sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ba3f4e3552db125475ec96a57c796d8489d0751469bd5cc908a4410abd65a515 | Shell | 1,321 | 44 | #!/bin/bash
# Usage: sbatch slurm-serial-job-script
# Prepared By: Kai Xi, Oct 2014
# help@massive.org.au
# NOTE: To activate a SLURM option, remove the whitespace between the '#' and 'SBATCH'
# $1: line counter
# Need to use variables OUTSIDE of this script, #SBATCH doesn't support variables: https://hel... |
c1fb7683eaa6fe9536fdbde3eb9ae74d4ec37d6ec16b509b14b5f895a51f29f2 | Shell | 1,321 | 17 | #!/bin/bash
#SBATCH --job-name=pred220331chrXII
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --nodes=1
#SBATCH --gres=gpu:1
#SBATCH --time=720
#SBATCH --mem=500G
#SBATCH --partition=gpu
#SBATCH --error=/private/groups/brookslab/gabai/projects/Add-seq/scripts/sbatch/log/lsf_%j_%x.err
#SBATCH --output=/private/gr... |
c2bc52d8279327f50deee1233c88ef7902ca039da81f440cd0bf35beb01994e1 | Shell | 1,321 | 17 | #!/bin/bash
#SBATCH --job-name=pred220331chrXVI
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --nodes=1
#SBATCH --gres=gpu:1
#SBATCH --time=720
#SBATCH --mem=500G
#SBATCH --partition=gpu
#SBATCH --error=/private/groups/brookslab/gabai/projects/Add-seq/scripts/sbatch/log/lsf_%j_%x.err
#SBATCH --output=/private/gr... |
c75925f6669ac80ad0183efff0f376bfc55f8169d3907502a71e1e6e663b792d | Shell | 1,321 | 17 | #!/bin/bash
#SBATCH --job-name=pred220331chrVII
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --nodes=1
#SBATCH --gres=gpu:1
#SBATCH --time=720
#SBATCH --mem=500G
#SBATCH --partition=gpu
#SBATCH --error=/private/groups/brookslab/gabai/projects/Add-seq/scripts/sbatch/log/lsf_%j_%x.err
#SBATCH --output=/private/gr... |
3ef21ddac7bfafdba5f02e2adb554fd4990ce441385372e2b7c52816ad1c479c | Shell | 1,324 | 17 | #!/bin/bash
#SBATCH --job-name=pred220331chrVIII
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --nodes=1
#SBATCH --gres=gpu:1
#SBATCH --time=720
#SBATCH --mem=500G
#SBATCH --partition=gpu
#SBATCH --error=/private/groups/brookslab/gabai/projects/Add-seq/scripts/sbatch/log/lsf_%j_%x.err
#SBATCH --output=/private/g... |
fea04b0ce904a317e95019b872e1bb50eb25957b8ef5cb5e3ed6e4e6bee84c26 | Shell | 1,324 | 17 | #!/bin/bash
#SBATCH --job-name=pred220331chrXIII
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --nodes=1
#SBATCH --gres=gpu:1
#SBATCH --time=720
#SBATCH --mem=500G
#SBATCH --partition=gpu
#SBATCH --error=/private/groups/brookslab/gabai/projects/Add-seq/scripts/sbatch/log/lsf_%j_%x.err
#SBATCH --output=/private/g... |
661dc5b72664ff20ae6a8dbb7e877921f8ee4ad98da188c51c34ffc9e21fcb8b | Shell | 1,335 | 36 | #!/bin/sh
#SBATCH --job-name=fmriprep
#SBATCH --mail-user=heejung.jung@colorado.edu
#SBATCH --mail-type=BEGIN,FAIL,END
#SBATCH --qos normal
#SBATCH --output ./log/fmriprep%j.out
#SBATCH --error ./log/fmriprep.e%j
#SBATCH --nodes 1
#SBATCH -c 6
#SBATCH -t 20:00:00
#SBATCH --exclusive
export OMP_NUM_THREADS=6
SUBJ=${1}
... |
aafbaae5b59e91fd3ed028c2507ccf17f50c8be8340325c0ab251605585a105f | Shell | 1,336 | 39 | #!/bin/bash
#PBS -l select=1:ncpus=4:mem=16gb
#PBS -l walltime=00:30:00
#PBS -N react
#PBS -J 1-16
module load anaconda3/personal
source activate graphtrp
# Parameters
study="psilodep1"
session="before"
receptor_set="Believeau-5"
# Define project directory and output directory
project_dir="/rds/general/user/hmt23/h... |
f43231389ab044c1023fc8944aeb2f577e0b7b55e5fd097c0b139fc3cb9a5175 | Shell | 1,339 | 39 | # !/bin/sh
set -e
# Benchmarks run on a Ubuntu 14.04 VM with 2 cores and 4 GiB of RAM.
# The VM is running on a Macbook Pro with a 3.1 GHz Intel Core i7 processor and
# 16 GB of RAM and an SSD.
# $BENCHMARK_DIR is generated with the following commands, from the Ubuntu image
# ubuntu-16.10-desktop-amd64.iso.
# > mkdir... |
65251bd92b139a3c9ad426cc3c0963400907b8d455e92963f8398ead352dc72b | Shell | 1,341 | 57 | #!/bin/sh
#
# Downloads sequence for the rn6 version of R. norvegicus (rat) from
# UCSC.
#
# Note that UCSC's rn6 build has two categories of compressed fasta
# files:
#
# 1. The base files, named chr??.fa.gz
# 2. The unplaced-sequence files, named chr??_random.fa.gz
#
# By default, this script indexes all these files... |
cc730e560e19b40b60e843b63cdd54f9d22dac2def6564861f4ea140af408d4e | Shell | 1,342 | 50 | #!/bin/bash
BAM_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/analysis/02_alignment/bowtie2/target/adjusted_replicated"
OUT_DIR="${BAM_DIR}/results/MACS2"
mkdir -p $OUT_DIR
run_macs2() {
local bam_file=$1
local output_prefix=$2
local additional_params=$3
... |
1d8d49d0d9ac791f52dbe98ad38324fd4bf00cd400a7e5a3fbb96be6aeee365e | Shell | 1,345 | 44 | #!/bin/bash
# Usage: sbatch slurm-serial-job-script
# Prepared By: Kai Xi, Oct 2014
# help@massive.org.au
# NOTE: To activate a SLURM option, remove the whitespace between the '#' and 'SBATCH'
# $1: line counter
# Need to use variables OUTSIDE of this script, #SBATCH doesn't support variables: https://hel... |
bf1ea269868aef3ac038be4426652b36d2a8b4f73c5dc086d5f41829ea04b30c | Shell | 1,345 | 44 | #!/bin/bash
# Usage: sbatch slurm-serial-job-script
# Prepared By: Kai Xi, Oct 2014
# help@massive.org.au
# NOTE: To activate a SLURM option, remove the whitespace between the '#' and 'SBATCH'
# $1: line counter
# Need to use variables OUTSIDE of this script, #SBATCH doesn't support variables: https://hel... |
5c6e403284dd569872873455fff5dcd168854f97f9b95f9fa48cb91ca738267b | Shell | 1,348 | 44 | #!/bin/bash
# Usage: sbatch slurm-serial-job-script
# Prepared By: Kai Xi, Oct 2014
# help@massive.org.au
# NOTE: To activate a SLURM option, remove the whitespace between the '#' and 'SBATCH'
# $1: line counter
# Need to use variables OUTSIDE of this script, #SBATCH doesn't support variables: https://hel... |
860086f9723a2a3eaa476341bd095df12ea53fb838c3bf65915dc5572a7399c2 | Shell | 1,353 | 63 | #!/bin/bash
usage() { echo "Usage: $0 [-a <gtf_file>] [-s <star_index] [-o <output_dir>] [-d <docker_image>] <rd1_fastq_gz|sample_csv> [<rd2_fastq_gz>]" 1>&2; exit 1; }
output_dir=corall_out
docker_img=corall:v1.0.1
while getopts ":a:s:o:d:" o; do
case "${o}" in
a)
gtf_file=${OPTARG}
... |
8f494c0a795bf080b8549b0013d011ecbf6befe65c7f6ab711017cac94484d33 | Shell | 1,353 | 46 | #!/bin/bash -l
#SBATCH --job-name=physio
#SBATCH --nodes=1
#SBATCH --task=4
#SBATCH --mem-per-cpu=8gb
#SBATCH --time=01:30:00
#SBATCH -o ./log/physio02_%A_%a.o
#SBATCH -e ./log/physio02_%A_%a.e
#SBATCH --account=DBIC
#SBATCH --partition=standard
#SBATCH --array=1-14%5
conda activate biopac
PROJECT_DIR="/dartfs-hpc/rc... |
534fcf396a6624aec3aca178310ec7df608050ca53b5c51577bf2ea5fff58d5e | Shell | 1,355 | 44 | #!/bin/bash
# Usage: sbatch slurm-serial-job-script
# Prepared By: Kai Xi, Oct 2014
# help@massive.org.au
# NOTE: To activate a SLURM option, remove the whitespace between the '#' and 'SBATCH'
# $1: line counter
# Need to use variables OUTSIDE of this script, #SBATCH doesn't support variables: https://hel... |
29da955f14523c175d0ab8412956c06cd435a9becbdbe0ac1175ba4babf0ccfa | Shell | 1,359 | 11 | wget https://bioinformatics.cse.unr.edu/software/scDHA/resource/Reproducibility/Data/deng.rds -O data/original/rds/deng.rds
wget https://bioinformatics.cse.unr.edu/software/scDHA/resource/Reproducibility/Data/hrvatin.rds -O data/original/rds/hrvatin.rds
wget https://bioinformatics.cse.unr.edu/software/scDHA/resource/Re... |
bf1583580eaf34d9a849cb53a0acf19a763bbdad51c29ed50962c8d70bd189ce | Shell | 1,362 | 43 | #!/bin/sh
# Ensure that zgrep -f - works like grep -f -
# Before gzip-1.4, it would fail.
# Copyright (C) 2009-2016 Free Software Foundation, Inc.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundatio... |
6aa613f3c20c56f1acdd3941e0784ba50d3db4a2b7634a5e7349ddcb5d56a3d6 | Shell | 1,372 | 71 | #!/bin/bash
set -eo pipefail
# Default values
INPUT_DATA=""
INPUT_LABELS=""
MODEL_FILES=""
OUTPUT_RESULTS=""
# Parse arguments
while [[ $# -gt 0 ]]; do
case $1 in
--input-data)
INPUT_DATA="$2"
shift 2
;;
--input-labels)
INPUT_LABELS="$2"
... |
bb47ee8e541cf9e750fceabaa59571186e9657d1c79446431fb599561fc54802 | Shell | 1,373 | 28 | #! /bin/bash
model=ScaleDense
batch_size=32
test_dirpath=./data/test
excel_dirpath=./data/dataset.xls
sorter_path=./TASN/Sodeep_pretrain_weight/best_lstmla_slen_${batch_size}.pth.tar
model_dirpath=./pretrained_model/ScaleDense/
# ------ train and set the parameter
CUDA_VISIBLE_DEVICES=0 python ./TSAN/prediction_first_... |
650f10727649e776bce47a3e7e37895b27b3b868830d082e9abbf759b1b1f27d | Shell | 1,378 | 55 | #!/bin/sh
#
# Downloads sequence for the GRCm38 release 81 version of M. Musculus (mouse) from
# Ensembl.
#
# By default, this script builds and index for just the base files,
# since alignments to those sequences are the most useful. To change
# which categories are built by this script, edit the CHRS_TO_INDEX
# var... |
229c1b3bb785e3a4933a53727a7e40c6c7c22efdd722b471a2f6e8045a51658e | Shell | 1,387 | 47 | #!/bin/bash
#BSUB -J homer_NICDmotifs
#BSUB -o logs/homer_NICDmotifs.%J.out
#BSUB -e logs/homer_NICDmotifs.%J.err
#BSUB -n 12
#BSUB -R rusage[mem=50]
# Create directories
mkdir -p logs
mkdir -p findMotifsGenome_motif_inst
# Load modules
. /usr/share/Modules/init/bash
module load modules modules-init
module lo... |
cb31ba6c6fb298e52823fb26c44872bcb7908b13dc953afa672b80edb7bac3e7 | Shell | 1,388 | 61 | while getopts c:k:d:g:r: flag
do
case "${flag}" in
c) CERT_FILE=${OPTARG};;
k) KEY_FILE=${OPTARG};;
d) DEPLOY=${OPTARG};;
g) CERT_GENERATE=${OPTARG};;
r) RESET_DB=${OPTARG};;
esac
done
DEPLOY="${DEPLOY:-1}"
CERT_GENERATE="${CERT_GENERATE:-1}"
CERT_FILE="${CERT_FILE:-cert... |
7879bc2a969b27d0617139136bd547aadb393785ec64fd1c1a5f6626f1084a5f | Shell | 1,391 | 32 | #!/bin/zsh
# the goal is to transfer handling of all URLs directly to web remote and not datalad
# one which initially was needed for handling shub:// urls.
# disable autoenabling of datalad remote
git annex enableremote datalad autoenable=false
# For those which are in shub:// resolve urls directly to the images
# H... |
1e2161c58dcb4a7e9c8745680a1849541a84ecee95327a68c6cb82a917e59505 | Shell | 1,393 | 59 | #!/bin/sh
# Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
#
# This file is part of the Kraken 2 taxonomic sequence classification system.
set -e
SCRIPT="$(realpath "$0")"
ROOT=$(dirname "$SCRIPT")
VERSION="$(cat "$ROOT/VERSION")"
cd "$ROOT"
if [ -z "$1" ] || [ -n "$2" ]
then
echo "Usage: $(basename "$SCRI... |
dc74834afa06a43266461c04fb7ff89eecb6b4354b3ab99685e50e1b2a6594b6 | Shell | 1,394 | 66 | #!/bin/bash
#SBATCH --array=1-8
#SBATCH -p 3090-gcondo
#SBATCH --gres=gpu:2
#SBATCH --gres-flags=enforce-binding
#SBATCH --exclude=gpu2262,gpu2112
#SBATCH -N 1
#SBATCH --cpus-per-gpu 2
#SBATCH --mem=128G
#SBATCH --time=24:00:00
#SBATCH --output=grid_llama_70b.%j.%A.%a.out
# Load modules
module load anaconda/2023.09-0-... |
d195be8288a515f2fa37335f9e688ecbb6616ee6df0b7ec7457e8e7200bc85e5 | Shell | 1,397 | 75 | #!/bin/bash
# Build MagellanMapper documentation
# Author: David Young 2018, 2019
HELP="
Build documentation files for MagellanMapper through the Sphinx package.
Arguments:
-a: Rebuild API .rst files.
-c: Clean docs before rebuilding.
-h: Show help and exit.
Usage:
- Clean and rebuild all doc files, including ... |
6187c8d848774049e568c1ab3bec47a342bb3b8eabe7aa00f53f750ee1ad7615 | Shell | 1,399 | 62 | MODEL_NAME="IDEA-CCNL/Erlangshen-Roberta-110M-NLI"
TEXTA_NAME=sentence1
TEXTB_NAME=sentence2
LABEL_NAME=label
ID_NAME=id
BATCH_SIZE=1
VAL_BATCH_SIZE=1
DATA_ARGS="\
--dataset_name IDEA-CCNL/AFQMC \
--train_batchsize $BATCH_SIZE \
--valid_batchsize $VAL_BATCH_SIZE \
--max_length 128 \
... |
899ef8390b82b5fb188ac3f9b0556ad5a0389eee5a869cc1faade6dcb025f4d2 | Shell | 1,399 | 53 | #!/bin/bash
echo ::::: Search hypotheses :::::
#mkdir all_hypotheses
cd /home/pvalenzuela/01_test/result_clusters_sdf/$dir/
#In the cycle, the best hypothesis is searched, considering the hyperscore phase, it is renamed with respect to the NameFolder_Cluster_CharacteristicsHypothesis and it is moved to a common fo... |
f5e7def0d59abc7160d0569943611fb26199b3d17197081a5a1ffd0eccf6e912 | Shell | 1,399 | 49 | #!/bin/bash
set -m
. /sh_libs/liblog.sh
info "Testing the base image."
info "Testing current user."
current_user=$(whoami)
if [[ $current_user == "encodermap" ]] ; then
info "Correct user selected."
else
error "Tests not running with the encodermap user. Current user is ${current_user}. Make sure to call docker w... |
7468107ed48a0a0ca0817ecdf27e480a8db2eafc56b630941d0f692247c8a4bb | Shell | 1,400 | 32 | #!/bin/bash
# Inject lib/libxgboost4j.so into JVM packages.
# This script is useful when the user opts to set skip.native.build=true
# option in the JVM package build. When this option is set, the JVM package
# build will not build libxgboost4j.so; instead it will expect to find the
# library in jvm-packages/xgboost4j/... |
117a5a2f9da9f70b193bf5cfc9c3bfd6e847b831603be6996a094a4aa2828640 | Shell | 1,414 | 48 | #!/bin/bash
#BSUB -J homer_CTRLmotifs
#BSUB -o logs/homer_CTRLmotifs.%J.out
#BSUB -e logs/homer_CTRLmotifs.%J.err
#BSUB -n 12
#BSUB -R rusage[mem=50]
# Create directories
mkdir -p logs
mkdir -p findMotifsGenome_motif_inst
# Load modules
. /usr/share/Modules/init/bash
module load modules modules-init
module lo... |
e4e0dcf48e1f3cad831cad035707613bf54b8f7785a631462c4242b44718ccfc | Shell | 1,414 | 71 | #!/bin/bash
set -eo pipefail
# Default values
INPUT_DATA=""
INPUT_LABELS=""
MODEL_FILES=""
OUTPUT_RESULTS=""
# Parse arguments
while [[ $# -gt 0 ]]; do
case $1 in
--input-data)
INPUT_DATA="$2"
shift 2
;;
--input-labels)
INPUT_LABELS="$2"
... |
0747dde7df7aa2beefebcdd8de9c65d4a40141e73f94fdd630322f3f545ecbc6 | Shell | 1,424 | 59 | #!/bin/bash
#
############################################################################
# Filename : load_config.sh
# Description : This script loads from configuration file "default.conf"
# Arguments : None
# Date : 08/01/2020
#####################################################################... |
bc54d6222850b2930491d893e0fd0a27816eabadd594dae2da95c4595cfef337 | Shell | 1,430 | 35 | #!/usr/bin/env bash
cd /workspaces/medperf/server
bash ./setup-dev-server.sh < /dev/null &>server.log &
sleep 10
docker pull mlcommons/chestxray-tutorial-prep:0.0.1
docker pull mlcommons/medperf-flower-fl:1.0.0
python seed.py --demo tutorial &>/dev/null
cd ..
# Create three instances of web UI
MEDPERF_CONFIG_STORAGE=... |
e272f496ef5b4eb62954942c77454b57ff0c953eb9b3e87e7f1d481afb68d1a3 | Shell | 1,430 | 40 | #!/bin/sh
#This script is intended for launch on *nix machines
#-Xmx8g indicates 8 gb of memory.
#To adjust this (or other Java options), edit the "$HOME/.igv/java_arguments"
#file. For more info, see the README at
#https://raw.githubusercontent.com/igvteam/igv/master/scripts/readme.txt
#Add the flag -Ddevelopmen... |
1e494a6eb70fabcdf156021009c69600cee86c4b6151cee21765cfc80a7be22a | Shell | 1,435 | 49 | #!/bin/bash
# Build Python wheels targeting MacOS (no federated learning)
set -euox pipefail
if [[ $# -ne 2 ]]; then
echo "Usage: $0 [platform_id] [commit ID]"
exit 1
fi
platform_id=$1
commit_id=$2
if [[ "$platform_id" == macosx_* ]]; then
if [[ "$platform_id" == macosx_arm64 ]]; then
# MacOS, Apple... |
31b97f35bf730f595fd243fb3751147ce6c2a5f745ed2d7647602bfd588d59c5 | Shell | 1,438 | 59 |
# Commandline arguments
SOURCE_INDEX="$1"
TARGET_LABEL="$2"
MODELID="$3"
# Configurable constants
ATTACK="poison_MNIST.py"
MAX_RETRIES=1
OUTPUT_BASE="MNIST_test_${MODELID}"
#MAX_RETRIES=10
#OUTPUT_BASE="MNIST-rand_test_${MODELID}"
#ARCH="basic"
#ARCH="adv"
#ARCH="MobileNet"
ARCH="RegNetX"
MODEL="mnist_${MODELID}.pt... |
e49abeebe6810f3b6dc7c3542b5ed02fdc5b40b1b3f41189662321c439305222 | Shell | 1,440 | 46 | dataset_name=soccer_dataset
model_name=yolov5n
size=1920
yolov5_path=/home/atom/MiRAI/submodules/yolov5
docker run \
--gpus all \
--ipc=host \
-v $PWD/:/PWD \
-v /mnt:/mnt \
-v /home:/home \
atomscott/all-in-one:latest \
/bin/bash -c " \
cd $yolov5_path/ && \
python train.py \
... |
354ca8b9c0dbfbe3b3f057964250ad892b4afea9887c9c4868358ba25319cb50 | Shell | 1,447 | 46 | #!/bin/sh
# Test the obsolescent GZIP environment variable.
# Copyright 2015-2016 Free Software Foundation, Inc.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... |
ebc468d57c8ca72a9fa3bc2c25b26d2afa9406e3e964ae835c1624bf7140ef7e | Shell | 1,455 | 47 | #!/bin/sh
# Ensure that zgrep -15 works. Before gzip-1.5, it would fail.
# Copyright (C) 2012-2016 Free Software Foundation, Inc.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versio... |
956a7deba24112b3c844d81830b0d1772a0bbf624a6fd3bb296d4b2ee10696b0 | Shell | 1,458 | 38 | set -eo pipefail
[[ -n "${DATA_CONFIG:-}" ]] || { echo "Error: DATA_CONFIG not set or empty" >&2; exit 1; }
[[ -n "${MODEL_CONFIG:-}" ]] || { echo "Error: MODEL_CONFIG not set or empty" >&2; exit 1; }
[[ -n "${RESULT_CONFIG:-}" ]] || { echo "Error: RESULT_CONFIG not set or empty" >&2; exit 1; }
[[ -n "${RESULT_COLLECT... |
fb0d91efaee77d78f2f75f113e2e84623305879dde394f8072a455d28b759fd1 | Shell | 1,462 | 48 | #!/bin/bash
#
# This script can be used to configure and run snakemake.
#
# It accepts up to 9 additional arguments, which are passed
# to the snakemake invocation, e.g.
# bash scripts/babel-build.sh --keep-incomplete anatomy_uberon_ids
#
# Number of cores to use.
export CORES=5
# Dry run: if true, run Snakemake in... |
a2e698d13ac1469f0135dd54fd7aa30a0c00a7db4142098f127bff31312dd531 | Shell | 1,468 | 54 | #!/bin/bash
#BSUB -J deeptools
#BSUB -o logs/computematrix_heatmap.%J.out
#BSUB -e logs/computematrix_heatmap.%J.err
#BSUB -n 12
#BSUB -R rusage[mem=50]
mkdir -p logs
#load modules and install deeptools
. /usr/share/Modules/init/bash
module load modules modules-init
module load python
# install macs2
pip install dee... |
a747cd1fe8865d5050fd9a059c767ef8d74b4043daa79268f3af6838bbf5dd13 | Shell | 1,469 | 41 | #!/bin/bash
#BSUB -o logs/bamCoverage.%J.out
#BSUB -e logs/bamCoverage.%J.err
#BSUB -n 12
#BSUB -R rusage[mem=50]
mkdir -p logs
. /usr/share/Modules/init/bash
module load modules modules-init
module load python
# install deepTools
pip install deeptools
# make arrays with the file names for each replicate for each c... |
5274e486aac47c48c28e6c57df173673c8522eebaf7c16546cfe35eb721a1b2d | Shell | 1,474 | 47 | #!/bin/sh
#This script is intended for launch on *nix machines
#-Xmx8g indicates 8 gb of memory.
#To adjust this (or other Java options), edit the "$HOME/.igv/java_arguments"
#file. For more info, see the README at
#https://raw.githubusercontent.com/igvteam/igv/master/scripts/readme.txt
#Add the flag -Ddevelopmen... |
e0a420f6ce844f683bbd29ad7a56ccd47c1c633b1839ddf33009d77358a12512 | Shell | 1,478 | 43 | #!/bin/bash
BAM_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/Four_DN/batch_2/sorted_bams/filese_renamed_adjusted"
OUTPUT_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/Four_DN/batch_2/sorted_bams/filese_renamed_adjusted/results_2/LANCEOTR... |
bb82f1d9b1c2de9eb2f5a5a5b1f886c8e660bf677eadeca0ce4a41f7f086f3f5 | Shell | 1,484 | 51 | #!/bin/sh
# Exercise the --keep option.
# Copyright (C) 2013-2016 Free Software Foundation, Inc.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your ... |
8651e01e9dd63ff348dc6b5d67fcb4be843d72c8fd85dadfc5c71c6ee2a89368 | Shell | 1,489 | 36 | #!/bin/sh
# gzip should report invalid 'unpack' input when uncompressing.
# With gzip-1.5, it would output invalid data instead.
# Copyright (C) 2012-2016 Free Software Foundation, Inc.
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as pub... |
99daf5016fbaa0384d4bff01c3782f3c64211c4e306da5b6880f613759fb526c | Shell | 1,493 | 50 | #!/bin/bash -l
#SBATCH --job-name=physio
#SBATCH --nodes=1
#SBATCH --task=4
#SBATCH --mem-per-cpu=8gb
#SBATCH --time=00:30:00
#SBATCH -o ./log/physio02_%A_%a.o
#SBATCH -e ./log/physio02_%A_%a.e
#SBATCH --account=DBIC
#SBATCH --partition=standard
#SBATCH --array=1-14
##1-14%5
conda activate biopac
# CLUSTER="discovery... |
2f0e8dcd00f803ee027225bee884c95f015693a7c1509da80d5d588d2005798a | Shell | 1,498 | 38 | #!/usr/bin/env bash
set -ex
echo "Adding official Postgres repository"
PG_URL="http://apt.postgresql.org/pub/repos/apt/"
APT_LINE="deb ${PG_URL} $(lsb_release -cs)-pgdg main"
echo "${APT_LINE}" | sudo tee "/etc/apt/sources.list.d/pgdg.list"
sudo apt-get install wget ca-certificates
PG_KEY_URL="https://www.postgresql.... |
bc0234d5a83754e4ec857ee44f9f6e8fc0838c4d797988314dc28f8284a87a4e | Shell | 1,503 | 58 | #!/usr/bin/env sh
# Create the imagenet lmdb inputs
# N.B. set the path to the imagenet train + val data dirs
set -e
EXAMPLE=examples/imagenet
DATA=data/ilsvrc12
TOOLS=build/tools
TRAIN_DATA_ROOT=/path/to/imagenet/train/
VAL_DATA_ROOT=/path/to/imagenet/val/
# Set RESIZE=true to resize the images to 256x256. Leave as... |
a15875085c0f46a786c020220ff002e306d93fe5bab10058a789ffb10ccee653 | Shell | 1,504 | 60 | #!/bin/sh
#
# Downloads sequence for the GRCh38 release 84 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh38 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
a5383a51e20d84527357f4828533afc6d53b2532109c144d93e4a26e28fe721c | Shell | 1,505 | 54 | #!/bin/bash
# Build Python wheels targeting manylinux2014 (no GPU, no federated learning)
set -euo pipefail
if [[ -z "${GITHUB_SHA:-}" ]]
then
echo "Make sure to set environment variable GITHUB_SHA"
exit 1
fi
if [[ "$#" -lt 1 ]]
then
echo "Usage: $0 {x86_64,aarch64}"
exit 1
fi
arch="$1"
source ops/pipeline... |
831e2b6e80bf18af3e4364d4a35207ba97ee5fbf22acdcd8989487c29d33596b | Shell | 1,506 | 60 | #!/bin/sh
#
# Downloads sequence for the RNor_6.0 release 84 version of rattus_norvegicus (rat) from
# Ensembl.
#
# Note that Ensembl's build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
f4ae40cc06d92b27b88c8b0a6b918015191489685b371215abd883e5b6fbb3e3 | Shell | 1,506 | 60 | #!/bin/sh
#
# Downloads sequence for the BDGP6 release 84 version of drosophila melanogaster (fly) from
# Ensembl.
#
# Note that Ensembl's build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments ... |
8a0f96ae3758e5495488e122db72f74a0073f24b6f2ba8e0ac5e63ad1bc50a40 | Shell | 1,510 | 60 | #!/bin/sh
#
# Downloads sequence for the WBcel235 release 84 version of caenorhabditis elegans (worm) from
# Ensembl.
#
# Note that Ensembl's build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignmen... |
bdc7f7e4c4178ae1a4a84333046e065a75e288c0a1f4a7462007dcdf82d11542 | Shell | 1,515 | 60 | #!/bin/sh
#
# Downloads sequence for the R64-1-1 release 84 version of saccharomyces cerevisiae (yeast) from
# Ensembl.
#
# Note that Ensembl's build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignm... |
e050a1ea6e7c6b808ff9c4d8858b107225ebc7428c0ae5645b89ade850de25c1 | Shell | 1,518 | 60 | #!/bin/sh
#
# Downloads sequence for the GRCh37 release 75 version of H. sapiens (human) from
# Ensembl.
#
# Note that Ensembl's GRCh37 build has three categories of compressed fasta
# files:
#
# The base files, named ??.fa.gz
#
# By default, this script builds and index for just the base files,
# since alignments to ... |
27548bbfffc56918bef13e752333df0df4a9416bf33360ea4ee2f5205d8c1873 | Shell | 1,520 | 47 | #!/bin/bash
set -e
set -x
# Finding whether os is Linux or MacOSX
OS=$(uname -s)
case ${OS} in
Linux*) OS=Linux;;
Darwin*) OS=MacOSX;;
*) echo "Unknown OS ${OS}; please use manual installation." && exit 1;;
esac
# Finding whether machine is 32bit or 64bit
case ${OS} in
Linux)
VER=$(u... |
54450e78619cb209ed5e1f9dcaddd16a6b930d9ecf6d0c6f03664a895a8b1ce7 | Shell | 1,532 | 47 | #!/bin/bash
#BSUB -J homer_RBPJmotifs
#BSUB -o logs/homer_NICDmotifs.%J.out
#BSUB -e logs/homer_NICDmotifs.%J.err
#BSUB -n 12
#BSUB -R rusage[mem=50]
# Create directories
mkdir -p logs
mkdir -p findMotifsGenome_motif_inst
# Load modules
. /usr/share/Modules/init/bash
module load modules modules-init
module lo... |
4000f43716092c5e253646da2abefaf2028ac0baf47d0e3f87b6255a5e54c665 | Shell | 1,534 | 63 |
# Commandline arguments
SOURCE_INDEX="$1"
TARGET_LABEL="$2"
MODELID="$3"
# Configurable constants
ATTACK="poison_CIFAR10.py"
MAX_RETRIES=1
OUTPUT_BASE="CIFAR10_test_${MODELID}"
#MAX_RETRIES=10
#OUTPUT_BASE="CIFAR10-rand_test_${MODELID}"
#ARCH="basic"
#ARCH="adv"
#ARCH="MobileNet"
ARCH="RegNetX"
MODEL="cifar10_${MOD... |
2c0feb01b28a55c37face6bd097fb5f34802a537c1462121588d6119d07f3fc8 | Shell | 1,542 | 76 | #!/bin/bash
# Read arguments
while [ "${1:-}" != "" ]; do
case "$1" in
"--ca_config"*)
ca_config="${1#*=}"
;;
"--pki_assets"*)
pki_assets="${1#*=}"
;;
*)
;;
esac
shift
done
# validate arguments
if [ -z "$ca_config" ]; then
ca_config="/mlcommons/volum... |
81569d68c6a24f6d5ceea36064dad95c4b205df809789d53481ad28e0f7e3cf4 | Shell | 1,547 | 52 | while getopts so: flag; do
case "${flag}" in
o) OUT=${OPTARG} ;;
s) EXT="v3_server" ;;
esac
done
EXT="${EXT:-v3_client}"
if [ -z "$OUT" ]; then
echo "-o is required"
exit 1
fi
if [ -z "$MEDPERF_INPUT_CN" ]; then
echo "MEDPERF_INPUT_CN env var is required"
exit 1
fi
if [ -z "$MEDPERF_... |
636b45a6fadd58b0060c0f121b7463b5b74ba52ce8dbf080ed2201633025ae32 | Shell | 1,548 | 58 | #!/bin/bash
# format_python.sh — lint and format Python scripts with Ruff
# Usage: ./format_python.sh [update|check]
# Default: check
set -u
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO_ROOT="$(cd "${SCRIPT_DIR}/.." && pwd)"
MODE="${1:-check}"
REQUIRED_RUFF_VERSION="0.16.5"
if [[ "${MODE}" != "upd... |
05e90f94d88d413ad40a1dea362e34bfb97cb8627370d9dde222ad330b60aef7 | Shell | 1,555 | 61 |
echo "#######################################"
echo "# Machine Details #"
echo "#######################################"
echo ""
echo "MEMORY USAGE:"
free
echo ""
echo "######################################"
echo "# User Details #"
echo "#####################################... |
5246786daa6fab1d36c6db03c3d6f3de8aef777a5a03c5543fc979d4b54ff0c2 | Shell | 1,568 | 53 | #!/bin/bash
# Usage: sbatch slurm-serial-job-script
# Prepared By: Kai Xi, Oct 2014
# help@massive.org.au
# NOTE: To activate a SLURM option, remove the whitespace between the '#' and 'SBATCH'
# $1: line counter
# Need to use variables OUTSIDE of this script, #SBATCH doesn't support variables: https://hel... |
b3310de70a1fb3f3d7ba3f3210c855b727c284162169266e99ad65c4ecc3ca0e | Shell | 1,574 | 48 | #!/bin/bash -l
#SBATCH --job-name=physio
#SBATCH --nodes=1
#SBATCH --task=4
#SBATCH --mem-per-cpu=100gb
#SBATCH --time=01:30:00
#SBATCH -o ./log/physio03_%A_%a.o
#SBATCH -e ./log/physio03_%A_%a.e
#SBATCH --account=DBIC
#SBATCH --partition=standard
#SBATCH --array=1
###%-14%5
conda activate biopac
PROJECT_DIR="/dartfs-... |
517ca7223d63e3bb2b010fdf59e7cd302cf7a65cc2287a899481dd2786cb2ee3 | Shell | 1,577 | 51 | #!/bin/bash -l
#SBATCH --job-name=physio
#SBATCH --nodes=1
#SBATCH --task=4
#SBATCH --mem-per-cpu=8gb
#SBATCH --time=01:30:00
#SBATCH -o ./log/physio03_%A_%a.o
#SBATCH -e ./log/physio03_%A_%a.e
#SBATCH --account=DBIC
#SBATCH --partition=standard
#SBATCH --array=1-14%5
conda activate biopac
PROJECT_DIR="/dartfs-hpc/rc... |
7af1f100a523160b813f07ba57617689abe08ba49882b4b97027e7c5c347d95c | Shell | 1,577 | 42 | #!/bin/bash
# turn on bash's job control
set -m
# bring up sshd
/usr/sbin/sshd
# print uid
id
# wait for the nodes to spin up and create passwordless ssh
/wait-for-it.sh slurm-node1.local.dev:22 --strict -- echo "slurm-node1.local.dev ssh(22) is up" ; sshpass -p adminpassword ssh-copy-id -i /etc/ssh/ssh_host_rsa_ke... |
e81ef4e6e6a5a1a84bb8b82cd8bed295fc1c5f8c7a2570e436d5ef27608981eb | Shell | 1,581 | 50 | #!/bin/bash
echo "Generating STAR index.."
mkdir ./test_data/star_index
conda_dir=$(which conda | grep -oP "^/.*(?=bin)")
echo "conda dir detected at: ${conda_dir}"
source ${conda_dir}/bin/activate corall
STAR --runMode genomeGenerate --genomeFastaFiles ./test_data/test_genome.fasta --genomeSAindexNbases 7 --sjdbGT... |
e1f6fcadf00b874ebe498c5e84ca13a39f852a2d9e33e7a33d5de2d07a5427fb | Shell | 1,584 | 51 | #!/bin/bash
## Build and test XGBoost with ARM64 CPU (no GPU, no federated learning)
set -euo pipefail
if [[ -z "${GITHUB_SHA:-}" ]]
then
echo "Make sure to set environment variable GITHUB_SHA"
exit 1
fi
source ops/pipeline/classify-git-branch.sh
source ops/pipeline/get-docker-registry-details.sh
source ops/pipe... |
3a45566e257bd9181946761e1fa313379b4f39679164a1747e3864be555aee96 | Shell | 1,593 | 55 | #!/bin/bash
#
# Adapted from https://github.com/nipy/nipype/blob/master/tools/update_changes.sh
#
# This is a script to be run before releasing a new version.
#
# Usage /bin/bash update_changes.sh 0.5.1
#
# Setting # $ help set
set -u # Treat unset variables as an error when substituting.
set -x #... |
94f1125d15e7d1f2dbe97e75463010248a15ddf226848ac34a6e519944059ed3 | Shell | 1,596 | 42 | #!/bin/bash
# Copyright 2013-2023, Derrick Wood <dwood@cs.jhu.edu>
#
# This file is part of the Kraken 2 taxonomic sequence classification system.
# Build the standard Kraken database
# Designed to be called by kraken_build
set -u # Protect against uninitialized vars.
set -e # Stop on error
set -o pipefail # Stop... |
8cbc00dcafa4a0528b009e71e807b1cf2bd62bbc4af57d8f017c92b3f4e3c43f | Shell | 1,600 | 46 | #!/bin/bash
# load libs
. /sh_libs/liblog.sh
# turn on bash's job control
set -m
# write the password
info "Running tests in EncoderMap's SLURM node with PROMETHEUS."
echo $LDAP_ADMIN_PASSWORD > /etc/ldap.secret
echo $LDAP_ADMIN_PASSWORD > /etc/pam_ldap.secret
echo $LDAP_ADMIN_PASSWORD > /etc/libnss-ldap.secret
unse... |
791a8c49289cc1f50b62a845e66a8e70648d4e3dc49c4e79330695a4cdf00587 | Shell | 1,608 | 51 | #!/bin/bash -e
#
############################################################################
# Filename : config_setup_load.sh
# Description : This script loads from config file "config/config_setup.conf"
# Arguments : None
# Date : 12/12/2020
#######################################################... |
1101f5a65fee8adb8c6e3c41ec3a9438ebb78166c21c1e1beffec72e1142b0c3 | Shell | 1,616 | 48 | #!/usr/bin/env bash
# Sample settings for MagellanMapper tasks
# Copy this script to your own file and change it to your own settings.
# choose file paths (relative to magellanmapper directory), channels, etc
PREFIXES=(. ../data) # add additional data folders
BASE=sample # replace with your sample file (without extens... |
9cff7ca7f455208ca7e68792910b3662086142b060d2f2a105d318560351e64b | Shell | 1,623 | 34 | #!/usr/bin/env bash
set -eu -o pipefail
printf '%s\n' "Checking for broken links in $# files:" "$@" '=========='
# Find and check each URL in the files provided as arguments to the script.
# The (($# == 0)) test is to prevent grep from using standard input if no files were given.
# The grep -H option is to output the... |
08f88974940a75a96319dcffe743e4940fde9c148735979e0a6179acac62383e | Shell | 1,639 | 73 | #!/bin/bash
export CUDA_VISIBLE_DEVICES=0,4,5,6,7
export DATA_DIR="eICU/"
export TF_ENABLE_ONEDNN_OPTS=0
export PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True
EXPIRED_LR=0.00011
EXPIRED_DROPOUT=0.72
FINE_TUNING_LR=0.00007
FINE_TUNING_DROPOUT=0.8
MDP_LR=2e-4
MDP_DROPOUT=0.5
OUTPUT_DIR="/dirs/gated_prompt"
mkd... |
bdf7d2648fe337ea784bd5c60703a8b25fe80df773b44521f20f542f2960f7f0 | Shell | 1,643 | 49 | #!/bin/bash
#PBS -l select=1:ncpus=4:mem=4gb
#PBS -l walltime=01:00:00
#PBS -N short_secondary_jobs
#PBS -J 0-19
# Regional attribution jobs.
# Each base job is run with 10 different seeds (0-9).
# Total: 2 versions × 10 seeds = 20 jobs (PBS_ARRAY_INDEX 0-19)
# Load environment
module load anaconda3/personal
source ... |
3b99ccf08c8c300195e05b96af2e9e31ae0718a58f8024a12363e7cb5281ab85 | Shell | 1,645 | 52 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
#pre processing
[ -z "$MMSEQS" ] && echo "Please set the environment variable \$MMSEQS to your MMSEQS binary." && exit 1;
# check number of input variables
[ "$#" -ne 4 ] && echo "Please provide <queryDB> <targetDB> <outputDB> <tmp... |
af8e09e46ed7792dc8c680cd6a822940ac98bf996962a5e56b639074f08e3d90 | Shell | 1,646 | 69 | set -o errexit
gpu=1;
version="01";
iter="no";
dataset="okvqa";
model_size="large";
stream=2;
use_fact="yes";
n_context=10;
text_maxlength=130;
# mean / max / 21mean /
attention_score_style="21mean";
use_last_half_layer_attention="no";
train_data="okvqa_train_t5_v5_frequent_bm25.json";
eval_data="okvqa_test_t5_v5_freq... |
363d3ec51b498ae547dc716a2019cd07ef3a1f36855ab8939c8de0ce15438249 | Shell | 1,649 | 68 | #!/bin/bash
export CUDA_VISIBLE_DEVICES=0,4,5,6,7
export DATA_DIR="eICU/"
export TF_ENABLE_ONEDNN_OPTS=0
export PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True
EXPIRED_LR=0.00011
EXPIRED_DROPOUT=0.72
FINE_TUNING_LR=0.00007
FINE_TUNING_DROPOUT=0.8
MDP_LR=2e-4
MDP_DROPOUT=0.5
OUTPUT_DIR="/dirs/gated_prompt"
mkdir... |
7bfb762a519602ba6ee31b65696b234ba85f970c9dcce084cd23d550b4213717 | Shell | 1,668 | 46 | #!/bin/bash
set -xe
if [[ ! -e ./ERR3240275/ERR3240275_1.fastq.gz ]]; then
mkdir -p ERR3240275
cd ERR3240275
echo "null" > null.txt
ls | grep -v -E 'ERR3240275_1.fastq.gz' | grep -v -E 'ERR3240275_2.fastq.gz' | xargs rm -r
cd ..
fi
if [[ ! -e ./SRR8315715/SRR8315715_1.fastq.gz ]]; then
mkdir -p SRR8315715
cd S... |
f53e369ee07e9073402b52ed87514c937069c096ebcf9c8e183e6ff4bf0a77b6 | Shell | 1,672 | 77 | while getopts "g:o:s:" opt
do
case "$opt" in
g ) parameterG="$OPTARG" ;;
o ) parameterO="$OPTARG" ;;
s ) parameterS="$OPTARG" ;;
? ) helpFunction ;; # Print helpFunction in case parameter is non-existent
esac
done
# This script needs to run with R
# Settings --------------------------... |
41798361f33db1992d9adb437c528774d1518d0a02978f836bc2672035546d39 | Shell | 1,674 | 59 | #!/bin/bash -l
#SBATCH --job-name=physio
#SBATCH --nodes=1
#SBATCH --task=4
#SBATCH --mem-per-cpu=8gb
#SBATCH --time=05:30:00
#SBATCH -o ./log/physio02_%A_%a.o
#SBATCH -e ./log/physio02_%A_%a.e
#SBATCH --account=DBIC
#SBATCH --partition=standard
#SBATCH --array=1-14%5
conda activate biopac
# CLUSTER="discovery" # loc... |
1abd15c7258e0a6b35e854913930a2aa85d63b0889c9847f51836591e70aec4e | Shell | 1,676 | 74 | #!/bin/bash
export CUDA_VISIBLE_DEVICES=0,1,4,5,6,7
export DATA_DIR="eICU/"
export TF_ENABLE_ONEDNN_OPTS=0
export PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True
EXPIRED_LR=0.00011
EXPIRED_DROPOUT=0.72
FINE_TUNING_LR=0.00007
FINE_TUNING_DROPOUT=0.8
MDP_LR=2e-4
MDP_DROPOUT=0.5
OUTPUT_DIR="dirs/gated_prompt"
m... |
bda84b0b77afe6d3674b453955f82c3ba966844a35b0c9f3aa7f577b45dea396 | Shell | 1,680 | 59 | #!/bin/bash -l
#SBATCH --job-name=physio
#SBATCH --nodes=1
#SBATCH --task=4
#SBATCH --mem-per-cpu=8gb
#SBATCH --time=05:30:00
#SBATCH -o ./log/physio02_%A_%a.o
#SBATCH -e ./log/physio02_%A_%a.e
#SBATCH --account=DBIC
#SBATCH --partition=standard
#SBATCH --array=3-14%5
conda activate biopac
# CLUSTER="discovery" # loc... |
7d12377cb968f491ccf71228660d0ad3cbde95918ed5ca70c52665716ea4a5b3 | Shell | 1,696 | 59 | #!/usr/bin/env bash
compiler_kind="$1"
runner_os="$2"
target_abi="$3"
target_system_name="$4"
target_arch="$5"
set -e
if [[ -z "$GITHUB_OUTPUT" ]]; then
echo "Error: This script should only be run in github actions environment"
exit 1
fi
if [[ -z "${runner_os}" || -z "${target_abi}" || -z "${target_arch}" ]]; t... |
46960a48855f75db6414c926a57d0bd2a2261adebc8edee71f0174f15b1f20da | Shell | 1,702 | 78 | #!/bin/bash
#SBATCH --array=1-40
#SBATCH -p 3090-gcondo
#SBATCH --gres=gpu:1
#SBATCH --gres-flags=enforce-binding
#SBATCH --exclude=gpu2262,gpu2112
#SBATCH -N 1
#SBATCH --mem=20G
#SBATCH --time=24:00:00
#SBATCH --output=cat_iwl_icl.%j.%A.%a.out
# Load modules
module load anaconda/2023.09-0-7nso27y
module load cuda/12.... |
4e1a5bb8c07eac60a2dc7274b5fba31f85544bf216f55d04bae4ace0d1bbaf42 | Shell | 1,702 | 32 | #!/bin/bash -l
#SBATCH --job-name=corr
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=12
#SBATCH --mem-per-cpu=40G
#SBATCH --time=01:00:00
#SBATCH -o ./logcorr/np_%A_%a.o
#SBATCH -e ./logcorr/np_%A_%a.e
#SBATCH --account=DBIC
#SBATCH --partition=standard
conda activate spacetop_env
/dartfs-hpc/rc/lab/C/CANlab/labdata/da... |
63421bf48f5f281e96a429dc34eb56564cf1a7428ee69bd08388e1c7b3c55e19 | Shell | 1,704 | 42 | #!/bin/bash
. sh_libs/liblog.sh
info "Killing gmx commands"
pkill gmx
info "Deleting test_sims/ and sims.h5 and .sims*"
rm -rf test_sims/
rm -f sims.h5
rm -f .sims*
info "Creating dirs"
mkdir -p test_sims/sim1
mkdir -p test_sims/sim2
mkdir -p test_sims/sim3
info "Running gmx"
gmx grompp -f water_simulation/production... |
42f5f758ef61d6dc0e52748d8a1a8b9887fa1ad46f7e01dafa1467fde64ebf4a | Shell | 1,710 | 35 | #NEED TO REMOVE PRIMARY and rename DUP as PRIMARY
# PRIMARYJSON="sub-0122_ses-03_acq-mb8_dir-ap_run-01_epi.json"
DUPJSON="./sub-0122/ses-03/fmapsub-0122_ses-03_acq-mb8_dir-ap_run-01_epi__dup-01.json"
DUPJSON_TR=$(jq '.AcquisitionTime' "${DUPJSON}")
PRIMARYJSON=$(echo "${DUPJSON}" | sed 's/__dup-[0-9]*//')
PRIMARYJSON_T... |
7f1b109ffdce6ec00a1bb628dfc08a2893dade8d8463eee0a0aac63b307996e6 | Shell | 1,714 | 47 | #!/bin/bash
# preprocess data
python ./preprocess/preprocess_chirbase_eo.py \
--input_eo ./data/ChirBase_eo/w_ena/ad_sr.sdf \
--input ./data/ChirBase/chirbase.sdf \
--csp_setting ./preprocess/chirality_stationary_phase_list.csv \
--output ./data/ChirBase_eo/exp/ad_sr_clean.sdf
python ./preprocess/preprocess_chirbase... |
aed9de0332e0ae56c957d5244bafdcab7e899166b252d63a00d081aef3a97838 | Shell | 1,715 | 52 | #!/bin/bash
cd /cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/analysis/02_alignment/bowtie2/target/adjusted_replicated/results/SEACR
BAM_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/analysis/02_alignment/bowtie2/target/adjusted_replicated"
OUT... |
b98f95a2d2cc5e3eb7ad5e000e83d9de930fbd5c1c6f6cb219610b243e94b3b8 | Shell | 1,715 | 79 | #!/bin/bash
#SBATCH --array=1-80
#SBATCH -p 3090-gcondo
#SBATCH --gres=gpu:1
#SBATCH --gres-flags=enforce-binding
#SBATCH --exclude=gpu2262,gpu2112
#SBATCH -N 1
#SBATCH --mem=20G
#SBATCH --time=24:00:00
#SBATCH --output=grid_iwl_icl.%j.%A.%a.out
# Load modules
module load anaconda/2023.09-0-7nso27y
module load cuda/12... |
a6823369b3d0918ef96e85a7dd7134889c283076e05523d8aac3f4d6310e29e7 | Shell | 1,721 | 46 | #!/bin/bash
set -xe
if [[ ! -e ./ERR3240275/ERR3240275_1.fastq.gz ]]; then
mkdir -p ERR3240275
cd ERR3240275
echo "null" > null.txt
ls | grep -v -E 'ERR3240275_1.fastq.gz' | grep -v -E 'ERR3240275_2.fastq.gz' | xargs rm -r
cd ..
fi
if [[ ! -e ./SRR8315715/SRR8315715_1.fastq.gz ]]; then
mkdir -p SRR8315715
cd S... |
f9a50976e5136588773fc7434fdcd988cfd4af712d2fb132b6dec4df826733d7 | Shell | 1,721 | 38 | #!/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: REPLACING ORIGINAL STRUCTURAL IMAGES WITH DEFACED STRUCTURAL IMAGES
# PROJECT: ZOO
# WRITTEN BY LENNART WITTKUHN, ... |
b49510af9c4f03e413f95243bd83e99525b58aaf05c68a49fc8f434be1ad28e3 | Shell | 1,724 | 49 | #!/bin/bash
SIF=/storage/group/bfp2/default/wkl2-WillLai/Adversarial_Project/Adversarial_Observation/manuscripts/POISON25/pytorch-captum.sif
WORKINGDIR=/storage/group/bfp2/default/wkl2-WillLai/Adversarial_Project/Adversarial_Observation/manuscripts/POISON25
# ==========================================
# CONFIGURATION... |
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