sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
cbd5cafd9d72e99f31235114307f92419b6ebc8888715945159e5ce64452fc1a | Shell | 4,538 | 89 | #!/bin/bash
# parse command-line arguments
if [ $# -ne 3 ]; then
echo Usage: $(basename "$0") assembly.fa input_fusions.tsv output_fusions.vcf
echo
echo "Description: This script converts fusion predictions from Arriba's custom tab-separated format to the standards-compliant VCF 4.3 format."
echo "Note: If a FastA... |
14390d3b292d431e9c0898f8e9b6b38af5f3dbe33f42a5923fdb2a85b92846ac | Shell | 4,551 | 62 | RAW_DIR="pdbs_raw"
CHAINS_DIR="pdbs_chains"
MISSING_AA_DIR="missing_aa"
# Step 1: Obtaining a list of proteins that satisfy our criteria.
## We obtained the list of proteins from the work by Kosciolek & Jones, PLOS One, 2014(https://doi.org/10.1371/journal.pone.0092197).
## 150 diverse globular proteins, with each pr... |
83d5096ccf8bdd5401fa8c72e6eff83dbd47db2dc34e1da6c4c557832665f6ec | Shell | 4,585 | 51 | #!/bin/bash
#$ -o /cbica/home/nishiom/qsub_output
#$ -l h_vmem=15G,s_vmem=15G
# based on https://github.com/timhartung/T1T2/blob/main/T1T2_script.sh
project_dir=/cbica/home/nishiom/202406_paper_T1T2/dataset/structural
sub=$1
ses=$2
T1coef=$3
T1sep=$4
T2coef=$5
T2sep=$6
# Calibration + create T1T2
#if ! [ -f ${project... |
8b422017f0992d1e8291139fc1586b19a5d093669a37c1759f57abf635698f81 | Shell | 4,585 | 111 | #!/bin/bash
# multi-resolution registration (MRR), using ANTs, to combine AXI+SAG+COR scans into one
# (the script was run on a server via SLURM)
# for details, see: https://direct.mit.edu/imag/article/doi/10.1162/IMAG.a.930
# František Váša, frantisek.vasa@kcl.ac.uk
# data directory
hype_dir=[path_to_folder]/HYPE ##... |
b8ac25398cb12769a8f2cd6575373dbdaa4eab1f156473ec57e145b82aba56e2 | Shell | 4,607 | 47 | #!/bin/bash
set -euo pipefail
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=${THREADS_PER_COMMAND:-$(nproc)}
movingfile=$1
fixedfile=$2
outputdir=$3
shift 3
fixedmask=$(dirname ${fixedfile})/$(basename ${fixedfile} _t1.nii.gz)_mask.nii.gz
movingmask=$(dirname $movingfile)/$(basename $movingfile _t1.nii.gz)_mask.nii.gz... |
71448b97a489070f1f92f8569cb4d80de0edc8799889916edd59349d951f5c55 | Shell | 4,628 | 115 | #!/bin/bash
# This script is used to register a T1 registration image with the helmet
# registration image. It performs the following steps:
# 1. Uses the 'bet' command to create a brain mask. Note, this may require setting
# the coordinates for the centre of the brain using the -c flag.
# 2. Inverts the brain... |
d709c11262d891a03aef0c41ada6f2d1f0216d24015010404072caf8664aef03 | Shell | 4,674 | 10 | #!/bin/bash
# usage: ./3dresample_mask.sh
# description: resamples brain mask to Wbgrndkm_func.nii.gz space
# author: amar ojha
# date: 20240821
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_20191011 10997_20180818... |
64f92b468a897a30806488034540b0ba93d2d7a163d5fc49fead2c730cd3ec10 | Shell | 4,675 | 207 | #!/bin/bash
##
## RNA-seq differential gene expression using DESeq2
##
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
route_name=${script_name/%.sh/}
echo -e "\n ========== ROUTE: $route_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 1 ] ; the... |
f5ff8ea8c73c742fc771382798e45f1ca791065e4bc8cb71363db3d3f212decc | Shell | 4,675 | 74 | ## The Wang et al. data object was processed with scRNAbox: https://github.com/neurobioinfo/scrnabox
############################################################################ Step 0
############################################################################
#########################################################... |
cdf1a361b732ca4f945fef34db2b07f35017af44181d4ea933c4deddd3172bc0 | Shell | 4,680 | 127 | #!/bin/sh
# Copyright (c) 2023 MIT Laboratory for Computational Physiology
# Copyright (c) 2021 Thomas Ward <thomas@thomasward.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without... |
6da3a0a47a90a7cad6dea59369f995fe10ce77a3d01687bf0c4b8cc298119e7f | Shell | 4,703 | 74 | ## The Kamath et al. data object was processed with scRNAbox: https://github.com/neurobioinfo/scrnabox
############################################################################ Step 0
############################################################################
#######################################################... |
7222daa10deca23d14d188f80980c8860c7435145067e3dd5328c6c534d339ff | Shell | 4,703 | 74 | ## The Smajic et al. data object was processed with scRNAbox: https://github.com/neurobioinfo/scrnabox
############################################################################ Step 0
############################################################################
#######################################################... |
0b3121efbd13ef3fe45bc05fde7bf7bead25b99c037a0d77325d099193ea7a2f | Shell | 4,719 | 113 | module purge
module load singularity/3.6.0
module use /projects/community/modulefiles/
module load connectome_wb/1.3.2-kholodvl
FSLDIR=/projects/f_mc1689_1/AnalysisTools/fsl
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh
####
subj=$1
subj=${subj}_V1_MR
projectDir=/projects/f_mc1689_1/R... |
44c575132a3ceb1b148d87e4e6b8785345c50d03f0def8a8c2a793c2194c4c25 | Shell | 4,746 | 145 | #!/bin/bash
# Siwei 10 May 2021
# customise code for genres01
# Siwei 20 Dec 2019
# updated WASP to 0.3.4 (30 Apr 2019)
# Set these environment vars to point to
# your local installation of WASP
export OMP_NUM_THREADS=1
WASP="/home/zhangs3/Data/Tools/WASP"
jre_8="/home/zhangs3/Data/Tools/jre1.8.0_291/bin/java"
pic... |
762c3024dac051a27829d8627afca4ed9f00a18c549a7408b834e0802efbc546 | Shell | 4,780 | 149 | #!/bin/bash
##
## ATAC-seq using Bowtie 2
##
# specify maximum runtime for sbatch job
# SBATCHTIME=48:00:00
# standard route header (validate args, print settings, prepare environment)
code_dir=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." && pwd)
source "${code_dir}/scripts/route-header.sh" "$@"
##############... |
3fc56874cc93b22c28e1cbdf503bdadd61c5a70bd81c91a1a5d73b8482c85e10 | Shell | 4,796 | 147 | #!/usr/bin/env bash
# common_setup.sh - Shared setup functions for deepRetinotopy tests
#################################################################################
# COMMON CONFIGURATION AND SETUP FUNCTIONS
#################################################################################
setup_environment() {
... |
4e24d7e6ac5b2b162b3aab2d8d154baf18b7142f1d3c323bbdb754249e3ccde9 | Shell | 4,824 | 96 | #!/bin/bash
set -euo pipefail
LOG_FILE="$PREFIX/menuinst_debug.log"
PYTHON_EXE="$PREFIX/bin/python"
PROJECT_ROOT="$PREFIX/CellTracksColab"
BASE_REQUIREMENTS="$PROJECT_ROOT/requirements.txt"
GPU_REQUIREMENTS="$PROJECT_ROOT/requirements_gpu.txt"
SELECTED_REQUIREMENTS="$BASE_REQUIREMENTS"
echo "Running post_install" > "... |
5054bfdff77da6e2c8bb0bb48053f3b122f9f54502863862af2a1cafb4d71767 | Shell | 4,824 | 96 | #!/bin/bash
set -euo pipefail
LOG_FILE="$PREFIX/menuinst_debug.log"
PYTHON_EXE="$PREFIX/bin/python"
PROJECT_ROOT="$PREFIX/PROJECT_NAME"
BASE_REQUIREMENTS="$PROJECT_ROOT/requirements.txt"
GPU_REQUIREMENTS="$PROJECT_ROOT/requirements_gpu.txt"
SELECTED_REQUIREMENTS="$BASE_REQUIREMENTS"
echo "Running post_install" > "$LO... |
c3b4c56fa285630d4ab5c0b840d2a1eb125f6695775571b1e031a68952308a22 | Shell | 4,853 | 204 | #!/bin/bash
# Bismark deduplicate_bismark
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 4 ] ; then
echo -e "\n $script_... |
3de500dcce9911fbc5aec002d31617550e67f7418017ec49c03aa235fdd71a5d | Shell | 4,854 | 124 | #!/bin/sh
# ============================================================
# 01.2_processing_for_roi2vox_structgradients_TRT.sh
# ============================================================
# This script performs pulvinar-targeted tractography and mapping
# for HCP-TRT (test-retest) data using MRtrix and FSL tools.
#
# ... |
85f7b72623983aadc732f614e543d9596643991d38150b155b758e2f74cb141a | Shell | 4,871 | 191 | #!/bin/bash
set -eo pipefail
workflow_path='/hpc/dbg_mz/production/DIMS'
R='\033[0;31m' # Red
G='\033[0;32m' # Green
Y='\033[0;33m' # Yellow
B='\033[0;34m' # Blue
P='\033[0;35m' # Pink
C='\033[0;36m' # Cyan
NC='\033[0m' # No Color
# Set input and output dirs
input=""
output=""
email=""
samplesheet=""
nr_replicates="... |
a5aa3442272bfa25c39cf937971e459ad82ea155f48ffd74c54d7d4c9d80e874 | Shell | 4,905 | 18 | #!/bin/bash
# usage: ./3dSeedCorr_lh.ln.sh
# description: runs seed-based connectivity analyses
# author: amar ojha (but Will wrote the OG function)
# date: 20240812
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_2... |
e5edcefe3a057ae6e2db4c9f8465746951c4f06d5db285928ade8b8cc4e86d4c | Shell | 4,907 | 18 | #!/bin/bash
# usage: ./3dSeedCorr_lh.cen.sh
# description: runs seed-based connectivity analyses
# author: amar ojha (but Will wrote the OG function)
# date: 20240812
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_... |
f6a4e982285a5f2de5374b8be8cc090dec32ae62a8d2f274b937a86f6364643f | Shell | 4,908 | 18 | #!/bin/bash
# usage: ./3dSeedCorr_rh.ln.sh
# description: runs seed-based connectivity analyses
# author: amar ojha (but Will wrote the OG function)
# date: 20240812
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_2... |
b4ac220ca35fc48759fbc0aeb3678b7a4a6ec82d04371fb2511904fb4db235f8 | Shell | 4,909 | 18 | #!/bin/bash
# usage: ./3dSeedCorr_lh.bn.sh
# description: runs seed-based connectivity analyses
# author: amar ojha (but Will wrote the OG function)
# date: 20240812
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_2... |
f73611a46515011c1e19028bc0371e80d7381340e0718ce5bf2a287dc362ea21 | Shell | 4,909 | 18 | #!/bin/bash
# usage: ./3dSeedCorr_rh.bn.sh
# description: runs seed-based connectivity analyses
# author: amar ojha (but Will wrote the OG function)
# date: 20240812
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_2... |
bc84503af70ff874f36fc816a27d5e0fbaf359f3c0ec52a1ae3914c145abeed2 | Shell | 4,910 | 18 | #!/bin/bash
# usage: ./3dSeedCorr_rh.cen.sh
# description: runs seed-based connectivity analyses
# author: amar ojha (but Will wrote the OG function)
# date: 20240812
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_... |
06eb11c26345eea330f226389ca5a4b47358e60566517a249a860ba13d77f2ed | Shell | 4,911 | 18 | #!/bin/bash
# usage: ./3dSeedCorr_lh.abn.sh
# description: runs seed-based connectivity analyses
# author: amar ojha (but Will wrote the OG function)
# date: 20240812
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_... |
3230fca16f5b2f9fdc60024f4b7a7c74628cde40ded152bd2943eaef61408d90 | Shell | 4,911 | 18 | #!/bin/bash
# usage: ./3dSeedCorr_rh.abn.sh
# description: runs seed-based connectivity analyses
# author: amar ojha (but Will wrote the OG function)
# date: 20240812
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_... |
3a4e299000a3ddd094cf1694b66d67474fae1203cbcb0b2e9f4b313af4b23100 | Shell | 4,911 | 18 | #!/bin/bash
# usage: ./3dSeedCorr_lh.cat.sh
# description: runs seed-based connectivity analyses
# author: amar ojha (but Will wrote the OG function)
# date: 20240812
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_... |
8dbd5d95e269ef4c7ad0f02c114536ea8aa8864c455c5821039b4b7563c60118 | Shell | 4,911 | 18 | #!/bin/bash
# usage: ./3dSeedCorr_rh.cat.sh
# description: runs seed-based connectivity analyses
# author: amar ojha (but Will wrote the OG function)
# date: 20240812
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644_20180216 10644_... |
2eb9033a183f0cc4fccf3bc835e035a47a553ea010051d984dc1d61349db3229 | Shell | 4,923 | 97 | #!/usr/bin/env bash
# "Source step #1": runs the "KB (v0.28.2)" wrapper "Kallisto (v0.50.1) + BUStools (v0.43.2)" for building the reference
## scRNA-seq: "10XV3" --> check Ivan emails about the AmpliDrop tech used!
### "CMDs" --> $ kb ref -i transcriptome.idx -g transcripts_to_genes.txt -f1 cdna.fa dna.primary_assemb... |
ab1cb285200bd2a73108689c5045b5a2814286ebc83384c18a5f6dcba51daee8 | Shell | 4,936 | 124 | #!/bin/bash
# This script runs inference on the dataset on the BIDS datasets using the sct seg_sc_epi model, sct_deepseg_sc and the sct_propseg model. The outputs of the models are saved in the derivatives folders with the following suffixes:
# sct_epi_seg --> _sct_epi_seg
# sct_deepseg_sc --> _sct_deepseg_sc
# sct_pr... |
9573dbd49f81829632a2e1a1f50a66b22c2c2eabe88f7725d563dc8e0b8c5763 | Shell | 5,009 | 191 | #!/bin/bash
#
#
# Created by Kenneth Weber on 6/7/2022.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS ... |
055cf34bfc3a4d3b8427a82c7e824494f8ad74fa407e6414291fec0252e9e446 | Shell | 5,016 | 135 | #!/bin/bash
# Parameters
#ACTION=$ACTION # install | remove
#SECRET_NAME=$SECRET_NAME
#SECRET_NAMESPACE=$SECRET_NAMESPACE
#COMMON_NAME=$COMMON_NAME
#EXPIRATION=$EXPIRATION
set -u
TLS_CERT_FILE="/cert/tls/tls.crt"
TLS_KEY_FILE="/cert/tls/tls.key"
function install_cert_files {
CERT_FILE=$1
KEY_FILE=$2
if ... |
547c9d357166c8c31278b1ac1bc0cf017d8f14980ef326c9994c956ef65d062b | Shell | 5,033 | 218 | #!/bin/bash
# remove duplicates using sambamba
# script filename
script_name=$(basename "${BASH_SOURCE[0]}")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 4 ] ; then
echo -e "\n $script_name ERROR: WRONG NUMB... |
bf19bc087a4f1b27af60ebdbc40b2ba850a7b3fe1bd6dcf6671bec0ae81184a0 | Shell | 5,054 | 205 | #!/bin/bash
# run Trim Galore (for MspI digested RRBS samples)
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ $# -lt 4 ] ; then
... |
5f07e17b8c2ec132781874f77f91e777f92a3c2572a15e0552a6b9bcebea695c | Shell | 5,055 | 72 | #!/bin/bash
# This script attempts to build MIMIC on an Oracle instance.
# You will likely need to modify it to fit your own system, for example,
# you may need to change the authentication, e.g. replace '\ as SYSDBA' with 'myusername/mypassword'
# The script requires sqlldr and sqlplus
# Create the tables
sqlplus ... |
d401a9f1974b18fccddbabfa5de2f1b016983a4bb7daf10cc08f2e041e4eeacc | Shell | 5,174 | 94 | ## Commencer par Denoising du T1 et du T2 avec sanlm
## Il sait faire ça David.
## T1xT2BET. Le crop est large (20) car le crop final sera fait quand l'anat se retrouvera dans le template.
## Ce crop sert seulement a gagner du temps de calcul pour les étapes suivantes.
## l'option -f épend du singe, ici j'ai mis la v... |
9321396162b98f0aa41918dd3f16d949e5381bcf0704ae1af22a4912ac88bdef | Shell | 5,178 | 143 | #!/bin/bash
# python -u "/home/lthpc/zhongzh/RFD4Hist/train_teacher.py" \
# --model ResNet50 \
# --batch_size 64 \
# --learning_rate 0.01 \
# --dataset ivygap \
# > 12_25_ResNet50_lr0.01_teacher.log &
# python -u "/home/lthpc/zhongzh/RFD4Hist/train_teacher.py" \
# --model ResNet18 \
# --batc... |
91695a7e66e352bb3a84d398d41e9d407c4f0f21f5e3d48984d15e432d3bcbb0 | Shell | 5,181 | 161 | #!/bin/bash
##
## WGBS using Bismark
##
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
route_name=${script_name/%.sh/}
echo -e "\n ========== ROUTE: $route_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 2 ] ; then
echo -e "\n $script_name ERR... |
01c44bccc94686270539450acb03fea75a73e033c51d5757718867444b2fe355 | Shell | 5,319 | 193 | #!/bin/bash
#
#
# Created by Kenneth Weber on 6/7/2022.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS ... |
16203777fc91a0eee950df8277e660683b50a8ca12373258f0b4557836cdc0d8 | Shell | 5,328 | 214 | #!/usr/bin/env bash
# Crop Volume based on a brain extraction
HELP() {
cat <<HELP
CropVolume. Crop image(s) based on a brain extraction. Multiple images can be cropped at once. Will crop each volume preceeded by the -i option
Usage:
bash ${0##*/} -i <input-file> -b <brain-file> [options]
Compulsory ar... |
b7d854570f1515cb24001273d5b98a02a1a11863c78b823e3839a8fbec370b94 | Shell | 5,344 | 155 | # First preprocessing of brain images - only one subject
# Segmentation of T1 structural scan in WM and CSF
# Motion correction of BOLD functional scan
# Fieldmap correction via TOPUP
# Registration of WM and CSF masks to functional scan
# Extraction of WM and CSF time-series
# Author: Valeria Oliva
echo "Which sub?... |
50f4d19b527d604d5db41891409e6c71c4372d55f5051a48a7b193ffc15f48e0 | Shell | 5,388 | 29 | #!/bin/bash
# usage: ./03_extract_timeseries_rest.sh
set -euo pipefail
#path=/Volumes/Hera/preproc/7TBrainMech_rest/MHRest_nost_nowarp_nosmooth
path=/Volumes/Hera/Amar/amyg_7T/data
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_20210924 10644... |
9c8c82da3e81434448a909263e3431cd95dcebbe9980bdcb81a68cd59e4dd150 | Shell | 5,434 | 153 | #!/bin/bash
## Siwei 14 Apr 2021
## modified from Rob's iMG analysis for Alena
############
# This script assumes you are aware of the tutorial on LDSC for cell specific analyses
# Requires that downloaded files from Broad are unpacked/unzipped in this same folder
# gene lists can be sourced elsewhere
############
... |
7214d69cd5c00a016b9c8c21ebd232f1d80b02d380cdb3332834fe322a6886eb | Shell | 5,452 | 29 | #!/bin/bash
# usage: ./01_extract_timeseries_background_nosmooth.sh
set -euo pipefail
#path=/Volumes/Hera/preproc/7TBrainMech_rest/MHRest_nost_nowarp_nosmooth
path=/Volumes/Hera/Amar/amyg_7T/data
for id in 10129_20180917 10173_20180802 10173_20200221 10173_20210830 10195_20180129 10195_20191205 10202_20200103 10202_... |
8790cc9a334052b8625f077512005673c6344c319713806e917d72f54eecdcb4 | Shell | 5,510 | 159 | #!/bin/bash
set -e # Exit on error
set -u # Exit on undefined variable
dataset_category="TDC"
declare -a dataset_names=("CYP1A2" "CYP2C9" "CYP2C19" "CYP2D6" "CYP3A4" "HIV" "AMES" "HERG")
declare -a split_types=("random" "scaffold" "scaffold_generic" "molecular_weight" "molecular_weight_reverse" "molecular_logp" "km... |
9b8523fed886af38a454c3086feb059ffd484d0d368942b93bdf8d69c6b88dc3 | Shell | 5,566 | 92 | # runVignette07.sh - Bayesian calibration (inverse modeling),
# forward simulations, path tracking
# --------------------------------------------------
# This vignette demonstrates use of Bayesian calibration
# for inferring unknown pressure boundary conditions, based
# on target blood flow directions and RBC velocitie... |
b5f8d352525ae3d4237e9eaf43e7d5a774d0f9163aee891ade0d8af10de26dff | Shell | 5,640 | 62 | # This config file contains the paths to all relevant data objects used by the ProteinNPT codebase. Only the next two lines should be updated based on your particular setup
export proteinnpt_data_path="Replace this string with the path to the folder where you downloaded the core ProteinNPT files (ProteinNPT_data.zip)"
... |
664fc2ce3dbd812d9820d3b01621d60cf4b84d0227d0eaf791d5f783aad49198 | Shell | 5,708 | 230 | #!/bin/bash
# This script builds a LAMMPS executable with graph-pes support.
# It sets up a conda environment, clones LAMMPS, patches it with graph-pes,
# and builds the executable for either CPU or GPU use.
# Fail if any command fails
set -e
show_help() {
echo "Usage: $0 [OPTIONS]"
echo
echo "This scrip... |
a8ee63b956438d23f1d429dca410af982b6a69b2c870bdee7a15395e81ee8b0f | Shell | 5,734 | 105 | #!/usr/bin/env bash
#
# model MGS task with dmblock
#
# may need new 1d files. see 020_task_onsets.R and output name
# see 'CHANGE ME' comments
# 20221212WF - copy of 021a_deconvolve_block.bash but intended to model with dmblock instead of block
# dryrun, iffmain defined in /opt/ni_tools/lncdtools/ (should be in path)... |
e15a426323b9012d291da92bf94a0124a04a5a1851df3080db955d519de33d15 | Shell | 5,755 | 167 | # First preprocessing of brain images - loop through all subjects
# Segmentation of T1 structural scan in WM and CSF
# Motion correction of BOLD functional scan
# Fieldmap correction via TOPUP
# Registration of WM and CSF masks to functional scan
# Extraction of WM and CSF time-series
# Author: Valeria Oliva
cd ../.... |
dfc9b09812a76987e25092ea34adf49c9300e50ee3fdef3702dd3037ee694194 | Shell | 5,786 | 152 | #!/usr/bin/env bash
# MIT License
#
# Copyright 2018 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, c... |
9f65b62738b3550a39c34f21ddc00691fddd6f51e47e299a9e12222313b664ff | Shell | 5,789 | 178 | #!/bin/bash
##
## RNA-seq using STAR aligner
##
# specify maximum runtime for sbatch job
# SBATCHTIME=12:00:00
# standard route header (validate args, print settings, prepare environment)
code_dir=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." && pwd)
source "${code_dir}/scripts/route-header.sh" "$@"
###########... |
363e43a351fff35aae46d8bae36f37a390af7e32de58131bbf780eee1f60d3c5 | Shell | 5,794 | 145 | #!/bin/bash
# Drive the KOKKOS sync detectors over the Tier-1 styles.
# ./run_checks.sh step0 thermo: plain CPU styles vs KOKKOS styles, same binary
# ./run_checks.sh detect watch/stale detectors on the KOKKOS runs
# Every KOKKOS run uses the settings a GPU would pick, per
# .github/dev-docs/kokkos-sync-debu... |
d7c1b7f42c881dffaf7509274b8c9f2272e99609aba2850848869d6cef193757 | Shell | 5,797 | 36 | #!/bin/bash
#
#SBATCH --job-name=MMRegBaseS
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-... |
6cb393e05008f74c5860d6d526af2ffd5791b51cd37832dd62e50f1f368c7b28 | Shell | 5,803 | 105 | #!/bin/bash
set -u -x -e
# GOAL: registration from fsaverage to hcp fs_lr
# Use this registration to resample the wang template to individual surfaces
#sub_id=$1
#path_bids_data=$2
#path_output_data=$3
#path_HCPtemplates_standardmeshatlases=$4
#path_fsaverage=$5
path_output_data="/data/p_02915/SPOT/00_HCP/template... |
b93e9893a6d5215da73945eab7b659492918a07fdc9a4c61c4287d51accb6cf7 | Shell | 5,837 | 137 | #!/bin/bash
###############################################################################
# ATAC-seq Analysis Pipeline
# Author: Alireza Ghahramani
# Contact: aghahram@uwo.ca
#
# Description:
# This script processes bulk ATAC-seq fastq files through adapter trimming,
# alignment, deduplication, peak calling, cov... |
b105b4312c712e25a0008297787d5bb47a23595de561919ab421489130264853 | Shell | 5,842 | 102 | #!/bin/bash
set -ev
# 01. Set up environment
exec_dir=$( pwd )
cd "${exec_dir}"
ct_dir="${exec_dir}/scripts"
# 02. Set up config files
# 02a. Specify config file path
cfg="${exec_dir}/configs/config_cell_type.yaml"
echo "${cfg}"
# 02b. Add root directory to config
# file if it does not exist in there
# yet (meaning ... |
bfeccc77f892eb2e1c2475a7e5153756a8c45b794969eae2e54b6c326cb92f2d | Shell | 5,862 | 253 | #!/bin/bash
# HMMRATAC peak calling for ATAC-seq data
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 3 ] ; then
echo -e ... |
5b0d42ef0cc38ffbafd1ccf265312498b12636a135a774b185195f1f1e237abf | Shell | 5,879 | 225 | #!/usr/bin/env bash
CAFFE=/cs/vml2/msibrahi/workspaces/caffe-lstm
GIT_PROJ_DIR=$CAFFE/examples/deep-activity-rec
DATASET_VIDEOS=$GIT_PROJ_DIR/volleyball-simple
DATASET_CONFIG=$GIT_PROJ_DIR/dataset-config-simple
OUTPUT_DIR=$GIT_PROJ_DIR/ibrahim16-cvpr-simple
TRAIN_SRC=trainval
TEST_SRC=test
WINDOW_NETWORK1=5
WINDOW_... |
edd12a4b254e637b03e2078dcab51ceae087e481d634062310ef8b60998e0493 | Shell | 5,885 | 194 | #!/bin/bash
# Build MIMIC-IV in PostgreSQL: create the schema, load the data, add the
# constraints and indexes, then derive the concepts.
#
# Usage:
# ./build_mimic.sh <mimic_data_dir>
#
# <mimic_data_dir> is the directory holding the hosp/ and icu/ subfolders.
# Compressed (.csv.gz) and uncompressed (.csv) data are... |
ea792118686868308d2c9650ac8f7a1857da5e1e987cc7d376a7a81b2029df85 | Shell | 5,905 | 225 | #!/usr/bin/env sh
CAFFE=/cs/vml2/msibrahi/workspaces/caffe-lstm
GIT_PROJ_DIR=$CAFFE/examples/deep-activity-rec
DATASET_VIDEOS=/cs/vml2/msibrahi/Datasets/Greg-Volleyball/volleyballVolleyball
DATASET_CONFIG=$GIT_PROJ_DIR/dataset-config
OUTPUT_DIR=$GIT_PROJ_DIR/ibrahim16-cvpr
TRAIN_SRC=trainval
TEST_SRC=test
WINDOW_NE... |
af272ef2122ad4bdc167eb9af7f54fb1afbf71bb4b6fdae88741e5384d124ab5 | Shell | 5,965 | 249 | #!/bin/bash
# call variants with GATK HaplotypeCaller
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 4 ] ; then
echo -e ... |
1a465a4d1f040d22e11dba7e84f4ef862576c18f38591e1ce9cfa1d6fd97b09f | Shell | 5,992 | 140 | #!/bin/bash
# Taku Ito
# 05/07/18
# Script that produces nifti masks for later nuisance regression
#### IMPORT AFNI
export PATH=$PATH:/projects/f_mc1689_1/HCP_v2_prereqs/afni
#########################
basedir="/projects/f_mc1689_1/ReliableFC"
datadir="${basedir}/data/preprocessed"
#########################
subjNums... |
58d5027b6244d4a30d2f58f5a798d8958ce447e206f1218f46042631f3bab0d7 | Shell | 6,005 | 36 | #!/bin/bash
#
#SBATCH --job-name=MMRegBaseS
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-... |
28e8d991045e9582bce90894d7b6972b09b89f08e451b1f93881efcebd82ce60 | Shell | 6,108 | 234 | #!/bin/bash
# merge fastqs or create symlinks to originals if no need to merge
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $... |
d8c324e930602ea6180c52f22612998e94a43d6cff9a12a27bdf84d6a6f4ec9b | Shell | 6,109 | 193 | #!/bin/bash
set -euxo pipefail
# Default values
PYTHON_VERSION="3.12"
PYTORCH_VERSION="2.10.0"
ENV_NAME="test"
MICROMAMBA_DIR="${HOME}/micromamba"
PIP_CACHE_DIR="${HOME}/.cache/pip"
CONDA_CREATE_ARGS=""
export MAMBA_ROOT_PREFIX="$MICROMAMBA_DIR"
# Parse command line arguments
while [[ $# -gt 0 ]]; do
case $1 in
... |
aa8b2bbb54eab60a09c0d5e9a8e0d4c90db78eaf64ac60d6dc6467f42a50c4d3 | Shell | 6,124 | 243 | #!/bin/bash
# GATK on-target coverage (capture efficiency)
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 4 ] ; then
ech... |
b7907a69bd28843a3246cd3d7ee9ac4d11a3f18f96dcf98d56c80d1dd63bcd28 | Shell | 6,133 | 209 | #!/bin/bash
# This script is used to preprocess images in a GCP bucket for use
# with PHAS, the PICSL Histology Annotation System.
function usage()
{
cat <<-USAGE
prep_bucket: image preprocessing script for PHAS
usage: prep_bucket <command> [options] ARGS
commands:
process_image: generate py... |
616d61b0be5be11c78e9a4a487213ec5de3b75c90bbb3872187cc00627c2f026 | Shell | 6,155 | 187 | #!/bin/bash
##
## whole genome/exome/targeted sequencing variant discovery using BWA-MEM and GATK
##
# specify maximum runtime for sbatch job
# SBATCHTIME=120:00:00
# standard route header (validate args, print settings, prepare environment)
code_dir=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." && pwd)
source "$... |
0675ac8b61e06e6af0700506a4263daf6ed70c55553bdc7cf863fe35b6bd183f | Shell | 6,165 | 151 | #!/bin/bash
# ===============================================================
# Gradient and Cluster Projection Script
# ---------------------------------------------------------------
# This script reconstructs parcel-wise gradient or cluster maps
# (in volumetric NIfTI format) by projecting scalar values
# derive... |
8448edb9c31ee6db6fbef4aa0c757f9bd180e840ec4305cc64d5d992034760d9 | Shell | 6,171 | 240 | #!/bin/bash
# run Trimmomatic
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ $# -lt 4 ] ; then
echo -e "\n $script_name ERROR: W... |
b504eab5dec4b720332895dc2ce2bbfffa6b439dfbe1010eb6a88b8e3aeb3920 | Shell | 6,175 | 118 | #!/bin/bash
# parse command-line arguments
if [ $# -ne 2 ]; then
echo Usage: $(basename "$0") alignments.bam virus_expression.tsv
echo
echo "Description: This script takes alignments in BAM format as input and counts the number of high-quality alignments mapping to viral contigs. It assumes that viral contigs start... |
41c99d5954763aee1dfd3b452ba3aa269ef3db73e1b346e3fbf0cca9a60b249a | Shell | 6,193 | 263 | #!/bin/bash
# run BWA-MEM
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ $# -lt 4 ] ; then
echo -e "\n $script_name ERROR: WRONG... |
e531a225bf30c0e5b76fb08df28c7db53b9101ae6df2fb0908c2d7dd88eadbd8 | Shell | 6,211 | 168 | #!/bin/bash
cifar_path="/user_data/weifanw/cifar-100-python" # cifar saving path
cwd="/user_data/weifanw/familiarity_clean" # project directory
# params =====================================================================================================
task="assoc"
wie=30
tau_train=150
gamma=30
num_epoch=5
... |
77166ad698f849346f3efac89f1df3b7ad56ade2f7dbca0f832dc6e442f5afa6 | Shell | 6,241 | 134 |
#!/bin/bash
#Quality filter 18S reads using the Trimmomatic version 0.38 and fastqc of trimmed reads
#Trimmomatic version 0.38 and FastQC v0.11.10.devel
#KCastellano
##Notes on flags used for trimming
#SLIDINGWINDOW:4:25 means that if at any point in a scan of the sequence the average quality drops below 25 in... |
a8bf803c170088c96b15a889f845fd348fe40fe47e2e613d237f558a3bf4ebfd | Shell | 6,251 | 160 | #!/bin/bash
set -ex
if [ "$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)
#------------------
echo "try to find tensorflow in the Python... |
f0cae19eb342df237ebc715459a429a867b4be167f6d991b298c6b769d2d115e | Shell | 6,256 | 130 | #!/bin/bash
# parse command-line arguments
if [ $# -ne 8 ]; then
echo Usage: $(basename "$0") STAR_genomeDir/ annotation.gtf assembly.fa blacklist.tsv known_fusions.tsv protein_domains.gff3 threads alignments.bam
echo
echo "Description: This script has a similar function as the main script 'run_arriba.sh'. But inst... |
36bc35cbd27398dcf5d6d7896345a2b3b1ce6d356ccd01849480bef8e12d564f | Shell | 6,272 | 34 | #!/bin/bash
#
#SBATCH --job-name=MMReg0s
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-per... |
f4576cacb1f16fb9c3dad2e2bf7980e1faf19626d3dafa6d7f783977d3ba5332 | Shell | 6,304 | 34 | #!/bin/bash
#
#SBATCH --job-name=MMReg1S
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-per... |
13def3fb2712d86ea02c54f73cc0250a976cd62cac8dc7111a9b9379ad1397d2 | Shell | 6,305 | 132 | #!/usr/bin/env bash
ml connectomeworkbench/1.5.0
ml freesurfer/7.3.2
ml deepretinotopy/1.0.11
source ~/miniforge3/etc/profile.d/conda.sh
conda activate deepretinotopy_validation
while getopts d:t:r: flag
do
case "${flag}" in
d) dataDir=${OPTARG};;
t) dirHCP=$(realpath "${OPTARG}");;
r) val... |
4b9539c4cd734e2134d4340e251f5187c0ef2776b2c87177d83bc459249abf5d | Shell | 6,313 | 223 | #!/bin/bash
function usage()
{
cat << EOF
Usage
This program creates a folder Data_MMDDYYYY in the directory /usr/g/research/cslaw
The folder contains raw data, DICOM data, shimming data, physiological data, png files, .mot & .physio files.
Can also save CUBE and BRAVO data
e.g. /usr/g/research/cslaw/savedata... |
ab581b4d4468435ea408e185577e40466f36c568a9fd8c3ebb0f300e4c288a5a | Shell | 6,321 | 34 | #!/bin/bash
#
#SBATCH --job-name=MMReg05S
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-pe... |
05ebabca6c56206d8989c6bcfa106e9d7fb27266e1a705da856536d6c783feb0 | Shell | 6,343 | 196 | #!/usr/bin/env bash
# "Source step #0": Quality Check (QC) Metrics of SE|PE-FASTQ reads with "FastQC" and, sometimes, adapter SEQ trimming with 'cutadapt'
## BONUS: summarizes the results with a new tool called "MultiQC"!
# 'Prints' message
echo -e "Setting up ENV..."
# Creates 'FUN'
## 'NICE LINK:' https://phoenixn... |
fbf00310552f0b22493c73af6bfd038ea34c61a939b604a8d3c3eb20e562d62b | Shell | 6,354 | 34 | #!/bin/bash
#
#SBATCH --job-name=MMReg025S
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-p... |
1912ec2a2a7eeae292e679f2857c9bac01c10605619aecc77cfa8cc631fa35ca | Shell | 6,369 | 144 | #!/bin/bash
# script for third data release
# script to align native surfaces with template space
set -x -u -e
Usage() {
echo "align_to_template.sh <topdir> <subjid> <session> <age> <volumetric template> <volumetric template name> <surface template> <surface template name> <pre_rotation> <outdir> <config> <script ... |
2ebf7408b2c4a57725a3865a3b3ba84c7cccc6181463a841357cc6f06f9ebe36 | Shell | 6,376 | 243 | #!/bin/bash
# run featureCounts
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 6 ] ; then
echo -e "\n $script_name ERROR... |
217556008d9353c451dfb23e0fb12dd03cd10ab982ed5f84050dafbc6bb003da | Shell | 6,387 | 34 | #!/bin/bash
#
#SBATCH --job-name=MMReg0125S
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-... |
41325efa70280f0ed2a1c6270478a880c83c30a186b0dae03c0509f03ddcd36a | Shell | 6,391 | 152 | #!/bin/bash
# script for third data release
# script to align native surfaces with template space
set -x -u -e
Usage() {
echo "align_to_template.sh <topdir> <subjid> <session> <age> <volumetric template> <volumetric template name> <surface template> <surface template name> <pre_rotation> <outdir> <config> <script ... |
c2ebbad4e37d08d45dfcbe4ed565c6759571ab3c3d6abaa2a632ed6743f07109 | Shell | 6,465 | 158 |
library("tidyverse")
library("sessioninfo")
library("BayesPrism")
library("here")
## prep dirs ##
data_dir <- here("processed-data", "08_bulk_deconvolution", "03_get_est_prop")
if (!dir.exists(data_dir)) dir.create(data_dir, recursive = TRUE)
#### data details ####
## dataset properties
dataset_lt <- tibble(Dataset ... |
d52ebe16644b8f8c977318777ab1232f598956ebbdeb4666e6ae434680d62a4f | Shell | 6,480 | 34 | #!/bin/bash
#
#SBATCH --job-name=MMReg0s
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-per... |
4c001f53cbb2ebe347586b25097d87baff2873502b7582a15e7e63498abea34e | Shell | 6,492 | 133 | #!/usr/bin/env bash
ml connectomeworkbench/1.5.0
ml freesurfer/7.3.2
ml deepretinotopy/1.0.11
source ~/miniforge3/etc/profile.d/conda.sh
conda activate deepretinotopy_validation
while getopts d:t:r: flag
do
case "${flag}" in
d) dataDir=${OPTARG};;
t) dirHCP=$(realpath "${OPTARG}");;
r) val... |
ab1d0d43e02974ff30de1a0768870a8506e192a7894eb89d0f29a49f633702a7 | Shell | 6,492 | 208 | #!/bin/bash
set -Eeuo pipefail
#-----------------------------------------------
# Argument parser
#-----------------------------------------------
usage() {
echo "Usage: $0 -s <sample_ID> -c <config_file> -d <sample_dir> [-m] [-t] [-b] [-e <int>]"
echo
echo "Options:"
echo " -s <sample_ID> Sample ID [requ... |
364c1084600d1d9b2b2f49564a123244fe0c4906430eb27759370e39058591d9 | Shell | 6,494 | 243 | #!/bin/bash
# run Picard CollectRnaSeqMetrics
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
segment_name=${script_name/%.sh/}
echo -e "\n ========== SEGMENT: $segment_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 3 ] ; then
echo -e "\n $scr... |
75feeec6b6480db9cdb2039f152cb17edf0591edf6331bc33afa1cae05a3d279 | Shell | 6,512 | 34 | #!/bin/bash
#
#SBATCH --job-name=MMReg1S
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-per... |
4b6683d0e514eddcedadad1e20a4ae12ade57f0e7c7ccef4682f36cdf3641652 | Shell | 6,521 | 165 | #!/usr/bin/env bash
# ------------------------------------------------------------
# Figure 5 – Deep-learning model benchmarking (IQ-paper)
# ------------------------------------------------------------
# This script lists ONE canonical training command per model /
# organism that was **actually used** to generate the ... |
369a0852cef01563b8568c46373e301547aa94d87f26b0d79cf0137eb6e79ba6 | Shell | 6,529 | 34 | #!/bin/bash
#
#SBATCH --job-name=MMReg05S
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-pe... |
09f5d0cd87239b952d26da043190720066f5a72abc9ec8aac9a6d6ceba92586b | Shell | 6,545 | 88 | #!/bin/bash
if [ "$#" -ne 1 ]; then
echo -e "\nUsage: vga_makeBoxPlotRsem.sh <geneName>\n"
exit 1;
fi
module load intel/18.0.2
module load impi/18.0.2
module load Rstats/3.5.1
module load RstatsPackages/3.5.1
DIR0="/work/02076/abacolla/stampede2/rnaSeq_tcga_18"
DIR1="$DIR0/hnsc/Part2_BasicDataProcessing"
... |
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