sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
79069e46c34474482f47f488dfb863c7616d1fc880e27b76edb6c787ef22d8b6 | Shell | 646 | 5 | cd MasterPool
~/.local/bin/bbmap/bbduk.sh -Xmx6g in1=R1.fq.gz in2=R2.fq.gz out=stdout.fq ref=adapters ktrim=r k=23 mink=11 hdist=1 tpe tbo 2> log_filtering.out | ~/.local/bin/bbmap/bbmap.sh -Xmx6g in=stdin.fq ref=design_files.fasta ordered interleaved nodisk outu=unmapped.fq.gz scafstats=scafstats.txt 2> log_mapping.ou... |
dd3038f970c23ccea98fbefb42c083af63e9c8ae0a6e2f124856b3c3dabfd0ca | Shell | 646 | 40 | #!/bin/bash
INPUT=$1
OUTPUT_PATH=$2
SMOOTHING=$3
NAME=$4
mkdir -p $OUTPUT_PATH
OUTPUT_VOL=$OUTPUT_PATH/$NAME.mgz
OUTPUT_SURF=$OUTPUT_PATH/$NAME.stl
TMP=$OUTPUT_PATH/tmp.mgz
TMP_OCN=$OUTPUT_PATH/tmp-ocn.mgz
num_closing=2
V_min=100
#if [ "$postprocess" == true ]; then
mri_binarize --i $INPUT --ventricles \
--o $TM... |
64812dfba72113c933e7a69320d1eba5cfd25a035459d41fc16b734214a90c58 | Shell | 647 | 25 | #! /bin/bash
# find all bams matching pattern and make index
mapfile -d $'\0' BAMs_to_index < <(find . -type f -name "Ast*WASPed.bam" -print0)
macs2 callpeak \
-t ${BAMs_to_index[@]} \
-g hs \
-f BAM \
-q 0.05 \
--nomodel \
... |
ee8ffa7420a765c7b2b20276490e3238d142e6b96688c7ea463f0fc1b0c8a04b | Shell | 647 | 29 | #!/bin/bash
function reg_linear_flirt {
image_original=$1
sub_name=$(basename $image_original __T1w.nii.gz)
fold_name=$(dirname $image_original)
mkdir ${fold_name}/to_MNI_flirt
flirt \
-in $image_original \
-ref $PWD/templates/MNI152_T1_manually_masked.nii.gz \
... |
16a4897c895d36b8655c4de52300cd39795f584fc089b2a79dad8527b1bcd90e | Shell | 650 | 27 | #!/bin/bash
if [[ ! -f ~/.kaggle/kaggle.json ]]; then
echo -n "Kaggle username: "
read USERNAME
echo
echo -n "Kaggle API key: "
read APIKEY
mkdir -p ~/.kaggle
echo "{\"username\":\"$USERNAME\",\"key\":\"$APIKEY\"}" > ~/.kaggle/kaggle.json
chmod 600 ~/.kaggle/kaggle.json
fi
pip install kaggle --upgrad... |
244a47c06c3204b68309b399a49717749210ddf61e3cbfec6cba0d8ec940bbd8 | Shell | 651 | 22 | #!/bin/zsh
WORK_DIRECTORY=/Volumes/LaCie/
flair collapse -g $WORK_DIRECTORY/DRS_basic/data/referance/dmel-all-chromosome-r6.43.fa \
--gtf $WORK_DIRECTORY/DRS_basic/data/referance/dm6_flybase_bdgp.gtf \
-q $WORK_DIRECTORY/DRS_compairison/results/flair/2_correction/all_reads.bed \
-r ctrl1_Nanopore.fastq.gz,ctrl2_N... |
3e0c7000cb47319e8cca2a6cae2fa97a4c7c3b3e4afb9bed2f6217118dc16b76 | Shell | 652 | 24 | #!/bin/bash
# Install Tensorflow with CUDA support
pip install tensorflow==2.8.4
# Install the learned optimization package from GitHub
pip install git+https://github.com/google/learned_optimization.git
# # Install Jax
pip install -U "jax==0.4.26[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_r... |
9a597e17ec3e1e8141dbd7b42f334c5c9365e2686e275241509820a537f9daec | Shell | 652 | 22 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=200
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
... |
397b720fafb0049d9bb0d186e5ba0a5f68a7eb50752cb64116b9d08d3bb5a3f2 | Shell | 653 | 25 | #!/bin/bash
# clean old res
rm res_*.dat
# test standard Lammps
./../../../../src/lmp_serial \
-in test-spin-precession.in
# test spin/kk with Kokkos Lammps
# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \
# -k on -sf kk -in test-spin-precession.in
# extract data from Lammps run
in="$(grep -n Step log.lam... |
86ab83ed47f95f83afe299aca3560067afdfe3219fefb786d95ffccc411e16a7 | Shell | 653 | 22 | set -e
read name fasta gtf bwa_index hisat2_index <<< "$@"
bwa_cmd="$(which bwa)"
hisat2_cmd="$(which hisat2)"
stringtie_cmd="$(which stringtie)"
samtools_cmd="$(which samtools)"
bwa_index=$(realpath $(dirname $bwa_index))/$(basename $bwa_index)
hisat2_index=$(realpath $(dirname $hisat2_index))/$(basename $hisat2_ind... |
ffb9cd12a0554470e37eb752760a749e3abc34a6706d030a95bb4b5979801542 | Shell | 653 | 11 | # GATv2
python -u run_regnn.py --dataset ACM --model regatv2 --save_postfix ACM-regatv2 --feats_type 2 --hidden 16 --weight_decay 0.005 --dropout 0.2 --repeat 10 --device $1
# MixHop
python -u run_regnn.py --dataset ACM --model remixhop --save_postfix ACM-remixhop --feats_type 2 --weight_decay 0.005 --dropout 0.7 ... |
e4ad5590fbcf71766d3972499cf9737772db883184ba7ce5d0e2a6de483c2edf | Shell | 654 | 24 | #!/bin/bash
# Install Tensorflow with CUDA support
pip install tensorflow==2.8.4
# Install the learned optimization package from GitHub
pip install git+https://github.com/google/learned_optimization.git
# # Install Jax
# pip install -U "jax==0.4.26[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda... |
9eb6cabf125e79c5cd448ded6e941397c57ab86b16ba9cd0ac91956faa410770 | Shell | 655 | 25 | #!/bin/bash
# clean old res
rm res_*.dat
# test standard Lammps
./../../../../src/lmp_serial \
-in test-spin-precession.in
# test spin/kk with Kokkos Lammps
# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \
# -k on -sf kk -in test-spin-precession.in
# extract data from Lammps run
in="$(grep -n Step log.lam... |
f333353ea54257a738726dab633895f9d6bea6dccdea702b34f153806391b90c | Shell | 655 | 19 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$SCRIPT_DIR"
export PYTHONPATH="${PYTHONPATH:+$PYTHONPATH:}$SCRIPT_DIR"
# Set default values for environment variables
WORKERS=${WORKERS:-1}
PORT=${PORT:-8080}
APPLICATION_ROOT=${APPLICATION_ROOT:-/}
echo "Starting ... |
a59f589cfb476e3372b91acf4efa9e027005c7b25a9606d21fb56afaadcab62c | Shell | 656 | 25 | torchrun --rdzv-backend=c10d --rdzv-endpoint=localhost:0 repl/scripts/cli.py \
--dataset libri \
--seq_len 20480 \
--encoder cpc \
--use_bn \
--enc_output_dim 512 \
--integrator lstm \
--ctx_dim 256 \
--predictor mlp \
--pred_hidden_dim 512 \
--pred_steps 16 \
--epochs 500 \
... |
b46cc0bd6e66ea23608ac8ab4f22f12b4913c36fdfc9cc04d927f58447387ccd | Shell | 656 | 24 | #!/bin/bash
### Ubuntu use pyinstall v3.0
THIS_SCRIPT_PATH=`readlink -f $0`
THIS_SCRIPT_DIR=`dirname ${THIS_SCRIPT_PATH}`
cd pyinstaller
git checkout v3.2
cd ${THIS_SCRIPT_DIR}
rm -r build
rm -r dist
rm labelImg.spec
python pyinstaller/pyinstaller.py --hidden-import=xml \
--hidden-import=xml.etree \
... |
5e52f272e2b8a79ae62bdb0d0c888cd4b583595e77daa7d5d3f517b287999ee9 | Shell | 660 | 26 | #!/bin/bash
source_folder=
sourceDir="${source_folder}/05.Star_mapped"
targetDir="${source_folder}/06.Feature_counts"
gtfFile="GRch38_p113.gtf"
nThreads=16
if [ ! -d $targetDir ]; then
mkdir -p $targetDir
fi
for sample in $(ls $sourceDir); do
# check if it starts with multiqc
if [[ $sample == FASTQC_sub_... |
390f1ffee26bed7a4e2b980111d436e616a2d6fd723cd48191b66568c8664150 | Shell | 661 | 31 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=5G
#SBATCH --job-name=02_deconvolution_MuSiC_cell_size
#SBATCH -c 1
#SBATCH -o logs/02_deconvolution_MuSiC_cell_size_%a.txt
#SBATCH -e logs/02_deconvolution_MuSiC_cell_size_%a.txt
#SBATCH --array=1-3%3
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
ech... |
73d234192b046bf47e608fc6ffb7ca8e6b544c5004889f9f338ae29bd4aa8c79 | Shell | 661 | 15 | #!/bin/bash
set -u -x -e
# RUN THIS TO CREATE FSAVERAGE MIDTHICKNESS FILES IF NEEDED
cd /data/p_02495/templates/template_fsaverage/fsaverage/surf
FREESURFER mris_expand -thickness lh.white 0.5 lh.midthickness
FREESURFER mris_expand -thickness rh.white 0.5 rh.midthickness
FREESURFER mris_convert \
/data/p_02495/te... |
18436c820311a99adce193a31bc8302f94a3682a428e3f95f0b052ab51d54904 | Shell | 662 | 16 | #!/bin/bash
set -u -x -e
# RUN THIS TO CREATE FSAVERAGE MIDTHICKNESS FILES IF NEEDED
cd /data/p_02495/templates/template_fsaverage/fsaverage/surf
FREESURFER mris_expand -thickness lh.white 0.5 lh.midthickness
FREESURFER mris_expand -thickness rh.white 0.5 rh.midthickness
FREESURFER mris_convert \
/data/p_02495/te... |
130fc6934bad7f8714668113532debb87690b5520e71f760415b34ddc67e4c61 | Shell | 663 | 33 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$"run_config"
fi
FOLDER=submissions/$(date +"%Y%m%d%H%M")
mkdir -... |
1b9671b7e4573f7de74677dad4db0e0b9c755f85d1a0689f646f630e5ee77486 | Shell | 663 | 33 | #!/bin/bash
# One sample t-test with fsl randomise
# seedlist.txt has been already produced with seed_subjects_correlation_maps.sh
function seed_group_level_map {
seed=$1
seed_name=$(basename $seed .nii.gz)
echo $seed_name
fslmerge -t ${seed_name}_4D.nii.gz $PWD/subject_maps/*${seed_name}_z*gz
... |
fcdd445dc3ca84d941642d709ccf7457f97ac53f495fb3662a81d6cf4f86f5e9 | Shell | 663 | 18 | # Train models later evaluated in papers
# Small model ~ VAE 128 with 0 skip connections and less hidden channels
train () {
rm -rf /data/cache
rm -rf $HOME/cache/
python3 -m scripts.train_model +dataset=alpha_multiscene ++dataset.root_folder="/data/local/worldfloods_change_no_duplicates/train" \
... |
ff82522fb843d357693bc2b45383d0c6186eaab939b304be8181cf416468be87 | Shell | 663 | 23 | set -e
if [ "$DP_VARIANT" = "cuda" ]; then
CUDA_ARGS="-DUSE_CUDA_TOOLKIT=TRUE"
elif [ "$DP_VARIANT" = "rocm" ]; then
CUDA_ARGS="-DUSE_ROCM_TOOLKIT=TRUE"
fi
#------------------
SCRIPT_PATH=$(dirname $(realpath -s $0))
NPROC=$(nproc --all)
#------------------
INSTALL_PREFIX=${SCRIPT_PATH}/../../dp_test
BUILD_TMP_D... |
2220cd560281837653b7285437f105bb90ed147dad933e750226997f60621c2a | Shell | 664 | 27 | #!/bin/bash
### RNA velocity: Generate loom file (velocyto)
pat=$1
### Sync in from AWS
# for sc
if [[ "$pat" == *"_sc"* ]]; then
aws s3 sync s3://scrna-seq/cellranger/v6.1.1/${pat}_CD45pos/ data/${pat}/ --exclude '*' \
--include 'possorted_genome_bam*' --quiet
fi
# for sn
if [[ "$pat" == *"_sn"* ]]; then
aw... |
2c7ca761ffe6b9bfb85ccdd18b694b65794a667d9e88355e474b1aaf244f7fdc | Shell | 664 | 38 | #!/bin/bash
echo Installing fmriprep
source .maint/ci/activate.sh
source .maint/ci/env.sh
set -eu
# Required variables
echo INSTALL_TYPE = $INSTALL_TYPE
echo CHECK_TYPE = $CHECK_TYPE
echo EXTRA_PIP_FLAGS = $EXTRA_PIP_FLAGS
set -x
if [ -n "$EXTRA_PIP_FLAGS" ]; then
EXTRA_PIP_FLAGS=${!EXTRA_PIP_FLAGS}
fi
if [ ... |
bbc2a6e2fb66bcc0da034aa8497251df282ad0eaa9b79a0450eab43c16220deb | Shell | 664 | 20 | #!/usr/bin/env bash
# This script generates two datasets for spatial and temporal scaling
# Both datasets will be dumped
SPATIAL_ROOT="/tmp/spatial" # Path to spatial scaling datasets
TEMPORAL_ROOT="/tmp/temporal" # Path to temporal scalingdatasets
# Generate spatial scaling dataset
SCALES="10 20 40 80"
SPATIAL_N=500... |
feeac4bcd95ceb7280c678c83e6dfe89ca896a953c4e72ce038d61034bd5138a | Shell | 664 | 14 | #!/bin/bash
set -euf -o pipefail
if [ ! -v WORKFLOW_NAME ]; then
echo WORKFLOW_NAME not set, setting it to the RUN_ID
WORKFLOW_NAME=$RUN_ID
echo $WORKFLOW_NAME
fi
echo 'Converting jupyter notebook file'
TIMESTAMP=$(date +%y-%m-%d-%H:%M:%S)
jupyter nbconvert --to pdf --execute --no-input /kaapana/app/otsu... |
6793f45d2feb93cf5ddedc6d4e69120b38201b595e8d2de909b46081684f681c | Shell | 665 | 35 | # Adding a fake registration folder containing an identity matrix for group feat analyses - for only one subject
# Author: Valeria Oliva
echo -n "Which sub? Only insert number >"
read subject
echo -n "session? 01 or 02 >"
read ses
cd ../../../data/BIDS/derivatives/sub-NSPilot${subject}/ses-${ses}brain/func/feat_an... |
186076a803a3024fe6f923cd8f44384bdd16c5458a37b1f272ef8d82aacb3fbb | Shell | 666 | 27 | #!/bin/bash
DATASET=human
# DATASET=celegans
# DATASET=yourdata
# radius=1
radius=2
# radius=3
# ngram=2
ngram=3
dim=10
layer_gnn=3
side=5
window=$((2*side+1))
layer_cnn=3
layer_output=3
lr=1e-3
lr_decay=0.5
decay_interval=10
weight_decay=1e-6
iteration=100
setting=$DATASET--radius$radius--ngram$ngram--dim$dim--la... |
32f7e6b5c7fc62b956fdd7da3ad3e2d0484aef3b019f18718a806d0744872893 | Shell | 666 | 12 | echo "Pulling featurized core pdbbind dataset from deepchem"
wget -c http://deepchem.io.s3-website-us-west-1.amazonaws.com/featurized_datasets/core_grid.tar.gz
echo "Extracting core pdbbind"
tar -zxvf core_grid.tar.gz
echo "Pulling featurized refined pdbbind dataset from deepchem"
wget -c http://deepchem.io.s3-website-... |
c30b04ebdc55b19951630af66ee1f47dbb7ad76e1bfbfcd8ffe538f274448e0e | Shell | 667 | 20 | #!/bin/bash
#SBATCH --job-name=downsample.job
#SBATCH --time=4:00:00
#SBATCH --export=ALL
#SBATCH --output logs/downsample-%j.out
#SBATCH --nodes=1 # Use 1 node
#SBATCH --ntasks=1 # 1 task
#SBATCH --cpus-per-task=32 # Allocate N CPUs for the task
#SBATCH --mem-per-cpu=10G ... |
10e65a70009fdbd81956678c1ecc2a452b7862b0cf0bd364ecedf80a2d0003cf | Shell | 671 | 22 | #!/usr/bin/env bash
echo "removing old files..."
rm -rf build
rm -rf dist
# Check if error introducing packages are still there
pip uninstall enum34
pip uninstall imagecodecs
echo "building app..."
#onefolder
pyinstaller -y --clean aydin.spec # -D -y --clean
mkdir -p dist/aydin_0.1.5rc12.app/Contents/MacOS
mkdir -p... |
9fda8137a21b63c2ef943fd5ddbdbab16e4b4dfca295b51cb6d8ba6f58feb845 | Shell | 671 | 33 | #!/bin/sh
set -e
rm -rf node_modules
rm -rf yarn.lock
cp development_package package.json
yarn global add yalc
[ ! -d "./geppetto-meta/" ] && git clone https://github.com/MetaCell/geppetto-meta/
cd geppetto-meta
#git checkout development
app=$(pwd)
cd $app/geppetto.js/geppetto-core
rm -rf node_modules
yarn && ya... |
9abd09852ee3507bdb974dbf2f38f7d455a7ba23ad061d86f54fddbfddb5bef5 | Shell | 674 | 34 | #!/bin/bash
#SBATCH --time=2:10:00
#SBATCH --mem=30GB
#SBATCH --nodes=1
#SBATCH --cpus-per-task=4
#SBATCH -o './logs/%A.out'
#SBATCH -e './logs/%A.err'
if [[ "$HOSTNAME" == *"tiger"* ]]
then
echo "It's tiger"
module load anaconda
source activate torch-env
elif [[ "$HOSTNAME" == *"della"* ]]
then
echo "... |
b551c39471ceb7d56995eeb74bed790ded1c0e813b54920be4dbfbd70c48e9c5 | Shell | 674 | 22 | #!/usr/bin/env bash
echo "removing old files..."
rm -rf build
rm -rf dist
# Check if error introducing packages are still there
pip uninstall enum34
pip uninstall imagecodecs
echo "building app..."
#onefolder
pyinstaller -D -y --clean aydin.spec # -D -y --clean
mkdir -p dist/aydin_0.1.5rc12.app/Contents/MacOS
mkdir... |
31c6790e161f7d2b7cbaa4fb54e351828d41baf48c20473725c362daa16e5575 | Shell | 675 | 26 | #!/bin/bash
# Sample script to export all annotated slices as SVG files
# Usage: TASK_ID DEST_PATH
TASK_ID=${1?}
DEST_PATH=${2?}
# Generate a listing of slides for this task
rm -rf /tmp/slides.csv
flask slides-list --min-paths 1 -C /tmp/slides.csv $TASK_ID
# Read all the slides
for line in $(cat /tmp/slides.csv); do... |
53cfa152351711d91184a57314587cde488bbef8f9dfb58cf8778ca6fd65dd59 | Shell | 675 | 21 | #!/bin/bash
declare -a REPLACEMENTS
# Value pattern replacements
REPLACEMENTS+=(-e 's/glcbt-.\{23\}/[MASKED]/g') # GitLab ... Token
REPLACEMENTS+=(-e 's/ghp_.\{36\}/[MASKED]/g') # GitHub Personal access Token
# Variable value replacements
if [ ! -z ${SITE_ID_TOKEN+x} ]; then
REPLACEMENTS+=(-e "s/$SITE_ID_... |
9f4294df4d217c1147fc2dbba9f908ee9503a0fbe49eed9ae10c6d8c84b5544d | Shell | 676 | 32 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=5G,h_vmem=5G,h_fsize=100G
#$ -N qc_pca
#$ -o logs/03_qc_pca.txt
#$ -e logs/03_qc_pca.txt
#$ -m e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
echo "Task id... |
1e0d83fb057c14d6307476e776afa808f670bd9da4e5ed2d4d2706c67b454cec | Shell | 680 | 17 | #!/bin/sh
# Packaging and Release
docker run --workdir=$(pwd)/ --volume="/home/$USER:/home/$USER" tzutalin/py2qt4 /bin/sh -c 'make qt4py2; make test;sudo python setup.py sdist;sudo python setup.py install'
while true; do
read -p "Do you wish to deploy this to PyPI(twine upload dist/* or pip install dist/*)?" yn
... |
c38e771851c15bdf9056550a7d0d848ad0e5a9e468a75e25f08dcec0a36d1a60 | Shell | 680 | 32 | #!/bin/bash
# Siwei 23 Jun 2023
# Siwei 07 Jun 2022
mkdir -p ld_scores
shopt -s nullglob
sumstats_list=(/home/zhangs3/Data/Databases/GWAS/MAGMA_ref_new/ldsc_sumstats/*.sumstats.gz)
shopt -u nullglob
echo "${#sumstats_list[@]}"
for eachfile in output_bed4/*.bed
do
base_bed_name=$(basename -- $eachfile)
... |
c485b397df853285eb44a2aae630b6a4a4e7b1466eb6e400c6106968cb72d558 | Shell | 681 | 20 | #!/bin/bash
#SBATCH --job-name=formatting
#SBATCH --output=logs/slurm/formatting.%A.%a.out
#SBATCH --error=logs/slurm/formatting.%A.%a.err
#SBATCH --partition=shared-cpu
#SBATCH --mem=128G
#SBATCH --ntasks=1 # run one thing per job
#SBATCH --time=1:00:00
# Potentially activate env here
##############################... |
1a33e6e92da9decd4f883cbc786b0b764ce5de4d4b711570bfefb77bba0889f4 | Shell | 682 | 32 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=$(date +"%Y%m%d%H%M")
WRITEFOLDER=submissions/$FOLDER... |
1ef726e600ae5583289693f2fdb87a6e90cd892d5b46b921738d6ef6e468b74e | Shell | 682 | 33 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=72:00:00,tmem=1.9G
# join stdout and stderr output
#$ -j y
#$ -sync y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME="run"
fi
FOLDER=submissions/$(date +"%Y%m%d%H%M")
mkdir -p ${FOLDER}
snake... |
6b193f799fe95a5a8b2baf7ae23228168bc3e07bd6246846c9330d9aa8667440 | Shell | 682 | 25 | #!/bin/bash
# Name of the tmux session
SESSION_NAME="chemcpa_training"
# Path to your Python script
SCRIPT_PATH="chemCPA/train_hydra.py"
# Check if the session already exists
if tmux has-session -t $SESSION_NAME 2>/dev/null; then
echo "Session $SESSION_NAME already exists. Attaching to it."
tmux attach-sessi... |
aba044cb817ad392a7e2009ba1a3c307eaae26511adfbf72fa6d607e08e4f55e | Shell | 684 | 31 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=01_deconvolution_Bisque_random_subset
#SBATCH -c 4
#SBATCH -o logs/01_deconvolution_Bisque_random_subset.txt
#SBATCH -e logs/01_deconvolution_Bisque_random_subset.txt
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${U... |
1887542283fe85ce0c37ff23962b357423bbb11f1140dd5ecd2137c467e22448 | Shell | 685 | 32 | #!/bin/bash
# Siwei 23 Jun 2023
# Siwei 07 Jun 2022
mkdir -p ld_scores
shopt -s nullglob
sumstats_list=(/home/zhangs3/Data/Databases/GWAS/MAGMA_ref_new/ldsc_sumstats/temp/*.sumstats.gz)
shopt -u nullglob
echo "${#sumstats_list[@]}"
for eachfile in output_bed4/*.bed
do
base_bed_name=$(basename -- $eachfile... |
b8ab2bb866f68ab2ee2331f0ec0df73979bd01c2339d1c32aae9d4f2bf0b107e | Shell | 685 | 22 | #!/bin/bash
set -ev
NPROC=$(nproc --all)
SCRIPT_PATH=$(dirname $(realpath -s $0))
export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
mkdir -p ${SCRIPT_PATH}/../buildcxx/
cd ${SCRIPT... |
cf3675800227814c338c8a6aaf3bcd5ce845ab3840aae936cf7ec8a5cf58cd6a | Shell | 686 | 23 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
#S... |
3f609e7fa5f26c8cc69a72da8a5a651c3b9c7084347ee5996b67322935548872 | Shell | 687 | 33 | #!/bin/bash
# One sample t-test with fsl randomise
# seedlist.txt has been already produced with seed_subjects_correlation_maps.sh
function seed_group_level_map {
seed=$1
seed_name=$(basename $seed .nii.gz)
echo $seed_name
fslmerge -t ${seed_name}_4D.nii.gz $PWD/inverted_subject_maps/*${seed_name}... |
4d72553a875283044c78937a90a99439731bc5a0bba65de0aefc6f2c1a354149 | Shell | 687 | 32 | #!/bin/bash -l
#SBATCH --job-name="EEG_1_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=142
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_1_CoordsV.out
##SBATCH --error=EEG_1_CoordsV.err
#SBATCH --exclusive... |
b43409d758215fc225dd3f4bf6befab14aefb7965a40c133655f54861a4524dd | Shell | 688 | 25 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_sonata_CoordsV.out
#SBATCH --error=EEG_sonata_CoordsV.err
#SBATCH --ex... |
d1ca4cc9aabf45820e977cc6253edc5da0a2354956f0fe8602c0de0bdc8b04e4 | Shell | 688 | 20 | #!/bin/bash
#SBATCH --job-name=decoding
#SBATCH --output=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodingformat.%A.%a.out
#SBATCH --error=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodingformat.%A.%a.err
#SBATCH --par... |
6e3d6152797f5f50305e1f36b166ca8b40df9b3957114d587ba112c8adb1e09e | Shell | 689 | 18 | #!/usr/bin/env bash
# Create the conda environment used for constructor builds.
set -euo pipefail
if ! command -v conda >/dev/null 2>&1; then
if [ -n "${CONDA:-}" ] && [ -f "${CONDA}/etc/profile.d/conda.sh" ]; then
# shellcheck disable=SC1090
source "${CONDA}/etc/profile.d/conda.sh"
elif [ -n "${MAMBA_ROOT... |
a80e6d6680132a12973b670a8f5e0d5d1967c053830aed2ee3109fc818ccc3e2 | Shell | 689 | 25 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_sonata_CoordsV.out
#SBATCH --error=EEG_sonata_CoordsV.err
#SBATCH --ex... |
82cdee5a1ccd6aae7034762cf0d7142962d03934a5afb77fe58b3e7523c6e982 | Shell | 692 | 37 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$3" != "" ]; then
RUN_NAME="PAPA"
else
RUN_NAME=$3
fi
FOLDER=submissions/$(date +"%Y%m%d%H%M")
mkdir -p ${FOL... |
85f29438923f0dd21f9e34b97483ab01e9bcf43153f3947c00e689588f7c7eeb | Shell | 692 | 32 | #!/bin/bash
#$ -cwd
#$ -l mem_free=5G,h_vmem=5G,h_fsize=100G
#$ -N fix_filenames
#$ -o logs/01_fix_filenames.txt
#$ -e logs/01_fix_filenames.txt
#$ -m e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}"
... |
41dbb01a0ec269daa7a3b31b97214e23fc11784e32ce384ee963c2bb564a2982 | Shell | 695 | 32 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=$(date +"%Y%m%d%H%M")
WRITEFOLDER=submissions/$FOLDER... |
59716fbd1198206bb585f950af935c931fbf2dd960d12396ba8292eb7ba0c414 | Shell | 695 | 20 | #!/bin/bash
#SBATCH --job-name=decoding
#SBATCH --output=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodingdatacaching.%A.%a.out
#SBATCH --error=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodingdatacaching.%A.%a.err
#SB... |
8a52e5b7e5133a29ecf2aaf8b3d43e6d989b5565f40ffef982ae8cb59e19557a | Shell | 696 | 25 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_sonata_CoordsV.out
#SBATCH --error=EEG_sonata_CoordsV.err
#SBATCH --ex... |
bcca45cf4065a11757bfba0551fcbf6a96b4f6aee3160ff4eaf13307e052d283 | Shell | 696 | 32 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=$(date +"%Y%m%d%H%M")
WRITEFOLDER=submissions/$FOLDER... |
c4b0b0be0a3030a9ce2ace19eee5394b2e8222bd50bbae6e431f24939e5cdf6f | Shell | 696 | 16 | #!/bin/bash
# input is protein (needs to be converted to pocket)
python genscore.py -p ./1qkt_p.pdb -l ./1qkt_decoys.sdf -rl ./1qkt_l.sdf -gen_pocket -c 10.0 -e gt -m ../trained_models/GT_0.0_1.pth
# input is pocket
python genscore.py -p ./1qkt_p_pocket_10.0.pdb -l ./1qkt_decoys.sdf -e gatedgcn -m ../trained_models/G... |
e6c90ee1aa987a856b9083657b2ecbf2f9d271b682e1de5541934b782166c6d8 | Shell | 697 | 27 | #!/bin/bash
source ~/.bashrc
conda activate kmol
run_path="/data_st01/drug/itosho/kmol/"
cd $run_path
train_base_path="/data_st01/drug/itosho/ADMET/configs/accuracy_drug/adme/singletask/train/*/*"
for folder in $train_base_path; do
if [ -d "$folder" ]; then
kmol train "$folder/config.json" > "$folder/tr... |
08a5296a09c025766101f56b846a601eb40f0d1d560d748e33048267a6f3460c | Shell | 699 | 30 | # Removing the first two volumes of functional images - brain and spinal cord
# Author: Valeria Oliva
echo "Which sub? Just input the number >"
read subject
echo -n "session? 01 or 02 >"
read ses
cd ../../../data/BIDS/derivatives/sub-NSPilot${subject}/ses-${ses}brain/func/
for scan in FingerTap ForceAbs ForcePerc... |
0f4c9822b9e3ad2dcb30c1217f7b0248e2c3cd904a6c7e602c12cb5cf1039139 | Shell | 699 | 35 | #!/bin/bash -e
if [ -z "${KMOL_UID}" ]; then
echo "KMOL_UID is not set"
exit 1
fi
if [ -z "${KMOL_GID}" ]; then
echo "KMOL_GID is not set"
exit 1
fi
chown ${KMOL_UID}:${KMOL_GID} /home/kmol
if ! getent group kmol > /dev/null; then
addgroup -q --gid ${KMOL_GID} kmol
fi
if ! getent passwd kmol > /dev/null;... |
108c24c1942f11133aff26a9bd84c1ea8c66c1b640c2d25de9db868b679800e2 | Shell | 699 | 15 | source config.sh # To get $proteinnpt_data_path
conda activate proteinnpt_env
#source $proteinnpt_data_path/proteinnpt_env/bin/activate # Uncomment if using python venv instead of conda env
export assay_data_location="Replace this string with the path to the assay data"
export MSA_location="Replace this string with t... |
e8d8f7f5b9148134ebf268343a8a994d7ee86efa8d79dee58914dfe0ddd22022 | Shell | 700 | 23 | #!/usr/bin/env bash
set -e
file_in=${1?"error: parameter FILE_IN missing"}
dir_out=${2?"error: parameter DIR_OUT missing"}
if [ ! -f "$file_in" ]; then
>&2 echo "error: '$file_in' does not exist"
exit 1
fi
if [ ! -d "$dir_out" ]; then
>&2 echo "error: '$dir_out' is not a directory"
exit 1
fi
set -x
... |
027a0501e10711fd4bdbdc91f538c83a405452d785e3b9f7f058fc1f927af839 | Shell | 701 | 12 | #!/bin/bash
echo "build models from folder " $1
NRNIVMODL_INCLUDE_FLAGS="-I${SONATAREPORT_DIR}/include -I/usr/include/hdf5/mpich -I/usr/lib/x86_64-linux-gnu/mpich"
NRNIVMODL_LOAD_FLAGS="-L${SONATAREPORT_DIR}/lib -lsonatareport -Wl,-rpath,${SONATAREPORT_DIR}/lib -L/usr/lib/x86_64-linux-gnu/hdf5/mpich -lhdf5 -Wl,-rpath... |
4a6b08d25bc42fa61c35048bc5705361c73ab12389a4d48664a44735484827bd | Shell | 701 | 19 | #!/bin/bash
ENV_NAME=${1:-alphadia}
TEST_TYPE=${2:-all}
case "$(echo $TEST_TYPE | tr '[:upper:]' '[:lower:]')" in
"all")
conda run -n $ENV_NAME --no-capture-output coverage run --source=../alphadia -m pytest
;;
"integration")
conda run -n $ENV_NAME --no-capture-output coverage run --source=../alphadia... |
849963455f3a2ecb933a79d352bd425fe14908fbb4bb42303b04f9dd33988a03 | Shell | 701 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=07_prep_sce
#SBATCH -c 1
#SBATCH -t 1:00:00
#SBATCH -o logs/07_prep_sce.txt
#SBATCH -e logs/07_prep_sce.txt
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Job name: ${SLUR... |
aa69caaccb63ad0a6715630b49b9dc2fca1c2f038fff87235402cd02dedf3cf8 | Shell | 702 | 18 | #!/usr/bin/env bash
#
# Usage: from directory for storing singularity image builds (e.g. /opt/singularity_images/)
# ./build.sh {yes/no for datalad}
# Datalad container install (yes or no)
DATALAD=$1
sudo rm -rf ./*.sif
sudo singularity build fsl-v6.0.6.4.sif fsl_v6.0.6.4.def
sudo singularity build freesurfer-v7.3.... |
e1bad1187757fa40a630aab2b6d849a71e27c4d15ee4fe33c3417de1433c67f8 | Shell | 702 | 34 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=80G
#SBATCH --job-name=05_1_CMC_data_prep
#SBATCH -c 1
#SBATCH -t 1-00:00:00
#SBATCH -o logs/05_1_CMC_data_prep.txt
#SBATCH -e logs/05_1_CMC_data_prep.txt
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}... |
9b1053e2357e125323bd330a8e15c88fd5b200f280af45a3acf46d855f18481a | Shell | 703 | 23 | #!/bin/bash -e
set -o pipefail
# Numba's on-disk JIT cache (NUMBA_CACHE_DIR) is invalidated whenever numba or
# llvmlite is upgraded, so CI cache keys have to include their versions in a form
# usable in a cache key. Prints "none" when numba is not installed, which just
# means the cache never gets populated for that... |
a0b2194a23139ec887e6a6281103a44a38ae213c03f27708a115a2109430db7b | Shell | 703 | 18 | #!/bin/bash
for dir in /$WORKFLOW_DIR/$BATCH_NAME/*
do
ELEMENT_INPUT_DIR="$dir/$OPERATOR_IN_DIR"
echo 'Here you find the files you want to work with on a batch element level'
echo ${ELEMENT_INPUT_DIR}
ELEMENT_OUTPUT_DIR="$dir/$OPERATOR_OUT_DIR"
echo 'Here you should write the fi... |
466afc78f9d46ed5a601b2fabbbd893501bc6c035bcc59726ce0e1954248694b | Shell | 704 | 12 | # GATv2
python -u run_regnn.py --dataset DBLP --model regatv2 --save_postfix DBLP-regatv2 --lr 0.005 --dropout 0.7 --repeat 10 --device $1
# MixHop
python -u run_regnn.py --dataset DBLP --model remixhop --save_postfix DBLP-remixhop --lr 0.001 --weight_decay 0.0005 --repeat 10 --device $1
python -u run_regnn.py --... |
8e5920d70b7762a6e9212ca627ae3430ebbced4e9240d936ec87aaf1303d6a8a | Shell | 704 | 14 | #!/bin/bash
SOURCECODE=/home/mayalen/code/my_packages
DESTINATIONCODE=<id_jeanzay>@jeanzay:/gpfswork/rech/zaj/<id_jeanzay>/code/
DESTINATIONEXPERIMENT=<id_jeanzay>@jeanzay:/gpfsscratch/rech/zaj/<id_jeanzay>/code/2021.04_experiments
echo Transfer code ...
rsync -azvh -e "ssh -i $HOME/.ssh/id_rsa_jeanzay" --exclude "*i... |
48bd309756a7fe15c4014ac7f1c872d13d172e1f54d968baa8369aa263812c72 | Shell | 706 | 32 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=5G,h_vmem=5G,h_fsize=100G
#$ -N prep_manifest
#$ -o logs/02_prep_manifest.txt
#$ -e logs/02_prep_manifest.txt
#$ -m e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOS... |
cb91aa9727cab96a82d89807956613ddc1112df2f7fcabc91d63d63e69172827 | Shell | 706 | 32 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=25G,h_vmem=25G,h_fsize=100G
#$ -N TREG_boxplots
#$ -o logs/07_TREG_boxplots.txt
#$ -e logs/07_TREG_boxplots.txt
#$ -m e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${H... |
2591688b348b81d6dec20e32f86841a994f98a4141c6be6daae3d965aa8a773d | Shell | 708 | 20 | #!/bin/bash
#SBATCH --job-name=decoding
#SBATCH --output=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodingimpostercaching.%A.%a.out
#SBATCH --error=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/decodingimpostercaching.%A.%a... |
6131f74d68f62e4c2664dd1f933cc010a34c98b24c14ef520de92859c34e3a09 | Shell | 709 | 32 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=$(date +"%Y%m%d%H%M")
WRITEFOLDER=submission/$FOLDER
... |
9e71d999646d3a9afeec45985adcc373ce0f66aab2e6301317f3599a4551a651 | Shell | 709 | 21 | #!/bin/bash
#Map trimmed RNA-seq reads to the L. variegatus 3.0 genome
#K. Castellano
module load histat2/v2.2.1
module load samtools/v1.18
fileList="trim_10FBS_D20_S277 trim_10FBS_D313_S283 trim_10FBS_D445_S286 trim_10FBS_D738_S289 trim_15FBS_D182_S281 trim_15FBS_D20_S278 trim_15FBS_D313_S284 trim_15FBS_D445_S287 tr... |
002b85a39f2d5d72600b9f2225002ac54a01614b97293f5dcbc41ec868328263 | Shell | 710 | 32 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=$(date +"%Y%m%d%H%M")
WRITEFOLDER=submissions/$FOLDER... |
b104a113b636709ad40b0b6881532e9bd384d56aa4bd7cb0543ba8971a7a66fc | Shell | 710 | 33 | #! /bin/bash
# find all bams matching pattern and make index
# mapfile -d $'\0' BAMs_to_index < <(find . -type f -name "*.bam" -print0)
for eachfile in *.bam
do
echo $eachfile
samtools index -@ 20 $eachfile
macs2 callpeak \
-t $eachfile \
-g hs \
-f BAMPE \
... |
74739179a55d2b61b8d9724cca85c75c3b2779ead1fcf869c631e497ebb37826 | Shell | 711 | 31 | #!/bin/bash -l
#SBATCH --output=logs/10_flexmix.txt
#SBATCH --error=logs/10_flexmix.txt
#SBATCH --partition=shared
#SBATCH --job-name=flexmix
#SBATCH --mem=5GB
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Job name: ${SLURM_JOB_NAME}"
echo "Host... |
cc2d59cb16e4d792f8660a948d4ce503da64cbc6146ac230ed4e1bbae567cae2 | Shell | 711 | 30 | cuda=$1
dataset=$2
ft=$3
hidden_channels_lst=(16 64)
n_layers_lst=(2 4)
lr_lst=(0.001 0.005)
weight_decay_lst=(0. 0.0005 0.001)
dropout_lst=(0.2 0.5 0.7)
R_list=(10. 100.)
for n_layer in "${n_layers_lst[@]}"; do
for hidden in "${hidden_channels_lst[@]}"; do
for lr in "${lr_lst[@]}"; do
for... |
2fe677c89592847f9358b3dfb14d0f838492174e03936011c1f5565ec8854f8c | Shell | 713 | 34 | #!/bin/bash
echo "Building archive"
source .maint/ci/activate.sh
set -eu
# Required dependencies
echo "INSTALL_TYPE = $INSTALL_TYPE"
set -x
if [ "$INSTALL_TYPE" = "sdist" -o "$INSTALL_TYPE" = "wheel" ]; then
python -m build
elif [ "$INSTALL_TYPE" = "archive" ]; then
ARCHIVE="/tmp/package.tar.gz"
git a... |
078be06315a6a9ac6446b6ee32b6761f5d2ae78672673642967ce4d15fef64f3 | Shell | 714 | 32 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=$(date +"%Y%m%d%H%M")
WRITEFOLDER=../submissions/$FOL... |
87a6a630bc625b1f0171c85429fe4600dff0fd431d8771977eee0f99ba379428 | Shell | 715 | 22 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$SCRIPT_DIR"
export PYTHONPATH="${PYTHONPATH:+$PYTHONPATH:}$SCRIPT_DIR"
# Set default values for environment variables
WORKERS=${WORKERS:-4}
PORT=${PORT:-8080}
APPLICATION_ROOT=${APPLICATION_ROOT:-/}
echo "Running d... |
f839824b947c7d1400e2775b32c30a1126617462600e077e503029346436687e | Shell | 715 | 31 | #!/bin/bash
function reg_linear_flirt {
image_original=$1
sub_name=$(basename $image_original __T1w.nii.gz)
fold_name=$(dirname $image_original)
if [[ ! -e ${fold_name}/to_MNI_flirt ]]; then
mkdir ${fold_name}/to_MNI_flirt
fi
flirt \
-in $image_original \
... |
660501a86765809f02ead5e32b1c5d5bfd8a90051e52253c63d51e7b7abf0780 | Shell | 717 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=02_GTEx_hspe
#SBATCH -c 1
#SBATCH -o logs/02_GTEx_hspe.txt
#SBATCH -e logs/02_GTEx_hspe.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Job name... |
363b46ccdb9c7eaf2f09646114b1d700ff765abc2102f3ae1cd9eb7b2b4e3dbe | Shell | 718 | 19 | #!/usr/bin/env bash
# Build the platform-specific installer using the prepared constructor env.
set -euo pipefail
if ! command -v conda >/dev/null 2>&1; then
if [ -n "${CONDA:-}" ] && [ -f "${CONDA}/etc/profile.d/conda.sh" ]; then
# shellcheck disable=SC1090
source "${CONDA}/etc/profile.d/conda.sh"
elif [ ... |
4aff0934a996f8eebc45564242660443d0b81002d57ece2b2ac1b93d711ace4f | Shell | 722 | 32 | #!/bin/bash
#$ -cwd
#$ -l mem_free=25G,h_vmem=25G,h_fsize=100G
#$ -N deconvolution_MuSiC
#$ -o logs/02_deconvolution_MuSiC.txt
#$ -e logs/02_deconvolution_MuSiC.txt
#$ -m e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hos... |
d3295246dab99d7765530382b1779855f776afa365c12a95124fb36f0ffb2344 | Shell | 722 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=5G
#SBATCH --job-name=03_add_colData
#SBATCH -c 1
#SBATCH -o logs/03_add_colData.txt
#SBATCH -e logs/03_add_colData.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Job... |
fe59b7489604b44dae3f9ca9266086bc2d632b2d65de6f2f892abe30fc0496ab | Shell | 722 | 34 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=60G
#SBATCH --job-name=05_2_CMC_replace_counts
#SBATCH -c 1
#SBATCH -t 1-00:00:00
#SBATCH -o logs/05_2_CMC_replace_counts.txt
#SBATCH -e logs/05_2_CMC_replace_counts.txt
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ... |
76d61936776c7043164d25ade29a1ae1ad880ac79907c584180971ce15db7a7a | Shell | 723 | 30 | cuda=$1
dataset=$2
ft=$3
hidden_channels_lst=(64)
n_layers_lst=(4)
lr_lst=(0.001 0.005)
weight_decay_lst=(0. 0.0005 0.001)
dropout_lst=(0. 0.2 0.5 0.7)
R_list=(10. 100.)
for n_layer in "${n_layers_lst[@]}"; do
for hidden in "${hidden_channels_lst[@]}"; do
for lr in "${lr_lst[@]}"; do
for w... |
ce045db0226c8da929a7a3c4779d182ca3377e4cb5e08299b973651737a1a390 | Shell | 723 | 27 | #!/bin/bash
SOURCE_REMOTE="origin"
ARCHIVE_REPO="git@codebase.helmholtz.cloud:kaapana/kaapana-archive.git"
BRANCH="$1"
if [ -z "$BRANCH" ]; then
echo "Usage: $(basename "$0") branch-to-move"
fi
echo "Branch $BRANCH will be moved to from $SOURCE_REMOTE to $ARCHIVE_REPO"
while true; do
read -r -p "Proceed? (y/n) "... |
325caf120b33e24afae0accdbc5f0d4fe640f9e25accd2ff57739ffd44d4262f | Shell | 724 | 30 | #!/bin/sh
brew install python@2
pip install --upgrade virtualenv
# clone labelimg source
rm -rf /tmp/labelImgSetup
mkdir /tmp/labelImgSetup
cd /tmp/labelImgSetup
curl https://codeload.github.com/tzutalin/labelImg/zip/master --output labelImg.zip
unzip labelImg.zip
rm labelImg.zip
# setup python3 space
virtualenv --s... |
c0183baeb2a00b08c6f7b252883c849080278129e43efd838aea0b476c424c73 | Shell | 725 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=50G
#SBATCH --job-name=01_GTEx_Bisque
#SBATCH -c 1
#SBATCH -o logs/01_GTEx_Bisque.txt
#SBATCH -e logs/01_GTEx_Bisque.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo "Jo... |
d50b061b9c40f31fadc704410a975b1c00651e106f3e81978002d3c330b78c4d | Shell | 725 | 32 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [ "$1" != "" ]; then
RUN_NAME=$1
else
RUN_NAME=$""
fi
FOLDER=$(date +"%Y%m%d%H%M")
WRITEFOLDER=submissions/$FOLDER... |
300bb1c8d5ccb79c188420b1b6b70f774c878a181434ca47b36396ef62e6a41d | Shell | 726 | 35 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=02_GTEx_hspe_rc
#SBATCH -c 1
#SBATCH -o logs/02_GTEx_hspe_rc.txt
#SBATCH -e logs/02_GTEx_hspe_rc.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${SLURM_JOB_ID}"
echo ... |
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