sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
abaf0630be6b64dc09b43beb15f65fab4b6871eb8735a51c21d0dbcfbc63ad47 | Shell | 5,537 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-58 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/C2_orca_min_hessian_n... |
220c458f6b7b3272f90ee6a2c37cf38bc1738c5aa17eccca50f49937fc7a0dfb | Shell | 5,540 | 170 | #!/bin/bash
#: Title : test_o2metab
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../o2metab
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
181bea476a3303c61880c5c334667f2071217184386172aa148dc4b945826abb | Shell | 5,542 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-361 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/B3_orca_min_hessian... |
6521ae93bdbc90344250ebca2ecd45a1222243899d32f9cee40af21f7d86a08f | Shell | 5,542 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-139 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/D3_orca_min_hessian... |
97f0b1fe934b91477d0b0bb6ee991b7687f2fef4bf2b100864d3ee9274e2d331 | Shell | 5,542 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-146 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/D4_orca_min_hessian... |
f9e977a5b15f45c267827539b512e7d9267ef08871d896b73fa62ea3d17e40b4 | Shell | 5,542 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-132 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/D2_orca_min_hessian... |
0d0a91ee93cff5479444b13c33f33abbfb45a4fd0469f34c5065c00cdabd0365 | Shell | 5,543 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-139 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/D3_orca_min_hessian... |
0e11bf1bd857ee42b942ddde6152119ca5216ad2823ab62d320f5dc16d22b597 | Shell | 5,543 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-146 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/D4_orca_min_hessian... |
bce2f1281f53e0a85249a425a7a7abd4b7decb63fa8b741be0f1a9ca2375576d | Shell | 5,543 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-361 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/B3_orca_min_hessian... |
d678c5bd2877550b6523f3995ac80b877a5b10f1b491ffebddc5a208e8b3b9de | Shell | 5,543 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-132 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/D2_orca_min_hessian... |
610cf91333bf21ff5a88222151a5768b68e33ab8fa46e129a6ce74fd97fce918 | Shell | 5,545 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-313 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/B4_orca_min_hessian_... |
78d2904f5ff2efc6be21eaaf112179ee7b8d11c72061c15a9a9eb3ce055d7218 | Shell | 5,545 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-184 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/A3_orca_min_hessian_... |
89082c07117430738b5bf61090b7abd9cbbe66802b1de53be0271bf9b38759f1 | Shell | 5,545 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-131 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/C7_orca_min_hessian_... |
1ebfa1aec35af0c00aba534e7517d9897a790790c05c14168ed7c1f1dc8bbbef | Shell | 5,554 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-139 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/D3_orca_min_hessian_... |
6fefac8d196d72593ca60a29b736f41b0ed3e4252d212cc1a091355301c4d7f4 | Shell | 5,554 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-361 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/B3_orca_min_hessian_... |
afa40097d7021fe0e93d3704d98fdc37503d39ab4b3450981a144ba1b8728c9b | Shell | 5,554 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-146 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/D4_orca_min_hessian_... |
d2ef001daeecd8a7bd815c249dc2baea90071d04bfcd2d58f58635a89f313c1f | Shell | 5,554 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-132 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/D2_orca_min_hessian_... |
b56d9e663c56f80cbc0e409350837a4a6acf2dce0edd053a529a73097b8bb8ce | Shell | 5,560 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-134 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/C6_orca_min_hessian... |
89d71152f3d733f29ebc19f2d499e0ef9f36a03a0fe55ce5b0f30dca1d92ed24 | Shell | 5,561 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-134 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/C6_orca_min_hessian... |
b50dc1135013e5d022a5f33c99db1f019db5f24488582927a2a912ad270f7c5f | Shell | 5,569 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-151 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/C5_orca_min_hessian... |
ba51880eeddee3aabfeab2955df03e458c132e5012cf6032f46275716085d169 | Shell | 5,569 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-267 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/D6_orca_min_hessian... |
735293521598c25e5cdb13c9681f264ae6ec1db89a1747e1491ad421c5810b26 | Shell | 5,570 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-151 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/C5_orca_min_hessian... |
94dd677103d8193d92c7af2c14695190d8bf7b4f9fd22c43765f7751b85c9738 | Shell | 5,570 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-267 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/D6_orca_min_hessian... |
12edaa1995161e04ca9d4358dfd3585e172c706c809da27250a8327c18714f46 | Shell | 5,571 | 225 | #!/bin/bash
# This script builds portable medaka binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, i... |
1397b105490176e70558f1e323e128063230f950483b9160e29ace626ebc01e9 | Shell | 5,572 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-134 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/C6_orca_min_hessian_... |
53d44c7e354e11a4926a4a7eaeff1101e718da2e4450a7b08fdefd48be337d26 | Shell | 5,578 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-348 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/D5_orca_min_hessian... |
504ffb04b1b92d9d29ad5bdf00702844454884a5638daeeea8b6a08de1192cb2 | Shell | 5,579 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-348 -n 16 --tmp=10000 --time=04:00:00 --mem-per-cpu=4000 --output=/cluster/project/igc/kpaul/MB_logs/D5_orca_min_hessian... |
6fc0646bdf73b8b9382009800c71f37c6b16dd8f7c4399c583df4b7dd57cfc2d | Shell | 5,581 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-267 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/D6_orca_min_hessian_... |
e73996341f8e03e166883f463f2fde176f1eaeb03e928e25b56261199a75fa1a | Shell | 5,581 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-151 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/C5_orca_min_hessian_... |
30d575ce764d036b28b943e5282cb1d6ef180dd093abd62a5dcf65f6fc2bd5de | Shell | 5,590 | 41 |
source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
jobidChloroform=$(sbatch --parsable --array=0-348 -n 2 --tmp=10000 --time=24:00:00 --mem-per-cpu=8000 --output=/cluster/project/igc/kpaul/MB_logs/D5_orca_min_hessian_... |
575bcde9bad925d76b02bcaed99c75f904a127060656ad845d1af7fa2b08a811 | Shell | 5,622 | 177 | #!/bin/bash
#: Title : test_abssexam
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../abssexam
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
383b2e8cbcd001fbc0396c205b779ae26d44000bb3ac707e0bc63c597d93d137 | Shell | 5,653 | 144 | #!/bin/bash
#
# Registers T1w --> FUNC space using a nonlinear SyN method applying the parameters given as input
#
#
# # INPUTS:
# $1 : id = num in (01..30)
# $2 : SES = num in 1, 2
# $3 : Convergence parameters
# $4 : Shrinkage parameters
# $5 : Smoothing sigmas
# $6 : Tag for saving files
#
#
#
# 2023 Mark ... |
821a57348cd9a66ff1d924166f1635d7d68032415d43302b4e2ce8976d142932 | Shell | 5,676 | 159 | #!/bin/bash
#
# Run inference (i.e., segment SC and lesions) using our nnUNet model on sci-zurich T2w axial images and generate QC report
#
# Note: conda environment with nnUNetV2 is required to run this script.
# For details how to install nnUNetV2, see:
# https://github.com/ivadomed/utilities/blob/main/quick_start_gu... |
a8820869419dfe98882219f42774bf2473caf426739d40a2ea2103c787c8eb26 | Shell | 5,678 | 163 | #!/bin/bash
#: Title : test_fit_rrtm
#: Date : 2022-03-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_rrtm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
34b3228350b426725ded243f023fb95785268e9a0666d496188d20e4fd7a9176 | Shell | 5,716 | 195 | # This script is meant to be sourced in a test script to start a docker container to test in
# it interprets the options:
# -i|-image|--image: docker image to start from
# -a|-arch|--arch: 64, x86_64 or linux-x86_64 for 64 bit Linux build (default); ix86, 32 or linux-ix86 for 32 bits Linux build; win, windows-x86_64 or... |
9bf4170bb85bfc2f7a1e3ee0edbef0a11462b1774e42006dfb02b8d2ae0dd701 | Shell | 5,746 | 182 | #!/bin/bash
#: Title : test_imgaumc
#: Date : 2019-09-18
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgaumc
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
6f36362de9332fe20d971cef5384ebdfbcace615918e5a94a45e1a3b1b758de1 | Shell | 5,769 | 158 | #!/bin/bash
#: Title : test_fit2auc
#: Date : 2021-02-04
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit2auc
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
cea206d753c7520ff294ec4ad0ba30cd11ab19ef3a0f1bab71dcb40f50406fc0 | Shell | 5,821 | 205 | #!/bin/bash
#: Title : test_imgmax
#: Date : 2016-06-03
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgmax
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
27837f8700d261e948f7885205423442dcfa0ba1f7328a305e8fdc1944e003be | Shell | 5,832 | 206 | #!/bin/bash
#: Title : test_imgafind
#: Date : 2016-06-03
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgafind
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
8ae689896c9ceb5e2a4ecaae7521174cf861411d21d9103603de1dd918da723f | Shell | 5,845 | 217 | #!/bin/bash
# engaging configs: L40S (mit_preemptable)
#SBATCH -n 10
#SBATCH -t 0-24:00:00
#SBATCH -J iceberg_atlas
#SBATCH --output=logs/iceberg_atlas_l40s_%A_%a.log
#SBATCH -p mit_preemptable
#SBATCH --mem-per-cpu=4000
#SBATCH -G l40s:1
#SBATCH --requeue
#SBATCH --array=0-240
MIN_ID=0
MAX_ID=3000
## engaging conf... |
151bd58b3d2831e12a6251d473a4dbe8795b0b7d5d971cb501f026aea2b60c64 | Shell | 5,867 | 182 | #!/bin/bash
#: Title : test_resdel
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../resdel
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
8c9101a4c7d588b8ae5f4b510cbbb80e1b19a5882faa8e5b69e858a45baa6f28 | Shell | 5,889 | 152 | #!/usr/bin/env bash
set -euo pipefail
umask 077
usage() {
echo 'usage: nsys_snn.sh capture [OPTIONS] OUTPUT_PREFIX -- COMMAND [ARGS...]' >&2
echo ' nsys_snn.sh capture-graph [OPTIONS] OUTPUT_PREFIX -- COMMAND [ARGS...]' >&2
echo 'options: --control=api|manual (default: api), --session=NAME (manual on... |
ab6175dbe06ff377432113ee548cb59890afafc1bd422869825f9375ba0a8805 | Shell | 5,898 | 212 | #!/bin/bash
# This script builds portable isoquant binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build,... |
2c5748f6b05839bbe490462aa81642fd5934daf78d2d34b8072ea30495e535b8 | Shell | 5,912 | 181 | #!/bin/bash
#: Title : test_ecatcat
#: Date : 2014-09-07
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../ecatcat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
b2dd9630418e36d2b6f533001a0d940914a0facf713ab12b8f67aceef6f51ec3 | Shell | 5,957 | 226 | #!/bin/bash
# This script builds portable lumpy binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, if... |
d2652aecbac0ab510bde157636973ba9b3668f1632e8f080356e299f0145f5d2 | Shell | 6,064 | 164 | #!/bin/bash
#
# The script crops the input image, spinal cord GT, and lesion GT around the spinal cord segmentation (based on the
# dilated spinal cord GT)
#
#
# Note that the script outputs the cropped images (images, SC GT, lesion GT) in the data_processed folder, which is
# not BIDS-compatible.
#
# Usage:
# sct_... |
de0d5257f95188435678dc35ea165373c6a21a88c3aea3ebf2c306bfabac1aa0 | Shell | 6,094 | 217 | #!/bin/bash
# This script builds portable flames binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, i... |
8ed8699acc133251392ac6a8bf19d62d506869b61c14c1f37cc1befb11288f5d | Shell | 6,098 | 201 | #!/bin/bash
#: Title : test_tacblend
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacblend
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
6828ed9c975e5b44bcf988f780258fbb474ecacf935eb9f084cdb5f6b29a0507 | Shell | 6,169 | 184 | #!/bin/bash
#: Title : test_imgmask
#: Date : 2016-09-26
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgmask
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
5a2d53041f69ade563e6c5e069d72b8edfcd9174769a43a5b6f3def757050113 | Shell | 6,186 | 158 | #!/bin/bash
#: Title : test_imgdysmo
#: Date : 2026-09-03
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgdysmo
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
69b8b46cf702515b834450aea2b02d6decf410f19329eaef0f89d6ef27b11d71 | Shell | 6,189 | 189 | #!/bin/bash
#: Title : test_taccut
#: Date : 2020-01-23
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../taccut
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
cecb535ceff49874297fb759f0f9c5a25f44e815ddfd998b845f0ab81755867b | Shell | 6,244 | 189 | #!/bin/bash
#: Title : test_imgwcbf
#: Date : 2025-12-18
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgwcbf
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
a39db86230796bb4f4ecf748d59cb5f719c984abda70a375b6654b8cf13a2f75 | Shell | 6,298 | 212 | #!/bin/bash
#: Title : test_iftisval
#: Date : 2014-10-17
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../iftisval
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
565f2634f3cd771d97ea0e5651efe5b771dc5e842d767b767c6c30a8450f07e9 | Shell | 6,367 | 133 | #!/bin/bash
#
# Compares methods for T1w to dwi registration using ANTs MeasureImageSimilarity
# Uses Mattes Mutual Information by default (larger negative values means better registration)
# Runs for all subjects and stores values in a .csv of shape subjects x methods
#
# See $ MeasureImageSimilarity --help for more i... |
4113c458c02086e08bc70dcaf378161cd180c635907d627104aad0631ccc4db7 | Shell | 6,380 | 216 | #!/bin/bash
# This script builds portable sqanti3 binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, ... |
fd0f0e6009cb190bd44009aad6a1c792d94a5553bc6c21bebef16766d96a7a8c | Shell | 6,381 | 206 | #!/bin/bash
#: Title : test_imgfrdyn
#: Date : 2019-11-10
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgfrdyn
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
49ac3e5a26e05c55703017c4ff62fc79ab1e82326ac9d0feccb9b2beb11b1674 | Shell | 6,400 | 224 | #!/bin/bash
#: Title : test_imglhk1
#: Date : 2021-12-16
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imglhk1
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
1b7bde635340ad9de22b7084fe4e9b65ec7272b2014590886013e3bb85beb219 | Shell | 6,490 | 196 | #!/bin/bash
#: Title : test_sim_pkcp
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../sim_pkcp
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
605bf220be07d36bc32e729626da1a3596c9a670b611aad7534d8a3a86483f43 | Shell | 6,501 | 224 | #!/bin/bash
#: Title : test_parmean
#: Date : 2019-09-15
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../parmean
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
44c9206787a350fbf824c5b157d8e17880729f6700a796c961db15a40bdc70e4 | Shell | 6,558 | 217 | #!/bin/bash
#: Title : test_tacadd
#: Date : 2020-01-23
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacadd
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
126d64a8bad8c3cca37bfe76332afef2053c3f996593f966564cc5dcd01f6ade | Shell | 6,567 | 205 | #!/bin/bash
#: Title : test_arlkup
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../arlkup
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
c876c4bb0f6b1ac4c5c486b79520dca5e579937d420b213914170df279c094cb | Shell | 6,581 | 137 | #!/bin/bash
#
# Registers T1w <--> FUNC space using the mri_synthseg function from newer freesurfer packages
#
# # INPUTS:
# $1 : id = num in (01..30)
# $2 : SES = num in 1, 2
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#-------------------------------------------------------------------... |
7333b06cc993982bf0f67ae3ed7f1b3bf46204108168e22bb46ad7317425b1b1 | Shell | 6,591 | 193 | #!/bin/bash
#: Title : test_imgflowb
#: Date : 2025-12-16
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgflowb
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
fcaefe36b7c9035c0462daab59560b448014892b4c65ba951718b28b47b7b110 | Shell | 6,598 | 165 | #!/bin/bash
#
# T1w Structural processing with bash:
#
# Preprocessing workflow for structural T1w.
#
# This workflow makes use of FREESURFER, FSL (fslchfiletype)
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micaopen/templates
#
# ARGUMENTS order:
# $1 : BIDS directory
# $2 : partici... |
59ebc1fade6935032b7cedfe0a7eee15f60d43837a1b9b503e1438df752d3c70 | Shell | 6,601 | 202 | #!/bin/bash
#: Title : test_fit_disp
#: Date : 2019-08-19
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
#: ToDo : Test options
# Set the name of executable to test
PROGRAM=../../fit_disp
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executa... |
792f57704cf13d33afda51bdbe74c8a088ddf81473fb760fb5738218c468ede2 | Shell | 6,604 | 205 | #!/bin/bash
#: Title : test_imgposv
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgposv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
6721c0b0c140e42e23acc75abce24dfcac9685ed54c5ff70a4f15e6dba33f4ad | Shell | 6,673 | 161 | #!/usr/bin/env bash
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless r... |
60c9a7e59e961d7e9db6c0723d53d58667a98d988308d0935cb19b0c3a54dacf | Shell | 6,700 | 180 | #!/bin/bash
#: Title : test_fit_blddr
#: Date : 2019-12-01
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_blddr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist... |
27b1e026a0e8a4e9f44694488e9c7fb231e000158c366b1665e495b74c6d375a | Shell | 6,716 | 208 | #!/bin/bash
#: Title : test_sim_mbf
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../sim_mbf
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
ec64ac3eba01aeea1a6bd23d7e0075b371f92ceebba3d423d78b3e06d58bc95a | Shell | 6,726 | 253 | #!/bin/bash
did_not_instrument() {
if grep "In Function: $1" $2 >/dev/null; then
echo "SHOULD NOT HAVE instrumented $1 in $2"
exit 1
else
echo "not instrumented $1 in $2"
fi
}
did_instrument() {
if grep "In Function: $1" $2 >/dev/null; then
echo "instrumented $1 in $2"
... |
e6d5b341d41e8aefbb140b45234351366466baa45cc7ca06b07b3ae2b76096b7 | Shell | 6,779 | 204 | #!/bin/bash
#: Title : test_iftdel
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../iftdel
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
3afb6ebfd92a8c4aeabdc67c3abd0f133b4c20ffadb8cd4c55a875401cd84f12 | Shell | 6,787 | 201 | #!/bin/bash
#: Title : test_sim_h2o
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../sim_h2o
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
a3bd4acc8d1819def96535cb9f577430b843734f4fab22a929161c047a9196b9 | Shell | 6,838 | 84 | python simulator_performance.py --num 10 --nt 10 --simulator with --append -1
python simulator_performance.py --num 10 --nt 10 --simulator without --append 1
python simulator_performance.py --num 10 --nt 100 --simulator with --append 1
python simulator_performance.py --num 10 --nt 100 --simulator without --append 1
pyt... |
8ae0d142f6a0d12780b2a9f083d5f795b91c3f1a946127a53911b9dded61dc5b | Shell | 6,907 | 212 | #!/bin/bash
#: Title : test_fit_o2bl
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_o2bl
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
68edca9c4e4c0e0338635b5a2cfc31d00cfa3dd7fdc518e41d8a11e4a8bfe041 | Shell | 6,914 | 175 | #!/bin/bash
# Checks run by the `test` stage of docker/fuzzy/Dockerfile:
#
# tests/run.sh <level> (x86-64-v1 ... x86-64-v4)
#
# For every package: the prism build varies under --mode=sr, the ieee build
# does not, and prism --mode=rn stays within MAX_ULP of ieee. PRISM's rn does
# not break ties like IEEE round-t... |
9f123f69971859ef7bb2f5ec765577e579fa3d2b8c61486637a9668d682fcad5 | Shell | 6,926 | 188 | #!/bin/bash
# Resting state preprocessing
# Written by Casey Paquola and Reinder Vos De Wael (Oct 2018).
# and a tiny bit from Sara (Feb 2019)...
# and a whole lot from Sara (August 2019)
# and incorporation to mica-pipe by Raul (August-September 2020)
# and addition of a bunch of fancy flags by Jessica (October-Novemb... |
0742ca45d5676a6eeda9b6f3fe30efb1cbadff074836cf364df28775a2c263c1 | Shell | 6,989 | 213 | #!/bin/bash
#: Title : test_fit_wrlv
#: Date : 2019-10-03
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_wrlv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
a597b79687417943f88bb74729c0abb91088e7592dc3fa705cddedc145781349 | Shell | 7,047 | 226 | #!/bin/bash
#: Title : test_tac2suv
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tac2suv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
fa8b18b5b0f6c96e7c1c595aa05cf7f9b19375bfebf728ac99afbdf03c34718f | Shell | 7,056 | 170 | #!/bin/bash
#
# Preprocess data.
#
# Dependencies (versions):
# - SCT (6.3.0)
#
# Usage:
# sct_run_batch -script preprocess_data.sh -path-data <PATH-TO-DATASET> -path-output <PATH-TO-OUTPUT> -jobs <num-cpu-cores>
# Manual segmentations or labels should be located under:
# PATH_DATA/derivatives/labels/SUBJECT/ses-0X/an... |
0f29b4dc6d09a002d7bd07f5099ecf8db776a2e24fcfcf3a1e235e908e088550 | Shell | 7,081 | 213 | # Settings file for FIX
# Modify these settings based on your system setup
FIXVERSION=1.06
# (actually this version is 1.068 - see wiki page for details)
# Get the OS and CPU type
FSL_FIX_OS=$(uname -s)
FSL_FIX_ARCH=$(uname -m)
if [ -z "${FSL_FIXDIR}" ]; then
if [ "X$0" = "X-bash" ]; then
FSL_FIXDIR=$(pwd)
else... |
4ba27a0983b5458fe7edfcc4063a1cc9ecf5d7f02fb191978bbddee7aeec0e4a | Shell | 7,096 | 232 | #!/bin/bash
#: Title : test_esetstrt
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../esetstrt
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
31e9f1f6a3317d586451883d0750e8455685d7a406374874f02b46f8ec58fb23 | Shell | 7,098 | 212 | #!/bin/bash
#: Title : test_fit_trtm
#: Date : 2022-03-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_trtm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
9b631b903902cdc098c3b4f6e9cae8f130d1ad69b8bc9b955946cf3c9a6eb2f1 | Shell | 7,116 | 203 | #!/bin/bash
#: Title : test_parcoll
#: Date : 2018-06-07
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../parcoll
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
f6df179b552891304e2f33210ef200faa89002cd4337c616c4ff61db2a7e6f02 | Shell | 7,120 | 212 | #!/bin/bash
#: Title : test_iftedit
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../iftedit
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
e97ea5997b334d62999250bc2b6c1f2a8fe6e2c208bbb1bcc3c2504636516d78 | Shell | 7,123 | 112 | #!/bin/bash
mkdir ../data/0_refs
#make list of transcriptomes
cat ../data/Adult_Table.txt | awk '{print $8}' | sort -u | grep -v "TranscriptomeRef" | tail -n 16 > ../data/0_refs/transcrList.txt
#get them, difficult to put in loop so manual
#Mus
wget https://ftp.ensembl.org/pub/release-104/gtf/mus_musculus/Mus_musculu... |
99f1a67f296e879e92428dc4ca43825b00d0c4474a386b3cfe1959c33c7b3709 | Shell | 7,160 | 218 | #!/bin/bash
#: Title : test_ecatnorm
#: Date : 2016-11-02
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../ecatnorm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
0d516345732f77c2d3daf38d812a268044b632c7b929b057eeea7ac823ed5ed8 | Shell | 7,165 | 141 | #!/bin/bash
#
# This script uses tools from MRtrix3 to prepare subject tractograms for COMMIT by removing all streamlines which do not connect 2 gray matter regions.
#
# 1. Computes a single connectome using the parcellation given by $parc_name
#
# 2. Reconstructs the tractogram using the node assignments from this sin... |
f446c163bd507f9879ddc238f40a773de26e691a4457bc8714ebed285699c9d6 | Shell | 7,168 | 205 | #!/bin/bash
# This script builds portable ont_vbz binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, ... |
82a151a2ba095e6aa5e106a04d05a4126364c3dedd0718501226331dd9666b34 | Shell | 7,237 | 270 | #!/bin/bash
#: Title : test_tacfcont
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacfcont
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
d53565053fb00f08dcf3c3757dc60e84e90b77037008f4f146a0b34ae060f33a | Shell | 7,325 | 219 | #!/bin/sh
# the next line restarts using tclsh \
exec cg source "$0" "$@"
# Script to download and prepare all reference databases (including genome) for hs1
# call using
# makedbs_hs1.sh ?options? ?dest? ?webcache?
# where
# * dest: the directory where the reference databases will be installed (default /complgen/ref... |
1a8703424676536475d7786bfdffa6c49122be20592a0ffd6ba79af2029ebed5 | Shell | 7,330 | 217 | #!/bin/bash
#: Title : test_imgadd
#: Date : 2016-11-18
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgadd
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
ef8e67c03488cb3eacd1f72f672bdb52bd1ca776f603537f824f577f2526c39f | Shell | 7,333 | 217 | #!/bin/bash
set +e
source /home/bdemedeiros/software/miniconda3/etc/profile.d/conda.sh
conda activate varKoder
mkdir -p /data/bdemedeiros/varKodes_allSRA
#ln -sf /data/bdemedeiros/varKodes_allSRA/ varKodes
# CSV file name
csv_file="train_valid_sets.csv"
# Function to list records already processed
export RUN_ID_FIL... |
9ee26aa5d1fb30ef22e41cbf39106cf63740f208b3a25d30493b10554a13bb90 | Shell | 7,336 | 185 | #!/bin/bash
#
# Registers T1w --> dwi space using a rigid approach applying the parameters given as input
#
#
# # INPUTS:
# $1 : id = num in (01..30)
# $2 : SES = num in 1, 2
#
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#----------------------------------------------------------------... |
d01d87532f70f61badfc7a220b0ea84618a4d8ec6cb8e0b6bec95d33a362127e | Shell | 7,385 | 286 | #!/bin/bash
# This script builds portable flair binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, if... |
533636343b5588d9e807f6e2e4ceba14f51b26da9ad174e8221fda3909fb2fc6 | Shell | 7,470 | 225 | #!/bin/bash
#: Title : test_iftren
#: Date : 2018-01-16
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../iftren
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
3f50ea9c504185c1271b41d89d12494fe092073c493bd8ed58a5f4ea559f9933 | Shell | 7,472 | 51 | #!/bin/bash
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=2
#SBATCH --time=48:00:00
#SBATCH --mem-per-cpu=60GB
#SBATCH --account=bbenayou_34
module purge
module load gcc/8.3.0
module load star/2.7.0e
WorkDir="/project/bbenayou_34/mcgill"
cd $WorkDir;
export GENIN="/project/bbenayou_34/mcgill/index"
... |
1c7c11133bcbdc99ff404258b37554c2a447bb76947e016837db32398d9116ef | Shell | 7,498 | 201 | #!/bin/bash
#: Title : test_imgfiltl
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgfiltl
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
dc9ccd619452180ecde2d21954d8abb189a88dd769d5dcb050536971c2e71aed | Shell | 7,521 | 186 | #!/bin/bash
#02_constants.sh
TESTDIR=Bembidion
TESTDIR_FASTA=Bembidion_fasta
prepend_text() {
local prefix="$1"
shift
eval "$@" 2> >(while read -r line; do echo "$prefix: $line"; done)
}
color=$(tput setaf 1)
reset=$(tput sgr0)
# Check if TMPDIR is not set
if [ -z "$TMPDIR" ]; then
TMPDIR=$(dirname $(m... |
5e43eccdc2f6704177876d86cf3706bbb659e6eed445bad68f87f4e246ff9108 | Shell | 7,524 | 209 | #!/bin/bash
#: Title : test_masklbl
#: Date : 2026-09-12
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../masklbl
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
d9af767a482662a966bdace4e2c27765851d3681e98b8a7c1c288510d435c3b5 | Shell | 7,593 | 219 | #!/bin/bash
#: Title : test_imgdelay
#: Date : 2023-03-22
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgdelay
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
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