sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
33a7c1e70b5650e72a34ae09566d6ff4b008f1db063510ba4e95d76424eab917 | Shell | 5,112 | 252 | echo "correctness tests -- general"
./datagen -s1 -g1GB > tmp
./adapt -otmp.zst tmp
zstd -d tmp.zst -o tmp2
diff -s -q tmp tmp2
rm tmp*
./datagen -s2 -g500MB > tmp
./adapt -otmp.zst tmp
zstd -d tmp.zst -o tmp2
diff -s -q tmp tmp2
rm tmp*
./datagen -s3 -g250MB > tmp
./adapt -otmp.zst tmp
zstd -d tmp.zst -o tmp2
diff -... |
ecad5128e2965c80fd11cbf32dbf3c4f75a5abe1d2bf03ca389cc4e832c5467e | Shell | 5,183 | 142 | while getopts t flag; do
case "${flag}" in
t) TWO_COL_SAME_CERT="true" ;;
esac
done
TWO_COL_SAME_CERT="${TWO_COL_SAME_CERT:-false}"
COL1_CN="col1@example.com"
COL2_CN="col2@example.com"
COL3_CN="col3@example.com"
COL1_LABEL="col1@example.com"
COL2_LABEL="col2@example.com"
COL3_LABEL="col3@example.com"
if ... |
78795907cad6dff8e4f728f15d851f2d89e867a8261f46598f232d7303a24426 | Shell | 5,252 | 135 | #!/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
[ "$#" -ne 4 ] && echo "Please provide <contigsDb> <taxSeqDB> <taxPerConti... |
7db64ec0aa54595d76f9e6e99ba12fe2c4252086c1ff7675d199280ae5fedf1c | Shell | 5,269 | 159 | #!/usr/bin/env bash
#
# release.sh — cut a new eggnog-mapper release.
#
# Steps: pre-flight checks → build sdist → smoke install in fresh venv
# → tag → push → gh release create (draft by default).
#
# Usage:
# scripts/release.sh --version 3.0.0
# scripts/release.sh --version 3.0.0 --dry-run
# scripts/release.sh ... |
92a0d09acc6c9894bebc4a05eaa3ae1cb28b1ff90604a7aac519c6215f77e20d | Shell | 5,296 | 190 | #!/bin/bash
# ============================================================================
# Rica - Production Build Script
# ============================================================================
#
# Purpose:
# Creates an optimized production build of rica with optional asset inlining
# for single-file HTML ... |
39d950fd328153b213a0aa0e05344da336b3cfeeb33e4584dce62ebcb61fb2be | Shell | 5,299 | 40 | python3.8 ./scripts/spikeAnalysis.py -w1 PEG_lr8_t0_w1_init -w2 PEG_lr8_t0_w2_init -o ./PEG_lr8/PEG_lr8 -t PEG_lr8_t0_init -s 4
python3.8 ./scripts/spikeAnalysis.py -w1 PEG_lr8_t1_w1_init -w2 PEG_lr8_t1_w2_init -o ./PEG_lr8/PEG_lr8 -t PEG_lr8_t1_init -s 4
python3.8 ./scripts/spikeAnalysis.py -w1 PEG_lr8_t2_w1_init -w2 ... |
6d2781746cbf5aaf4904a58b8611d4e1982d4fa3c700d2cc046067e7e46e530b | Shell | 5,447 | 192 | #!/bin/bash
# Sets up the MagellanMapper environment using venv
# Author: David Young 2019
HELP="
Sets up the MagellanMapper environment using the Python built-in
venv environment manager.
Also handles package updates for existing environments.
Arguments:
-h: Show help and exit.
-e [path]: Path to folder where t... |
65be2174aafedce31ddb05847174adb0653b0843386d299f542a4bd2b51c2660 | Shell | 5,488 | 125 | #!/bin/bash
module load python/3.6.4-anaconda
source activate ldsc
type=TOP20K_EXPAND_50kb
cd /home2/s422159/workdir/pr5/05_LDSC/$type
# Copy files required for ldsc
cp ../ADULT.ldcts ADULT.ldcts
mkdir RESULTS
cp -r ../BCG/ADULT_BCG .
# Run the regressions
for i in $(ls -d ADULT_* | grep 'ADULT' |... |
03d5da75f7051375a8dafe3f2110033314b8deb391b064331a42213d745c4b43 | Shell | 5,506 | 221 | #!/bin/bash
#
# Bitnami LDAP library
# shellcheck disable=SC1090,SC1091
# Load libraries
. /scripts/libfs.sh
. /scripts/liblog.sh
. /scripts/libos.sh
########################
# Loads global variables used on LDAP configuration.
# Globals:
# LDAP_*
# Arguments:
# None
# Returns:
# Series of exports to be used a... |
f1226024021c46436c2cb9621561712575363c45927ea6d5ae8a2a60aaa15e94 | Shell | 5,525 | 160 | #!/bin/sh -e
# Iterative sequence search workflow script
fail() {
echo "Error: $1"
exit 1
}
abspath() {
if [ -d "$1" ]; then
(cd "$1"; pwd)
elif [ -f "$1" ]; then
if [ -z "${1##*/*}" ]; then
echo "$(cd "${1%/*}"; pwd)/${1##*/}"
else
echo "$(pwd)/$1"
... |
6e493f6be3c67ac99b3dc022a428357eac4c3d2ff0b6b491ee37ac62bacef2b8 | Shell | 5,662 | 158 | while getopts t flag; do
case "${flag}" in
t) TWO_COL_SAME_CERT="true" ;;
esac
done
TWO_COL_SAME_CERT="${TWO_COL_SAME_CERT:-false}"
COL1_CN="col1@example.com"
COL2_CN="col2@example.com"
COL3_CN="col3@example.com"
COL1_LABEL="col1@example.com"
COL2_LABEL="col2@example.com"
COL3_LABEL="col3@example.com"
if ... |
e6319a08d708f4c97862c888583705d8205602a4c1ef1671f8ccf3535d7d5b1e | Shell | 5,698 | 163 | #!/bin/sh -e
# Sequence search workflow script
fail() {
echo "Error: $1"
exit 1
}
abspath() {
if [ -d "$1" ]; then
(cd "$1"; pwd)
elif [ -f "$1" ]; then
if [ -z "${1##*/*}" ]; then
echo "$(cd "${1%/*}"; pwd)/${1##*/}"
else
echo "$(pwd)/$1"
fi
... |
027b0b30988ce40b11d1f78f2345706d63643d3df6e566813dbe8fc7b18198eb | Shell | 5,723 | 264 | #!/bin/bash
#
# Validation functions library
# shellcheck disable=SC1091
# Load Generic Libraries
. /scripts/liblog.sh
# Functions
########################
# Check if the provided argument is an integer
# Arguments:
# $1 - Value to check
# Returns:
# Boolean
#########################
is_int() {
local -r int... |
bd781112c9a875f21f9418471f40fae0ee9fa311d24f87e660a9630cbe63c1e8 | Shell | 5,741 | 185 | #!/bin/bash
# Stitch files using ImageJ/Fiji plugin
# Author: David Young 2017, 2020
HELP="
Stitch files using ImageJ/Fiji plugin.
Arguments:
-h: Show help and exit.
-f [path]: Path to image file.
-j [path]: Path to custom JAVA_HOME for ImageJ/Fiji. If not given
empty, the JAVA_HOME environment variable wi... |
68a72fb1bee3d1972c6f65459523ecaa80bd642debed54a06702e96af71657b8 | Shell | 5,751 | 162 | # IMPORTANT: This script is outdated
# import setup
. "$(dirname $(realpath "$0"))/tests_setup.sh"
# This script is for manual testing only.
# It prompts the user with Synapse credentials
# And it expects certain assets to be already uploaded on Synapse
# overwrite some variables
MODEL_ADD="synapse:syn51089171"
MODEL... |
d10386dcdf4f8e1aab44b1efd0ad73bd0844b430a662e7d605ec91131db46225 | Shell | 5,821 | 140 | #!/usr/bin/env bash
# bump_version.sh — update version.py, commit, and tag a new emapper release.
#
# Usage:
# ./bump_version.sh [BUMP] [OPTIONS]
#
# BUMP types:
# pre — increment pre-release counter: 3.0.0-beta1 → 3.0.0-beta2
# if not currently on a pre-release, starts at label1: 3.0.0 → 3.0.0-... |
ecbb4436368a9e9ac0fad239307a0e40099222b59b456586bc282cce4187c736 | Shell | 6,008 | 177 | #!/usr/bin/env bash
#
# release-db.sh — publish a versioned eggnog-mapper DB set with manifest+checksum.
#
# Steps: validate source-dir → compress → sha256 + manifest.json + SHA256SUMS
# → upload (rsync or local) → re-fetch manifest from public URL and verify.
#
# Usage:
# scripts/release-db.sh \
# --db-ve... |
442cfc767baaebc4885e21acbfe6e254debe2a50f6d2ff1603b3e8fd6ad16757 | Shell | 6,018 | 163 | #!/bin/bash
#SBATCH --partition=imgcomputeq
#SBATCH --qos=img
# This specifies type of node job will use
#SBATCH --nodes=1
# This specifies job uses 1 node
#SBATCH --ntasks-per-node=1
# This specifies job only use 1 core on the node
#SBATCH --mem=4g
# This specifies maximum memory use will be 4 gigabytes
#SBA... |
5089085804e7ab1650a5689ae0bc641306e2f344f39ebe8d1cd95739ee07b3fa | Shell | 6,024 | 180 | #!/bin/bash
venv() {
if ! test -d "$1" ; then
if command -v virtualenv > /dev/null; then
virtualenv -p python3 "$1"
else
python3 -m venv "$1"
fi
fi
# shellcheck source=/dev/null
source "$1"/bin/activate
}
# Set these variables when running the script, e.g.:
# VERSION=v1.2 GIT_TARGET=ma... |
8b4b3af733db4c128fa14c1d99a6cf0e1788000672ad974789221750d892461c | Shell | 6,046 | 134 | #!/bin/bash
#SBATCH --partition=imgcomputeq
#SBATCH --qos=img
# This specifies type of node job will use
#SBATCH --nodes=1
# This specifies job uses 1 node
#SBATCH --ntasks-per-node=1
# This specifies job only use 1 core on the node
#SBATCH --mem=10g
# This specifies maximum memory use will be 4 gigabytes
#SB... |
9f1dde840115c7b5b4b658181ea753a228a580db8ad6ec75f9b61945a7539ba5 | Shell | 6,181 | 246 | #!/bin/bash
# Prepare a server the MagellanMapper pipeline
# Author: David Young 2018, 2023
HELP="
Sets up a server for processing files in the MagellanMapper pipeline.
Both initial setup and re-setup of existing servers is supported.
Arguments:
-d [/dev/name]: Set path of data device. If an empty string, data m... |
6304f5e0424e025a9b4eac5752bccc44e90d3e8d0c76e046f0a1d0be03570154 | Shell | 6,247 | 135 | #!/bin/bash -l
# Bash usage:
# ls -d C001*/job_00* | while read i; do prefix=$(echo $(dirname $i) | awk '{print tolower(substr($0, length($0)-3, 4))}')$(basename $i | sed 's|job||g'); if [ -f /disk3b/yzhang/traj75/${prefix}.nc ]; then echo "Skipping $prefix"; else echo "Processing: $prefix"; bash /MieT5/Nearl/script... |
bf8501722f9b1017d79fcd8cc1b1399a040f3f85208e8b2a28de9f3e9a68f80b | Shell | 6,263 | 139 | #!/bin/sh -ex
# Iterative sequence search workflow script
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
[ "$#" -ne 6 ] && echo "Plea... |
6214ed06413cf955f16300ce516164cb3ca905fb3e9807c16926783870f0bf75 | Shell | 6,451 | 184 | #!/bin/bash
#SBATCH --partition=imghmemq
#SBATCH --qos=img
# This specifies type of node job will use
#SBATCH --nodes=1
# This specifies job uses 1 node
#SBATCH --ntasks-per-node=1
# This specifies job only use 1 core on the node
#SBATCH --mem=10g
# This specifies maximum memory use will be 5 gigabytes
#SBATC... |
975b4332d7c4343ec674797ef1e270052649eae8aa7bb9bfac4e8d9cef685d4c | Shell | 6,654 | 212 | ## Internal script for compiling and packaging DMG and EXE
## Compiles with appropriate properties file depending on if
## -b flag is set (if set, compile for BCM)
## Set the two globals at the top for your system
#!/bin/bash
set -e
shopt -s extglob
## GLOBALS: Set for your system
# executable for launch4j, which bun... |
3ae0273e52c17b3cba42fadb20e2f003ab7f1207ee3aece2ee49da9182a64c74 | Shell | 6,666 | 212 | while getopts ":d:" opt
do
case "$opt" in
d ) parameterD="$OPTARG" ;;
? ) helpFunction ;; # Print helpFunction in case parameter is non-existent
esac
done
############################## Prep #################################
plink_file=$parameterD
# Set up folders and logging process -----... |
d2ebb91a3d7d655926422cb2279bb82274e154c4b88f598c2b905d9e621b0933 | Shell | 6,677 | 150 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
if notExists "${TMP_PATH}/input.dbtype"; then
# shellcheck disable=SC2086
"$MMSEQS" createdb "$@" "${TMP_PATH}/input" ${CREATEDB_PAR} \
|| fail "query createdb died"
fi
if notExists "${TMP_PATH}/clu.dbtype"; the... |
ee22fc0d684338b4f98101576cf88ad5355fcb9f2fe9fbec902390b580d9e1d4 | Shell | 7,188 | 198 | # import setup
. "$(dirname $(realpath "$0"))/tests_setup.sh"
##########################################################
################### Start Testing ########################
##########################################################
##########################################################
echo "==============... |
1ceb511858215923f680eacedf33a4b3af467664798de63e9c0e7b8f7e77e67e | Shell | 7,366 | 171 | #!/bin/bash
#
# Process data of different neck positions (extension, flexion and straight).
#
# Usage:
# ./process_data.sh <SUBJECT>
#
# Manual segmentations and labels (discs, PMJ, nerve rootlets) should be located under:
# PATH_DATA/derivatives/labels/SUBJECT/anat/
#
# Authors: Sandrine Bédard
set -x
# Immediatel... |
4bc238ba8e3f781565616c461489e3315a98b03115a182593e566a2f0cab3fa3 | Shell | 7,428 | 170 | set -eo pipefail
####################################################
#################### Config ########################
####################################################
# Project ID
export PROJECT_ID="project_id"
# User email (the GCP email address of the user who will be using MedPerf)
export USER_EMAIL="user... |
7c0714c6690578b21b8831bb220734a5460303c8f1992f3d410715575b5adc3c | Shell | 7,456 | 234 | #!/bin/bash
#set -x
#set -e
# script to run shiny app in the beginning
# How to run
# cd <project_dir>
# bash scripts/run_shiny_analysis.sh
# Examples:
# bash scripts/run_shiny_analysis.sh
# <project_dir> is where the fastq and outputs directory are
# project directory where the fastq and outputs directory are
#
# to r... |
44ab1c9cc3c220e6a91ba8b7adf5c058ea1f54034c317810e5ec0eb50b093c76 | Shell | 7,626 | 40 | PARTITION=$1
echo 'configs/hrnet/fcn_hr18s_512x512_160k_ade20k.py' &
GPUS=4 GPUS_PER_NODE=4 CPUS_PER_TASK=2 ./tools/slurm_train.sh $PARTITION fcn_hr18s_512x512_160k_ade20k configs/hrnet/fcn_hr18s_512x512_160k_ade20k.py --cfg-options checkpoint_config.max_keep_ckpts=1 dist_params.port=24727 --work-dir work_dirs/hrnet... |
f1c08472c509c77e5894f4373ee7e63365b76c52b48be5677759acfcbdbb3d47 | Shell | 8,199 | 270 | #! /bin/sh
# Make sure all these programs work properly
# when invoked with --help or --version.
# Copyright (C) 2000-2016 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 Fo... |
4aa18ea0ee95268e488e948fd6d15768352972531fa1f42ec9ce742020e36d0e | Shell | 8,257 | 208 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
hasCommand () {
command -v "$1" >/dev/null 2>&1 || { echo "Please make sure that $1 is in \$PATH."; exit 1; }
}
abspath() {
if [ -d "$1" ]; then
(cd "$1"; pwd)
elif [ -f "$1" ]; then
if [ -z "${1##*/*}"... |
9d0cd0a5134b89271b4bf60be72e1c1383e1ef9d35361ce8936841f4cdd34031 | Shell | 8,423 | 137 | #!/usr/bin/env bash
if [ $# -ne 2 ]; then
exit 1;
fi
# argument parsing
filename=$1
URL=$2
echo -e "\n${filename}: Checking URL ${URL}..."
###############################################################################
# Run `curl` to resolve URLs and status code #
##############... |
66f5da678c69350023bd1d7e08b80e4f4053f63396144298f2bc4b3d0ff68606 | Shell | 8,673 | 100 | #!/bin/bash
# RNAseq WT hiPSC
computeMatrixOperations relabel -m FL_L1PAs_WT_hiPSC_positive.mtx --groupLabels L1HS L1PA2 L1PA3 L1PA4 -o FL_L1PAs_WT_hiPSC_positive_relabel.mtx
computeMatrixOperations relabel -m FL_L1PAs_WT_hiPSC_reverse.mtx --groupLabels L1HS L1PA2 L1PA3 L1PA4 -o FL_L1PAs_WT_hiPSC_reverse_relabel.mtx
... |
161d854da3562eb3f4ac1a3e7434aa9765e213208098029948fbc2d936d851a9 | Shell | 8,702 | 282 | while getopts "d:" opt
do
case "$opt" in
d ) parameterD="$OPTARG" ;;
? ) helpFunction ;; # Print helpFunction in case parameter is non-existent
esac
done
plink_file=$parameterD
# Set up folders and logging process ------------------------------------
mkdir -p PRS
if [ ! -f "PRS/log.txt" ]
then
... |
c7fc03a8cbdc0d7257e81566ecf48de8a56202e225380f6351332bd3e6e94d97 | Shell | 8,715 | 187 | #!/bin/bash
#
# Process data of different neck positions (extension, flexion and straight).
#
# Usage:
# ./process_data.sh <SUBJECT>
#
# Manual segmentations and labels (discs, PMJ, nerve rootlets) should be located under:
# PATH_DATA/derivatives/labels/SUBJECT/anat/
#
# Authors: Sandrine Bédard
set -x
# Immediatel... |
47fca03774db588b39ea7ae198231ba731b281a3002901357b9b68342c58f49a | Shell | 8,747 | 41 | PARTITION=$1
CHECKPOINT_DIR=$2
echo 'configs/hrnet/fcn_hr18s_512x512_160k_ade20k.py' &
GPUS=4 GPUS_PER_NODE=4 CPUS_PER_TASK=2 tools/slurm_test.sh $PARTITION fcn_hr18s_512x512_160k_ade20k configs/hrnet/fcn_hr18s_512x512_160k_ade20k.py $CHECKPOINT_DIR/fcn_hr18s_512x512_160k_ade20k_20200614_214413-870f65ac.pth --eval m... |
983b2c39372ea65e0fc513293602f04ad9063fb56e48f23f93d46186f68eb286 | Shell | 8,775 | 189 | #!/bin/bash
#
# Process data of different neck positions (extension, flexion and straight).
#
# Usage:
# ./process_data.sh <SUBJECT>
#
# Manual segmentations and labels (discs, PMJ, nerve rootlets) should be located under:
# PATH_DATA/derivatives/labels/SUBJECT/anat/
#
# Authors: Sandrine Bédard
set -x
# Immediatel... |
b2ce22d173e55b9ec825af0910bf0f7dbb202877816f2c2cfa5bf4d12eb080a0 | Shell | 9,053 | 187 | #!/bin/bash
#
# Process data of different neck positions (extension, flexion and straight).
#
# Usage:
# ./process_data.sh <SUBJECT>
#
# Manual segmentations and labels (discs, PMJ, nerve rootlets) should be located under:
# PATH_DATA/derivatives/labels/SUBJECT/anat/
#
# Authors: Sandrine Bédard
set -x
# Immediatel... |
389fd9f54926f412675c20fbb605b844f7502aca182f8618192b5dbc5d7af7d4 | Shell | 9,062 | 231 | #!/bin/sh
sambamba=$1
if [ ! -f $sambamba ]; then
sambamba=./bin/sambamba
fi
opts="-q --DRT-testmode=run-main"
outdir=output
mkdir -p $outdir
md5sum=`which md5sum`
[ -z $md5sum ] && md5sum="md5 -r " # for OSX
# Name sorted and pos sorted
nsortedbam=$outdir/ex1_header.nsorted.bam
sortedbam=$outdir/ex1_header.sor... |
584727cec7a4850b4130388bf4e40cdbb01eac7e4fea75d2638bf8a3ac260bbc | Shell | 9,071 | 219 | #! /bin/sh
while getopts s:d:c:ft:rl: flag; do
case "${flag}" in
s) SERVER_URL=${OPTARG} ;;
d) DIRECTORY=${OPTARG} ;;
c) CLEANUP="true" ;;
f) FRESH="true" ;;
t) TIMEOUT=${OPTARG} ;;
r) RESUME_TEST="true" ;;
l) TEST_FROM_LINE=${OPTARG} ;;
esac
done
SERVER_URL="${SERVER_URL:-https://localhost:8000}"
DI... |
b07f6301afe1aff79f048e8a993dd3e07a4e0fab6a174c3a26d476b1ac9337e4 | Shell | 9,289 | 199 | #!/bin/bash
#
# Process data of different neck positions (extension, flexion and straight).
#
# Usage:
# ./process_data.sh <SUBJECT>
#
# Manual segmentations and labels (discs, PMJ, nerve rootlets) should be located under:
# PATH_DATA/derivatives/labels/SUBJECT/anat/
#
# Authors: Sandrine Bédard
set -x
# Immediatel... |
b286626bcf51d0e99680a54966dcd08d881f97f7200e5923148baadb3b56a6c5 | Shell | 9,338 | 296 | #!/bin/bash
# script to trim fastq files and run quality control
# How to run:
# cd <project_dir>
# bash scripts/run_trim_qc.sh &> run_trim_qc.out &
# DO NOT change the name or location of run_trim_qc.out
# Examples:
# cd project1
# bash scripts/run_trim_qc.sh &> run_trim_qc.out &
#
# or to run with specific time limi... |
444cda1d81db08975b26ef3c36be7280e97f035b8e31bc23dd972beef0a6a5f5 | Shell | 9,366 | 235 | #!/bin/bash
module load bedtools
module load samtools
BAM_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/Four_DN/batch_2/sorted_bams/filese_renamed_adjusted"
PEAK_DIR="/cluster/projects/epigenomics/Aminnn/CNR/EpigenomeLab/EPI_P003_CNR_MM10_07172022/Four_DN/batch_2/sorted_bams/... |
fbd6608d4eff8fcecfdca2775cac8d40c74bc942b48f3f323db8126acf26494b | Shell | 9,420 | 270 | #!/bin/bash -e
############################################################################
# @ Filename : setup.sh
# @ Description : Setup the experimental environment
# @ Arguments :
# @ Date :
############################################################################
. config/config_setup_lo... |
6b293b6aae86bfeae80114f734d43106763e4f0e28ec8f58470302808cffad07 | Shell | 9,669 | 250 | #!/usr/bin/env bash
######################################
#
# dependencies and versions tested:
# umi_tools 1.0.0
# samtools 1.9
# cutadapt 2.5
# STAR 2.6.1b
# GNU Awk 5.0.0
# FastQC 0.11.8
# multiQC 1.7
# mix-square 1.4.0.1
#
# last change: 15/01/2021
#
############... |
525c7d5bace903b015f737cb21e9501fd5fea38258dc9293266b92b4082927d5 | Shell | 9,672 | 261 | # import setup
. "$(dirname $(realpath "$0"))/tests_setup.sh"
##########################################################
################### Start Testing ########################
##########################################################
echo "====================================="
echo "Retrieving mock dataset"
ech... |
9edde5fd046776e29b5564dfe77c6015a73c98ff952a47c7c367ad5d6966db49 | Shell | 9,821 | 206 | #!/usr/bin/env bash
# Declare an associative array
declare -A myArray=(
["task-narratives_acq-mb8_run-01"]=967
["task-narratives_acq-mb8_run-02"]=1098
["task-narratives_acq-mb8_run-03"]=1298
["task-narratives_acq-mb8_run-04"]=1156
["task-social"]=872
["task-fractional_acq-mb8_run-01"]=1323
["task-fractional_acq-mb8_run... |
ab4e07fdfe03d194b29b6fba8eb5d269b98e9ddde58054f3b21cff90c1348c36 | Shell | 9,920 | 200 | # Declare an associative array
declare -A myArray=(
["task-narratives_acq-mb8_run-01"]=967
["task-narratives_acq-mb8_run-02"]=1098
["task-narratives_acq-mb8_run-03"]=1298
["task-narratives_acq-mb8_run-04"]=1156
["task-social"]=872
["task-fractional_acq-mb8_run-01"]=1323
["task-fractional_acq-mb8_run-02"]=1322
["task-sh... |
e276e5ab9060ee99992589603816061bad553ddbe9680125453aad1269384b78 | Shell | 10,036 | 268 | # import setup
. "$(dirname $(realpath "$0"))/tests_setup.sh"
##########################################################
################### Start Testing ########################
##########################################################
##########################################################
echo "==============... |
fcdc457bedfe469ad7557b6ef1b3ae6cbf53f7aaaff477cfba785fa2af330daf | Shell | 10,040 | 315 | #!/bin/bash
# script to trim fastq files and run quality control
# How to run:
# cd <project_dir>
# bash scripts/run_trim_qc.sh &> run_trim_qc.out &
# DO NOT change the name or location of run_trim_qc.out
# Examples:
# cd project1
# bash scripts/run_trim_qc.sh &> run_trim_qc.out &
#
# or to run with specific time limi... |
3470659d950dd007e24dcfd09b0940c051960d08f5b7bf56378702fdf31ae397 | Shell | 10,496 | 315 | #!/bin/bash
# script to create genome STAR index
# How to run:
# cd <my_project_dir>
# bash scripts/run_star_index.sh &> run_star_index.out &
# DO NOT change the name or location of run_star_index.out
# Examples:
# cd ~/project1
# bash scripts/run_star_index.sh &> run_star_index.out &
#
# or to run with specific time ... |
104419a1a120b320c98d596f46c0f118f9310d764d91b8ec0c84fbb548b4f466 | Shell | 10,644 | 209 | #!/usr/bin/env bash
# Declare an associative array
declare -A myArray=(
["task-narratives_acq-mb8_run-01"]=967
["task-narratives_acq-mb8_run-02"]=1098
["task-narratives_acq-mb8_run-03"]=1298
["task-narratives_acq-mb8_run-04"]=1156
["task-social"]=872
["task-fractional_acq-mb8_run-01"]=1323
["task-fractional_acq-mb8_run... |
be6e9b604b517572d018cd3137e7cb1454904a3c6f1f50275f642228f83815bd | Shell | 10,680 | 333 | #!/bin/bash
# How to run
# cd <project_dir>
# bash scripts/run_differential_analysis_rna.sh &> run_differential_analysis_rna.out &
# DO NOT change the name or location of run_differential_analysis_rna.out
# Examples:
# bash scripts/run_differential_analysis_rna.sh &> run_differential_analysis_rna.out &
#
# or to chang... |
21f0aa472d6164be2f643c071272e550b327768c10aec08f9346f8314ddc4847 | Shell | 10,820 | 322 | #!/bin/bash
# script to create genome STAR index
# How to run:
# cd <my_project_dir>
# bash scripts/run_star_index.sh &> run_star_index.out &
# DO NOT change the name or location of run_star_index.out
# Examples:
# cd ~/project1
# bash scripts/run_star_index.sh &> run_star_index.out &
#
# or to run with specific time ... |
577ef4efa6fab1b865d06688e8b392b5f1c70a342a0815a3c695566271da6b14 | Shell | 10,858 | 254 | #!/usr/bin/env bash
# Sample commands for MagellanMapper tasks
# Author: David Young, 2020
# WARNING (2020-09-18): We are brainstorming ways to reorganize the sample
# scripts with the goal of exposing MagellanMapper functionality, keeping
# commands up to date, and minimize setup required by the user. Any and all
# f... |
65b9a6349d3171ee3c1ec84d31e5294a0adf2784262d79d15122f511cfebed66 | Shell | 11,036 | 345 | #!/bin/bash
# How to run
# cd <project_dir>
# bash scripts/run_differential_analysis_rna.sh &> run_differential_analysis_rna.out &
# DO NOT change the name or location of run_differential_analysis_rna.out
# Examples:
# bash scripts/run_differential_analysis_rna.sh &> run_differential_analysis_rna.out &
#
# or to chang... |
6dd6dcef85c576d7ae9732afecf6bec4bfebc090a0a3ea5771497ecc3a16014d | Shell | 11,407 | 263 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
log() {
if [ "${VERBOSITY}" = "-v 3" ]; then
echo "$@"
fi
}
abspath() {
if [ -d "$1" ]; then
(cd "$1"; pwd)
elif [ -f "$1" ]; then
if [ -z "${1##*/*}" ]; then
echo "$(cd "${1... |
3bf597b369f348d8531fdaf2852ef7db9f5994a151d7dc9db58102ba354b2021 | Shell | 11,925 | 186 | # Commands for Illumina BaseSpace Sequence Hub command line interface (CLI)
cd ~
# authenticate account
$HOME/bs auth --api-server https://api.aps2.sh.basespace.illumina.com
# get config details
$HOME/bs load config
#export BASESPACE_API_SERVER="https://api.aps2.sh.basespace.illumina.com"
#export BASESPACE_ACCESS_T... |
12aaf6afbd41abc07d6b3ebbadfcb1ef4e847d2c5f76e358be3c343bfb4951d6 | Shell | 11,970 | 372 | set -o errexit
gpu=1;
version="01";
iter="no";
dataset="okvqa";
model_size="large";
stream=1;
use_fact="no";
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_frequ... |
8f0d5e0df6501c3937817837a93c2e651e1e6435168ee742ce0b51bf50dba09e | Shell | 12,173 | 274 | set -eo pipefail
####################################################
#################### Config ########################
####################################################
# Project ID
export PROJECT_ID="project_id"
# User email (the GCP email address of the user who will be using MedPerf)
export USER_EMAIL="user... |
85ddfb08c59eac3e9df653b50116ab8fdb086a0d79c40521800af25b8e927bc3 | Shell | 12,198 | 275 | set -eo pipefail
####################################################
#################### Config ########################
####################################################
# Project ID
export PROJECT_ID="project_id"
# User email (the GCP email address of the user who will be using MedPerf)
export USER_EMAIL="user... |
f520d40adeeb457a92a8130fdc6d7a4c4800492ca91af1855316bbf2c85fadb2 | Shell | 12,347 | 425 | #!/usr/bin/env bash
# Bash library functions for MagellanMapper
# Author: David Young 2018, 2020
############################################
# Backup a file or directory if necessary.
# Globals:
# NONE
# Arguments:
# 1: Path of file/directory to back up. The backed up file will have the
# same name with th... |
698f5a5b2f2b0a13abd39d567b5b714b5256aa6b5ab4a8b2d097b6d17f05fb3e | Shell | 13,106 | 555 | #!/bin/bash
#
# Library for operating system actions
# shellcheck disable=SC1091
# Load Generic Libraries
. /scripts/liblog.sh
. /scripts/libfs.sh
. /scripts/libvalidations.sh
# Functions
########################
# Check if an user exists in the system
# Arguments:
# $1 - user
# Returns:
# Boolean
#############... |
f0cfd498f51db77c0b8208bc840abf9514f99ea507912e97171dbebdb238c156 | Shell | 13,977 | 325 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
[ "$#" -ne 3 ] && echo "Please provide <sequenceDB> <outDB> <tmp>" && exit 1;
# check if files exist
[ ! -f "$1.dbtype" ] && echo "$1.dbtype not found!" && exit 1;
[ -f "$2.dbtype" ] && echo "$2.dbtype exists already!" && exit 1;... |
58b1e5530f7dac8efe46a9aa61bed890d7e8238efe7fd8f23248c4fe9cb43861 | Shell | 14,020 | 156 | #!/bin/bash
#SBATCH -A bbse-delta-gpu
#SBATCH --partition=gpuA100x4
#SBATCH --gpus=1
#SBATCH --nodes=1
#SBATCH --tasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=60g
#SBATCH --time=8:00:00
SIF=/work/hdd/bbse/wklai/AdversarialData/Adversarial_Observation/manuscripts/POISON26/singularity/pytorch-captum.sif
cd /work/hdd/b... |
04cd62af6f24e40a4a852ea5a7d189d5d892bbbefe322eba1614158a27a6cf08 | Shell | 14,618 | 128 | python -u train.py Chinatown UCR --loader UCR --batch-size 8 --repr-dims 320 --max-threads 8 --seed 42 --eval
python -u train.py SonyAIBORobotSurface1 UCR --loader UCR --batch-size 8 --repr-dims 320 --max-threads 8 --seed 42 --eval
python -u train.py ItalyPowerDemand UCR --loader UCR --batch-size 8 --repr-dims 320 --ma... |
d4491cd8c5c2fc16dad23d13c6990fcb3eb44478bda4147299cec49a7889ce99 | Shell | 14,925 | 365 | #!/bin/bash
# We want job control to optionally start Celery in parallel.
set -m
# Remove quotes around a string
sanitize() { echo "$1" | sed "s/^[\"']\?\(.*[^\"']\)[\"']\?$/\1/"; }
# Get environment configuration or use defaults if unavailable.
DB_HOST=$(sanitize "${DB_HOST:-localhost}")
DB_PORT=$(sanitize "${DB_PO... |
2a7e744d54eb8b68072a17466b21ed6cb37a0255e811c1c7d9869489fc430906 | Shell | 15,313 | 399 | # import setup
. "$(dirname $(realpath "$0"))/tests_setup.sh"
##########################################################
################### Start Testing ########################
##########################################################
##########################################################
echo "==============... |
f406fc9117c6e9ccd78752697e80ce726b0c5fabf05df08fcb30216a587e68ae | Shell | 15,460 | 423 | #!/bin/bash
#
# NCP processing pipeline
# Gregory Way, 2019 (adapted by Shantanu Singh)
#
# Instructions to generate cell painting profiles for the NCP pilot experiments
# Pipeline generated using the profiling handbook:
# https://cytomining.github.io/profiling-handbook/
############################
# Step 1 - Con... |
f47046f651bdd7f12802dc0a6d9c4a657110bccabcad5fc9ccdf177fbf66b408 | Shell | 15,918 | 430 | #!/bin/bash
# print linenumber when set -x is set
export PS4='+${LINENO}:${BASH_SOURCE}: '
# script connecting all the individual scripts to do full rnaseq analysis
# How to run
# cd <project_dir>
# bash scripts/run_rnaseq_full.sh &> run_rnaseq_full.out &
# DO NOT change the name or location of run_rnaseq_full.out
# ... |
4030d460c93b0bd724f0c5266f6cabea46c043838e8e6f0e38dfe74b81acf9c8 | Shell | 16,327 | 444 | #!/bin/bash
# print linenumber when set -x is set
export PS4='+${LINENO}:${BASH_SOURCE}: '
# script connecting all the individual scripts to do full rnaseq analysis
# How to run
# cd <project_dir>
# bash scripts/run_rnaseq_full.sh &> run_rnaseq_full.out &
# DO NOT change the name or location of run_rnaseq_full.out
# ... |
e8f4b47f76ee96cd9155b8083003d7b49788796fb5de7084f316a70d00f5bdf2 | Shell | 16,422 | 411 | # import setup
. "$(dirname $(realpath "$0"))/tests_setup.sh"
##########################################################
################### Start Testing ########################
##########################################################
##########################################################
echo "==============... |
5bb29ed38b1d8749803f82ab2b59ba77fc440c920b5afe49fbc27ba514cb9fed | Shell | 17,586 | 361 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
abspath() {
if [ -d "$1" ]; then
(cd "$1"; pwd)
elif [ -f "$1" ]; then
if [ -z "${1##*/*}" ]; then
echo "$(cd "${1%/*}"; pwd)/${1##*/}"
else
echo "$(pwd)/$1"
fi
el... |
7e5bb2a8eedfa273a71a355a8cb8e5f492568cd22e82e71f52047ebf131c3125 | Shell | 19,515 | 571 | #!/bin/bash
# How to run:
# cd <project_dir>
# bash scripts/run_align_create_tracks_rna.sh &> run_align_create_tracks_rna.out &
# DO NOT change the name or location of run_align_create_tracks_rna.out
# Examples:
# cd project1
# bash scripts/run_align_create_tracks_rna.sh &> run_align_create_tracks_rna.out &
#
# by def... |
371c6eebb1ade743ac8464482b65a776f35f395b5bef52d8df5fceb9ec2afb44 | Shell | 19,595 | 543 | # import setup
. "$(dirname $(realpath "$0"))/tests_setup.sh"
##########################################################
################### Start Testing ########################
##########################################################
##########################################################
echo "==============... |
d681d6e7a8edbdee0434c80b5cbdc3a48fa980d0f34ce646073d5b3ec68c5118 | Shell | 19,982 | 616 | # source this file; set up for tests
# 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 Foundation, either version 3 of the License, or
# (at your opt... |
014a4060ca1c7635c4a3bb6d7db8f7b21fa42ea6b68bd20b4227c08b4c19ff5f | Shell | 20,263 | 597 | #!/bin/bash
# How to run:
# cd <project_dir>
# bash scripts/run_align_create_tracks_rna.sh &> run_align_create_tracks_rna.out &
# DO NOT change the name or location of run_align_create_tracks_rna.out
# Examples:
# cd project1
# bash scripts/run_align_create_tracks_rna.sh &> run_align_create_tracks_rna.out &
#
# by def... |
49ad4646929f681c61a6a9e8e41de3a876afc238c5ef19e6a3001d341c9f4c55 | Shell | 22,103 | 593 | #!/bin/bash
# This is a rather minimal example Argbash potential
# Example taken from http://argbash.readthedocs.io/en/stable/example.html
#
# ARG_OPTIONAL_BOOLEAN([push],[],[Push the containers])
# ARG_OPTIONAL_BOOLEAN([pull],[],[Pull upstream images. Might be time-consuming to rebuild everything.])
# ARG_OPTIONAL_BO... |
40e4f6f04dbca2b58b07336a4ebd30c52daf229860f01cc32dab3b6433f534dd | Shell | 23,112 | 751 | #!/bin/bash
# MagellanMapper pipelines script
# Author: David Young 2017, 2020
HELP="
Run MagellanMapper pipelines. Choose various pathways from simple viewing to
stitching and full volumetric image detection.
Note that currently not all options are settable through at
command-line and will need to be set manually ... |
1a80913df22acf37d6b1aae621dfb7b3840c9fa42abb80b23bee62b589f2bc74 | Shell | 23,736 | 587 | # import setup
. "$(dirname $(realpath "$0"))/tests_setup.sh"
##########################################################
################### Start Testing ########################
##########################################################
##########################################################
echo "==============... |
903231a1151aa7ab5401dc38e0771b1b6027ea56a07f03bb3cbb2dc266b795ab | Shell | 25,628 | 540 | #!/bin/sh -e
fail() {
echo "Error: $1"
exit 1
}
notExists() {
[ ! -f "$1" ]
}
hasCommand () {
command -v "$1" >/dev/null 2>&1
}
ARR=""
push_back() {
# shellcheck disable=SC1003
CURR="$(printf '%s' "$1" | awk '{ gsub(/'\''/, "'\''\\'\'''\''"); print; }')"
if [ -z "$ARR" ]; then
ARR... |
100c79eb4a1c04e175f2d0bcc7ad5008e42f943599695274538a8ba898a8f5d9 | Shell | 25,735 | 669 | # import setup
. "$(dirname $(realpath "$0"))/tests_setup.sh"
##########################################################
################### Start Testing ########################
##########################################################
##########################################################
echo "==============... |
8f9138635a46245a7f91402b1ce96590a540e4b6e1b37f05f50b61f828bad656 | Shell | 31,248 | 941 | #!/bin/sh -e
die() {
$ECHO "$@" 1>&2
exit 1
}
roundTripTest() {
if [ -n "$3" ]; then
cLevel="$3"
proba="$2"
else
cLevel="$2"
proba=""
fi
if [ -n "$4" ]; then
dLevel="$4"
else
dLevel="$cLevel"
fi
rm -f tmp1 tmp2
$ECHO "roundTripTe... |
c2514a3897fb2b9e5fbf497bfbb4136946c0f11267e308d5ded19586e88725fb | Shell | 35,406 | 588 | #!/bin/bash
#
# Example of commands to process multi-parametric data of the spinal cord
# For information about acquisition parameters, see: www.spinalcordmri.org/protocols
#
# Notes:
# - Many of the commands in this script are commented out (start with "# "). These commands won't be run by default,
# as many of ... |
2b060a5ac1ede711bc87a3a441892ed77e2e20bc579dd44ed60ab0c90d3c8f3a | Shell | 44,218 | 788 | #!/bin/bash
# Run first script/function of CICADA
# NOTE: make sure your version of FSl is creating .nii.gz files before opening Matlab and running any scripts.
# e.g.,: in bash_profile:
# FSLOUTPUTTYPE=NIFTI_GZ
# export FSLOUTPUTTYPE
# immediately exit upon common error
set -euo pipefail
echo
usage(){
>&2 cat << E... |
ebd75f830a47b2d7bdbba51f1308917efe8a0dda08750c33adbee3f51600f86a | Stan | 2,161 | 63 | data {
int n;
int n_subject;
int n_bins;
int<lower=0, upper=1> choice[n];
int subject[n];
vector[n] avg_outcome;
vector[n] avg_accuracy;
int bin_b_subject[n_bins];
int trial_bin1_b[n];
int trial_bin2_b[n];
vector[n] trial_bin1_b_p;
vector[n] trial_bin2_b_p;
}
parameters {
re... |
aee3a1e0f8461c269794b733341a68aa154865e28d7100a76118b1ebc8585084 | Stan | 4,581 | 92 | data {
int n;
int n_subject;
int n_bins_learning;
int n_bins_decision;
int<lower=0, upper=1> choice[n];
int subject[n];
vector[n] avg_outcome;
vector[n] avg_accuracy;
int bin_b_subject_learning[n_bins_learning];
int bin_b_subject_decision[n_bins_decision];
int trial_bin11_learning_b[n];... |
2cddeef8c0e97569efe864ad9310759dbed54549de4e5819878ae49d22ddcece | Text | 7 | 1 | # FAHMM |
55e6cf47f96f3fb37f6faae02f511b56691d321595177795c26e1568c8c1313f | Text | 13 | 1 | # Rescreener
|
0f5bd742559d52ce555d09d669e6b5916b7928c00d9671dbf4eb5ed6d960cac7 | Text | 24 | 2 | # C_P
Averaged MEG data
|
6fbb0384bd6ddfdbfe77f4e4d10fea3fb2b03d78afb14c175ee4e9d848dbda45 | Text | 24 | 1 | # Notch3_retina_software |
dc7df6aa3e954fe0d7aea49e93ace2669be3c6a93374e28febe05ff632eff68d | Text | 25 | 1 | this is work for mspaths
|
a1443dc64fc7650a3bed33c90c8320b697915493635b563f4127f92fa1f53e38 | Text | 26 | 1 | # Synapse_OneColorLineScan |
c6fecfe22d090917c0ce5d72ca12348b851cb1e828b966ce2f551368af25cb13 | Text | 43 | 2 | # FiberPhotometry
Fiber photometry scripts
|
c869c1eac50fef146ee1c477147ea2554e457fbfe85ff2116ddf2df3c0857862 | Text | 68 | 1 | Minimal implementation of a MACE model for hydrogenating molecules.
|
962fa84bece0bee01a890f59b9c91e64468db6736d165757bb154d660d9cef28 | Text | 77 | 2 | # hypodetect
Photoacoustic perinatal hypoxia detection with SSS localization
|
b3bae82ef2bad88dca1ea8affab54e2b6e76f98a346035f6571add959e0e060f | Text | 77 | 2 | # EsophagealPeristalsisModel
Mathematical model of human esophageal motility
|
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