO 1- Make a list of your sumstats (or change this script to loop over them)
#TODO 2- Update paths to sumstats_lis... |
e293b8adaddbf7b896666db6c700c1bbb7107cb63ecbd98f42b14c145412a2d4 | Shell | 1,270 | 52 | #!/usr/bin/env Rscript
#
# This script will parallelize Overlap Analysis
# jobs over annotations.
# The R script works only with R version >4.0.3.
# Thus, run this script on gridportal1 instead of
# gridmaster.
#
# Gokberk Alagoz
# Created on: 02.07.2021
#--------------------------------------------------#
# VARIABLES... |
95c7c134b0a47ccbe1aa8329da10d2a8e485256afe8e0fc69a5666b442492f5a | Shell | 1,275 | 34 | #!/bin/bash -x
# This script is for running the preparation workflow to create a pdb file that is compatible for parsing by openmm
# It reads in a pdb provided in the supplementary information from 10.1021/ja512751q always of the form:
# {target}_protein.pdb and runs pdb4amber and pdbfixer to generate a new pdb file w... |
7163eefdd3ff9b5760115dcda535d3568c81eba4411e32c0d8252caab708253b | Shell | 1,306 | 57 | #!/bin/sh
# set -x
. ./variables.sh
exit_code=0
$vips im_benchmarkn || exit_code=$?
if [ $exit_code -ne 0 ]; then
echo "im_benchmark is not available, skipping test"
exit 0
fi
chain=1
# im_benchmark needs a labq
$vips colourspace $image $tmp/t3.v labq
for tile in 10 64 128 512; do
# benchmark includes a dithe... |
439437614b6801a0069b41c94914edb8859a371622f91ad83d581e6a3a625c0c | Shell | 1,323 | 31 | #!/bin/bash
# start this script from repository root as working directory
##############
# Simulations
##############
# for full reproduction, uncomment this line to delete results
#rm simulated/results/*
simulated/run_all.sh
simulated/h0_simulate_normviol_lin.py
simulated/h0_simulate_normviol_sig.py
simulated/h1_... |
26d5d96d22424659ad60141d1b9460378519fce1d64baa2ed624021e042baf45 | Shell | 1,411 | 39 | #!/bin/bash
# run this script locally in the 'quarterly report' folder
# Indicate the date and time for last stat generation
current_time=$(date +"%Y-%m-%d %H:%M:%S.%3N")
echo "#Book stats for chapters and subchapters, \
generated on: $current_time" > book-stats.md
# add table header
echo "guide name; number of chapt... |
137bc705e356883c70e926c60acce44c77d57a0221f51ede28792983d1ad03f1 | Shell | 1,419 | 29 | #!/bin/sh
#copy files after subsetting and variant QC from cluster to workspace
for sample in european replication; do
#-----------------------------------------------------------------------------------------------
#set paths
#-------------------------------------------------------------------------------------... |
818dc73e4b62f8d1a1feee423dd731d699ebcdd38e7261e317b572bd9f75b542 | Shell | 1,435 | 48 | # Copyright 2025 The Magenta Authors.
#
# 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... |
23dc9b1339bfbd7f880efa121add72315f6037593405896ad27a9ce558de0a0f | Shell | 1,463 | 56 | #!/bin/sh
## This script assumes that it has already been run for a set of patients,
# and it just needs to run the modificed
# CreateBoxFromOpticNerveNoEye
# to create the data augmentation scans.
## AUTHOR: Aran Garcia-Vidal
# Project
Projecte=FAT_SAT
Ext=nii.gz
RunDir=/home/extop/GERARD/RunNas
if [ ! -d $RunDir ... |
18a6932b84b7a50151f27e3d0b7dfb2c84fa5e877bd18c951cdcfe7dc052b1fa | Shell | 1,491 | 29 | #!/bin/sh
set -ex
starcluster put ani_cluster aws_datapath.sh /root
starcluster sshmaster ani_cluster "sh aws_datapath.sh" > aws_log
starcluster sshmaster ani_cluster "rm aws_datapath.sh"
for line in $(<aws_log);
do
aws_path=$line
CELL_ID=${aws_path##*/}
mkdir -p $CELL_ID
starclu... |
7efcbc8cf79bc33e59361de2c02c22775ecf45234107f44b9360543c1bc3cd99 | Shell | 1,504 | 40 | #!/bin/bash
#-----run_1000G_PC_cor_BJK_noGC.sh-----
# Run correlation analysis between 1000G phase 3 PC loadings and sumstats BETAs for all phenotypes
# /usr/local/lib64/R/bin/
#-----Variables-----
# $rdataDir - Directory containing GWAS summary statistics (in Rdata format)
# $outDir - Directory to write Spearman's ... |
499cb3def01a84c0808773ca08519eba12b7342af67248b12d88edce109019d8 | Shell | 1,510 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc5
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc5.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
698d9080547b0ba409596cb2ab61bc14adff181fd612366dd64fdcf1a80e389a | Shell | 1,510 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc3
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc3.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
da02360f8f99b1df277814a8955d4b92a321cc5d686ecbf37cc32181c3e406db | Shell | 1,510 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc4
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc4.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
4eee64813d4c74f74d6fc66c4947e56ea9cb29e8237ddbf3ec5ae7788a82b904 | Shell | 1,524 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc6
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc6.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
5efa76686f55b87e0955fd199a62e4741db902df28d70429258f7d86e0d17d59 | Shell | 1,524 | 45 | #!/bin/bash
set -eu
# Either to build against to-be-released heudiconv
dev_build=
generate() {
if [ "$dev_build" = "1" ]; then
apt_pkgs=python3-pip
run_cmd="pip install git+https://github.com/nipy/heudiconv@master"
else
apt_pkgs="heudiconv=0.13.1-1~nd120+1"
run_cmd=":"
fi
# more details might come on htt... |
e43791c3e56a377f09c6fe98ae741f164916776ddbab9e4a079c8d20844ac333 | Shell | 1,538 | 47 | # Copyright 2025 The Magenta Authors.
#
# 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... |
9ae738b15eade46fd1d6805d7ed084dc3749df2635a6b8b571fd3c77aa436538 | Shell | 1,539 | 49 | # Copyright 2025 The Magenta Authors.
#
# 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... |
fb147ef87f1af06f682b895994ee3b55f4ae17a51962618a91b7920afac04629 | Shell | 1,562 | 39 | #!/bin/bash
# On Mac, builds and deploys VoxSim for iOS platform
# Requires Xcode to run to completion and deploy, will not run on Windows
# Pass -b with a build configuration XML file (required)
# Pass -a with a path to Unity (optional: defaults to assumed known location in Applications)
# use this if you have Hub in... |
158542e6059e6ac3cc23394d827e443b994dfa8db7d4c3b43c188809ad345127 | Shell | 1,583 | 50 | # Copyright 2025 The Magenta Authors.
#
# 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... |
fcb63784882abc8e0cbcc1daf4682ef3138226c60d94bc5e68ddaf4aad334b51 | Shell | 1,583 | 36 | #!/bin/bash
# Run it on bash -> bash run_1000G_PC_cor_ancreg_BJK_noGC_par.sh
#-----1000G_PC_cor_ancreg_BJK_noGC_par.sh-----
# Run correlation analysis between 1000G phase 3 PC loadings and ancestry regressed sumstats for all phenotypes
#-----Variables-----
# $rdataDir - Directory containing GWAS summary statistics (... |
e2e68308cc57e661e2d7c2f73d52c514748dbd8093331e2dad760ab3e545af2c | Shell | 1,654 | 10 | findMotifsGenome.pl 'female precocious DMRs - age_m_unique_neuron.bed' mm10 female_precocious_DMRs_age_m_unique_neuron_rev3/ -size given -bg 'control dmrs - female precocious dmrs - age_m_neuron - 10.bed'
findMotifsGenome.pl 'control dmrs - female precocious dmrs - age_m_neuron - 1.bed' mm10 control_dmrs_female_precoci... |
b0ae778ac6d9b78f7ed52a55ec8bce3225d91d4560384f56a8d7c038ae3666a1 | Shell | 1,695 | 50 | #!/bin/bash
set -eu
# Either to build against to-be-released heudiconv
dev_build=
generate() {
if [ "$dev_build" = "1" ]; then
apt_pkgs=python-pip
run_cmd="pip install git+https://github.com/nipy/heudiconv@master"
else
apt_pkgs=heudiconv
run_cmd=":"
fi
#neurodocker generate "$1" \
docker run --rm kaczma... |
6867d2cbfe9a6aba7b4f074872024ead7d08ced3fa406b3416006c2cb03a96dc | Shell | 1,697 | 71 | #!/bin/sh
# resize a 1000x1000 image to every size in [100,1000], check for black
# see https://github.com/libvips/libvips/issues/131
# set -x
. ./variables.sh
# make a 1000x1000 mono test image ... add a bit so the image should not
# contain any zeros, helps to spot missing tiles and bad pixels
echo building te... |
062ebc2dcabce52672bfb52237544c17f0a14d0619eb6a41e643a074f5e1495e | Shell | 1,708 | 38 | #!/bin/sh
#-----------------------------------------------------------------------------
# WRAPPER script: submit all BGENIE jobs to the cluster:
# Will run BGENIE on global FS metrics for different samples (Replication, European, different metrics and covariates)
# Written and adapted by B. Molz, Nov 2021
#-----------... |
fb2caf8fde44374edb6ea9095f69f92e2a792f12644a813eb2ba1a1a03c8d175 | Shell | 1,708 | 11 | findMotifsGenome.pl 'female precocious DMRs - age_m_unique_neuron.bed' mm10 female_precocious_DMRs_age_m_unique_neuron/ -size given -cpg
findMotifsGenome.pl 'control dmrs - female precocious dmrs - age_m_neuron - 1.bed' mm10 control_dmrs_female_precocious_dmrs_age_m_neuron_1/ -size given -cpg
findMotifsGenome.pl 'contr... |
1f232174f1bf4ccb21c10a754617c326b889f5351cff327e892a926c713cec44 | Shell | 1,767 | 9 | #!/bin/bash
mv /Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55AP_dwi.nii.gz /Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_acq-HASC55APVARIANTEchoTimeFlipAngle_dwi.nii.gz
mv /Users/scovitz/BIDS_Dataset_Datalad/sub-02/ses-phdiff/dwi/sub-02_ses-phdiff_ac... |
e8751ae3b17300e5add0d256e4476cad7e82584740db43562cd532cf001cc2b9 | Shell | 1,785 | 34 | #!/usr/bin/env bash
set \
-o errexit \
-o nounset \
-o pipefail
if [ ! -f lin_all.peaks.final.bed ] || [ ! -f GM.peaks.final.bed ]; then
wget 'https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE66386&format=file&file=GSE66386_all_nucleosome_calling.tar.gz' -O - | gzip -cd | tar xvf -
rm osmotic.peaks.final.b... |
3d33e10a0416ee6f3337f7dbea06484532c1cda2c705ef1a60938a03df9d1ca6 | Shell | 1,797 | 53 | #!/bin/sh
# Gokberk Alagoz, 2020
#-----Munge Sumstats-----
# Reformat GWAS summary stats before computing LDSC intercept
# munge_sumstats.py is from github.com/bulik/ldsc
# Based on the tutorial at github.com/bulik/ldsc/wiki/Heritability-and-Genetic-Correlation
# WARNING: Run it on single.q, other queues won't work b... |
f839e3ea885c5cba65f1caa4616719b1149037eea3ecf1edff4f0b7accd3a6d6 | Shell | 1,834 | 32 | #!/bin/sh
set -ex
nersc_host=ani@cori.nersc.gov
scp -i /local1/nersc_ssh/mynersc nersc_datapath.sh $nersc_host:~/
ssh -i /local1/nersc_ssh/mynersc $nersc_host "sh nersc_datapath.sh" > nersc_log
ssh -i /local1/nersc_ssh/mynersc $nersc_host "rm nersc_datapath.sh"
for line in $(<nersc_log);
do
nersc_path=... |
6b470f5343d5b83c7903044537c4cc7a3fdf05e78476b3d66db42c03fdd551b5 | Shell | 1,852 | 59 | #!/bin/sh
# SKIP_IN_V6
set -e
OLD_PWD=$PWD
# BOILERPLATE
#% EXAMPLE START
#
# Getting started
# ***************
#
# The Datalad container extension provides a few commands to register
# containers with a dataset and use them for execution of arbitray
# commands. In order to get going quickly, we only need a dataset... |
016dca2191ee5261b4d9cf78382088cf7940db18e471a2ed8d434dac4be90940 | Shell | 1,854 | 59 | #!/bin/sh
# SKIP_IN_V6
set -e
OLD_PWD=$PWD
# BOILERPLATE
#% EXAMPLE START
#
# Getting started
# ***************
#
# The Datalad container extension provides a few commands to register
# containers with a dataset and use them for execution of arbitrary
# commands. In order to get going quickly, we only need a datase... |
48dfcf02a3ec17ccac6bf70f57d6f1f49cdaff9ea961398d77a48d4df41e9aa1 | Shell | 1,883 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc5
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc5.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
63d4fdbcb82c825066a71475c81a380cb498fe75cf1b7292411d42201fbd7e9e | Shell | 1,883 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc3
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc3.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
79458e53f31751b992171480a1a8a265333157262ecbd89799bcce8ae5043324 | Shell | 1,883 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc4
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc4.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
cdf231309f69063a7531fe96271e76c273b340df0d8b14d4cf923ba422548d54 | Shell | 1,883 | 16 | #!/bin/bash
#SBATCH --qos short
#SBATCH -N 1
#SBATCH -c 4
#SBATCH -t 2-00:00
#SBATCH --mem 8G
#SBATCH -p res-gpu-small
#SBATCH --job-name ensemble-mocc6
#SBATCH --gres gpu:1
#SBATCH -o ../../../.results/ensemble-mocc6.out
cd ../../..
source venv/bin/activate
python main.py --lr=-4.8 --optimiser=Adam --ensemble \
--... |
86a981dd1d57fa1acb6832a3d000eed3c91461d5be8fe7630a0a7b590ff664fe | Shell | 1,891 | 54 | #!/bin/sh
#-----Run ldsc-----
# Estimating heritability, genetic correlation and the LD Score Regression Intercept
# ldsc function is from github.com/bulik/ldsc
# For interpreting results, check the tutorial at github.com/bulik/ldsc/wiki/Heritability-and-Genetic-Correlation
#-----Variables-----
# $ss1 - munged summar... |
700690a7c0329f732a784c634fded132ff1bfc5b276017af22c217bcefc4f326 | Shell | 1,901 | 55 | #!/bin/sh
set -ex
# Can be run from any location on CentOS
aibs_datapath='/allen/programs/celltypes/workgroups/humancolumn_ephysmodeling/anin/Optimizations_HPC/Mouse'
aibs_runpath='/allen/aibs/mat/anin/hpc_trials'
aibs_metricpath='/allen/aibs/mat/ateam_shared/Mouse_Model_Fit_Metrics'
cell_complete_path=""
cd $aibs_r... |
fdf6c890983e4355acea10f166a2ce263bf92de80ea00ed01a42fc04ab45c095 | Shell | 1,916 | 46 | #!/bin/bash
# Builds VoxSim for OSX platform
# Requires MinGW to run on Windows
# Pass -b with a build configuration XML file (required)
# Pass -a with a path to Unity (optional: defaults to assumed known location in Applications on OSX or Program Files on Windows)
# use this if you have Hub installed and need to make... |
4770e63c45c36ca1191deed7291c484c03ec35e4e28607b47d7cb2a9394ee125 | Shell | 1,917 | 46 | #!/bin/bash
# Builds VoxSim for Windows platform
# Requires MinGW to run on Windows
# Pass -b with a build configuration XML file (required)
# Pass -a with a path to Unity (optional: defaults to assumed known location in Applications on OSX or Program Files on Windows)
# use this if you have Hub installed and need to ... |
344ee1b3c5f72e213ff44aeebb88bcae5db862892499711ac760cd7922a3feac | Shell | 1,919 | 39 | #----------------------------------------------------------------------------------------------------------
# script for the calculation of the number of independent phenotypes in GenLang
# by Else Eising, 11 June 2019
# adabted by Barbara Molz, May 2022
# The script uses PhenoSpD
# see https://github.com/MRCIEU/... |
6f48984c1dc2b95d0227cf9706269509a1536c2176e2ba4245600d70efaa082a | Shell | 2,004 | 67 | # Copyright 2025 The Magenta Authors.
#
# 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.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... |
73e7af9a2a2ceff61c327f858289eb94582a80bd2b9851968e81efff88bc897d | Shell | 2,019 | 19 | #!/bin/bash
python ldsc.py --h2 bip.sumstats.gz --ref-ld-chr lister_anno. --w-ld-chr weights. --overlap-annot --frqfile-chr 1000G.mac5eur. --out bip_lister
python ldsc.py --h2 pubertal_growth.sumstats.gz --ref-ld-chr lister_anno. --w-ld-chr weights. --overlap-annot --frqfile-chr 1000G.mac5eur. --out pubertal_growth_li... |
fcd5a78f9b5012a336e8004510780fa6fc9e43b1efba882f62f078f87fa14d80 | Shell | 2,061 | 31 | DIR=`dirname $0`
# H0
python3 $DIR/simulate_H0.py --out=$DIR/results/h0_ccc_partial_d1e0_linear.csv --mode=partial --delta=1 --epsilon=0 --nonlin-trf=identity --repetitions=1000
python3 $DIR/simulate_H0.py --out=$DIR/results/h0_ccc_partial_d01e2_linear.csv --mode=partial --delta=0.1 --epsilon=2 --nonlin-trf=identity ... |
212662c8f8d4614cd8b5decc1a4470e2ce1ab357561875f6aab59212c7f9b643 | Shell | 2,073 | 58 | #!/bin/bash
#
# Script for running code coverage of ldpred tests.
#
# For this script to work, the coverage tool must have previously been installed
# via `pip install coverage` .
#
# Coverage files will be stored in subdirectories under ${TMPDIR}/ldpred or, if
# TMPDIR is not defined, /tmp/ldpred.
#
# By default, all ... |
bc397e98d8bf2cf723248e288bad66cdb590c78dadc058d3bdd0ce1c86604e4e | Shell | 2,080 | 53 | #!/bin/bash
#emacs: -*- mode: shell-script; c-basic-offset: 4; tab-width: 4; indent-tabs-mode: t -*-
#ex: set sts=4 ts=4 sw=4 noet:
#
# A sample script to test correct operation for a prototypical/recommended
# setup etc
#
# COPYRIGHT: Yaroslav Halchenko 2019
#
# LICENSE: MIT
#
# Permission is hereby granted, free of... |
b0eaf6030c764672f436801e483b21396f3c0f67b5604f3c80a149bbab808e65 | Shell | 2,107 | 67 | #!/bin/sh
## AUTHOR: Aran Garcia-Vidal
# Name of project folder
Projecte=FAT_SAT
#Extension of images
Ext=nii.gz
# Directory where the scripts will run
RunDir=/mnt/DADES/Gerard/RunNas
if [ ! -d $RunDir ]
then
mkdir $RunDir
fi
export PYTHONNOUSERSITE=True
# path to the images
NiftisPostProc=/mnt/Bessel/Gproj/Ge... |
e6177fc29cf2223e4267df02e3f0a1fcbf74571af53bd11518e7d57c02e8e20f | Shell | 2,111 | 91 | # GAT Enrichments
# Ben Laufer
# Human ASD
cd /share/lasallelab/Ben/Obesity/meta/GAT/hg38
echo "Sorting bed files"
parallel --dry-run --will-cite "sort -k1,1 -k2,2n {} > {.}_sorted.bed" ::: *.bed
parallel --verbose --will-cite "sort -k1,1 -k2,2n {} > {.}_sorted.bed" ::: *.bed
echo "Done sorting bed files"
GAT(){
... |
d18e1b4f463588c9b8af494649388a43fe02e976a9263559c5e37408a712ef18 | Shell | 2,114 | 52 | #----------------------------------------------------------------------
#!/bin/sh
#$ -q single15.q
#$ -S /bin/bash
#$ -e /data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/final/log
#$ -o /data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/final/log
#$ -m eas
#$ -M Barbara.Molz@mpi.nl
#----... |
44581cdf141900c42f91d9be494d64a6b15367056fb913f43a71a19e74356234 | Shell | 2,252 | 117 | #!/bin/bash
#
#SBATCH --job-name=CpG_QC
#SBATCH --ntasks=2 # Number of cores/threads
#SBATCH --mem-per-cpu=4000 # Ram in Mb
#SBATCH --partition=production
#SBATCH --output=CpG_Me_PE_QC_%j.out # File to which STDOUT will be written
#SBATCH --error=CpG_Me_PE_QC_%j.err # File to which STDERR will be written
#SBATCH --ti... |
e772e23c89536b33acf28f367cc622e1a51bf1c9e37fa25c8c475fff55a57df0 | Shell | 2,253 | 117 | #!/bin/bash
#
#SBATCH --job-name=CpG_QC
#SBATCH --ntasks=2 # Number of cores/threads
#SBATCH --mem-per-cpu=4000 # Ram in Mb
#SBATCH --partition=production
#SBATCH --output=CpG_Me_SE_QC_%j.out # File to which STDOUT will be written
#SBATCH --error=CpG_Me_SE_QC_%j.err # File to which STDERR will be written
#SBATCH --... |
dca4aaee2ee08ea4b4e886d1200320d824a44f136de9b8d54ad0d1b6cae77b6b | Shell | 2,278 | 55 | #!/bin/bash
set -euo pipefail
if [ ! -d "tmp" ]; then
mkdir tmp
fi
WINDOW_SIZE="${1:-}"
INTERVAL_FILE="${2:-}"
IDX="${3:-}"
if [ -z "$WINDOW_SIZE" ] || [ -z "$INTERVAL_FILE" ] || [ -z "$IDX" ]; then
echo "Usage: $0 WINDOW_SIZE peaks.bed genome.fa.fai" >&2
exit 1
fi
INTERVAL_FILE_BASE=$(basename $INTERVAL_FIL... |
3844f7c0c54b16b015e936354ab0c72a32fd92cb43c95311f16a33714d055333 | Shell | 2,285 | 118 | #!/bin/bash
#
#SBATCH --job-name=CpG_QC
#SBATCH --ntasks=2 # Number of cores/threads
#SBATCH --mem-per-cpu=4000 # Ram in Mb
#SBATCH --partition=production
#SBATCH --output=CpG_Me_PE_QC_%j.out # File to which STDOUT will be written
#SBATCH --error=CpG_Me_PE_QC_%j.err # File to which STDERR will be written
#SBATCH --ti... |
dd5ffbb37f5e433d61283ac13e1f33e934b87aaeea5c1282f3f24a4beae1f64b | Shell | 2,288 | 118 | #!/bin/bash
#
#SBATCH --job-name=CpG_QC
#SBATCH --ntasks=2 # Number of cores/threads
#SBATCH --mem-per-cpu=4000 # Ram in Mb
#SBATCH --partition=production
#SBATCH --output=CpG_Me_SE_QC_%j.out # File to which STDOUT will be written
#SBATCH --error=CpG_Me_SE_QC_%j.err # File to which STDERR will be written
#SBATCH --... |
ee5677abde5a91daa15a35d949e9fc532f10556df9a9e7116f489a9b9c511ebe | Shell | 2,291 | 60 | #----------------------------------------------------------------------
#!/bin/sh
#$ -N bgenie_enigmaEvo_DTI
#$ -q single15.q
#$ -S /bin/bash
#$ -e /data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/final/log
#$ -o /data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/final/log
#$ -m e... |
cc33915605ec530d3de4c1113fb7db87e9bad3ed5f64479e90ad44873ffec757 | Shell | 2,294 | 23 | #!/bin/bash
python ldsc.py --l2 --bfile 1000G.mac5eur.1 --ld-wind-cm 1 --annot cg_anno.1.annot.gz --out cg_anno.1
python ldsc.py --l2 --bfile 1000G.mac5eur.2 --ld-wind-cm 1 --annot cg_anno.2.annot.gz --out cg_anno.2
python ldsc.py --l2 --bfile 1000G.mac5eur.3 --ld-wind-cm 1 --annot cg_anno.3.annot.gz --out cg_anno.3
py... |
7a894eda0acd7044d08c92db3e18d70e19417a0cc7b8f5d5a7b29a05e93b1d21 | Shell | 2,307 | 61 | #!/bin/bash
set -euo pipefail
data_dir="../../data/marand_2021_scATAC"
if [ ! -d "tmp" ]; then
mkdir tmp
fi
if [ -z "${1:-}" ]; then
echo "Usage: $0 CONFIG_PATH" >&2
exit 1
fi
PREPROCESSING_CONFIG="$1"
WINDOW_SIZE=$(jq --raw-output '.preprocessing.window_size' < "$PREPROCESSING_CONFIG")
if (( (WINDOW_SIZE %... |
6a9c7c7788f17758e3889dbc14fb2f6940be22018caa73bbefba41d7ff93cc18 | Shell | 2,323 | 68 | #!/bin/bash
#########################################################
# Make .annot and .l2 files for LDSC part. heritability
# Download the latest version of bedtools to your local
# directory. Set path to that dir. with:
# export PATH="/home/gokala/bedtools2/bin:$PATH"
# Then you will not have any issues.
# You're we... |
dc7331eea13841927503b454788091704f3bacb3df528081360e3b9c22043e08 | Shell | 2,332 | 57 | #$ -q single15.q
#$ -S /bin/bash
#$ -e /data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/final/log
#$ -o /data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/final/log
#$ -m eas
#$ -M Barbara.Molz@mpi.nl
#----------------------------------------------------------------------
# this... |
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