sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ca5b25cc698311110cc1f74ae99b4c48cca8f8d32cdfd08ff83cc2676186ba31 | Shell | 11,260 | 267 | #!/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
#----------------------------------------------------------------... |
0466e80660cc84d687ed3af2db1559337da9aae4453914882cca03c225bd8be5 | Shell | 11,302 | 343 | #!/bin/bash
#: Title : test_imgbkgrm
#: Date : 2018-11-15
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgbkgrm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
9c202c98d6548c168b390659143daec9cf0edb62741501b25eaadbed65824261 | Shell | 11,329 | 306 | #!/bin/bash
#
# Automatic bundle segmentation
#
export FSLOUTPUTTYPE=NIFTI_GZ
dir_functions=$(dirname $(realpath "$0"))
MICAPIPE=$(dirname $(realpath "$dir_functions"))
source "${MICAPIPE}/functions/utilities.sh"
version() {
echo -e "\nMICAPIPE (${Version})\n"
}
help() {
echo -e "
COMMAND:
$(basename "$0")
... |
8197580272dc82bb073f532e2cb40bea04f3552a31cc2c8dbf203d7cb3dbdb33 | Shell | 11,461 | 249 | #!/bin/bash
#
# DWI structural processing with bash:
#
# Preprocessing workflow for diffusion MRI.
#
# This workflow makes use of freesurfer, FSL workbench and MRtrix3
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micaopen/templates
#
# ARGUMENTS order:
# $1 : BIDS directory
# $2 : pa... |
0496860eef4926113e5040b8493c3ab977a633de15d5a227413ea1042b4e4f02 | Shell | 11,502 | 268 | #!/bin/bash
#
# T1w Structural processing with bash:
#
# Preprocessing workflow for structural T1w.
#
# This workflow makes use of ANTS, FSL and AFNI
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micaopen/templates
#
# ARGUMENTS order:
# $1 : BIDS directory
# $2 : participant
# $3 :... |
ac2f9d5b8932fd9f9da0382b232b21860a82b6b94ae54086f7542cd5bbda4829 | Shell | 11,535 | 234 | #!/bin/bash
#
# This script works to reconcile the classification of white matter (WM) hypointensities
# as cortical gray matter (CGM) or cerebrospinal fluid (CSF) within a subject's 5TT image
# by replacing the original CGM volume generated by FSL FAST with the cortical ribbon
# generated by Freesurfer. Additionally... |
2a02d4de5a17b2e1c1aab32349edd028282f313ead136d1e137b2b4d01cf3ef8 | Shell | 11,547 | 348 | #!/bin/bash
#: Title : test_imghist
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imghist
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
6ba38f4ae48ec730f9f56f6145597bcb72c2103bee0d06fc64cdb37375c76891 | Shell | 11,625 | 398 | #!/bin/bash
#: Title : test_imgdelpl
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgdelpl
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
c2f8a6518ef0b2f167b1154370ee327d506db092fd845f99798ef2ed3edf67b5 | Shell | 11,706 | 308 | #!/bin/bash
#: Title : test_imgbfk2
#: Date : 2020-02-27
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
#: Todo : Error situations
# Set the name of executable to test
PROGRAM=../../imgbfk2
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: execu... |
29e83772211d391b598927e977e3e9ed57bb2c14b070530f6e65a9f52f56afef | Shell | 11,728 | 339 | #!/bin/bash
#: Title : test_svar4tac
#: Date : 2019-09-13
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../svar4tac
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
b3edaa727fc31b2d3577394f981aac106f1c7089138f460cde76d57c82f328f1 | Shell | 11,781 | 290 | #!/bin/bash
#
# Compare our nnUNet model with other methods (nnUNet-2D and nnUNet-3D) on sci-zurich and
# sci-colorado datasets
# Note: subjects from both datasets have to be located in the same BIDS-like folder, example:
# ├── derivatives
# │ └── labels
# │ ├── sub-5416 # sci-colorado subject
# │ │ └── a... |
bfbc6f813174ac3bb5c1ec8a44f175d03ca19cbd7ae1b9884c9f728f352616e3 | Shell | 11,782 | 363 | #!/bin/bash
#: Title : test_var4tac
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../var4tac
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
53e4286d98290b6855457aac3daf8bc2cde3e2ccce8f1fd7006f9da3616c57b1 | Shell | 11,876 | 380 | #!/bin/bash
#: Title : test_dftweigh
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dftweigh
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
ee377b3661c137ae1c15955d7ae787418fc97d5c76bf001cf944c537fbc08580 | Shell | 11,896 | 424 | #! /bin/bash
# copyright John Maddock 2005
# Use, modification and distribution are subject to the
# Boost Software License, Version 1.0. (See accompanying file
# LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
libname=""
src=""
header=""
all_dep=""
# current makefile:
out=""
# temporary file:
tout... |
becb506e49a04014995d167c1347988a100fbcf314643d1b19a03324ddb62f2c | Shell | 12,054 | 312 | #!/bin/bash
#: Title : test_spillinp
#: Date : 2026-03-23
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../spillinp
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
f8ac73aca85252f33970a940c472ea951856d3e0a6427e5e7aab573e8c445346 | Shell | 12,201 | 401 | #!/bin/bash
#: Title : test_fvar4tac
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fvar4tac
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
d9befa408a6e12519a5902307fa515bf558c60b3aaa71fba56c0a3abafda2241 | Shell | 12,220 | 428 | #!/bin/bash
#: Title : test_tacrange
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacrange
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
6100b3a621ecb655bacae2cf01ccbd72ebb836fe9e00fe49ccb68ff33e1f6948 | Shell | 12,256 | 344 | #!/bin/bash
#: Title : test_imgpeak
#: Date : 2019-09-02
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgpeak
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
b8c7ceba9fe659db637b70037c3ccc1d6cd4450e4382eef28bfebdef4f49a0d9 | Shell | 12,270 | 351 | #!/bin/bash
#: Title : test_tacmove
#: Date : 2025-11-28
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacmove
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
0f25e5db3e096616a47211746db143bce7fd664f377e783f215cfc41d97e30ea | Shell | 12,302 | 357 | #!/bin/bash
#: Title : test_liverpv
#: Date : 2018-05-11
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../liverpv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
6f4669b55aee6494669bef04d4d616919c256e74c2e6597d788fa44927a4e383 | Shell | 12,340 | 339 | #!/bin/bash
#: Title : test_img2dft
#: Date : 2018-12-20
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../img2dft
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
7360ba8f5d303b6bf2f1ecc544168c053e3f24eedcc19bf94fe552a97bd4d236 | Shell | 12,394 | 361 | #!/bin/bash
#: Title : test_imgfsegm
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgfsegm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
aa7eeefa7a08cefa374ee42b78514cd18db40535d272d66d87a27547133f9445 | Shell | 12,473 | 410 | #!/bin/bash -ex
# title notice
echo "HTK training for TIMIT from Cantab Research"
echo "See http://www.cantabResearch.com/HTKtimit.html"
# (C) Cantab Research: Permission is granted for free distribution and
# usage provided the copyright notice and the title notice are not
# altered.
#
# version 1.0: 22Jun06 - first... |
e27777c66fbc5b44513ff9e599937a1d5dfa20a86bd12969a49a6981d844b8d1 | Shell | 12,496 | 342 | #!/bin/bash
#: Title : test_tacmean
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacmean
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
c79793b286a4ad8b3cc717c933082fda1dfdbcd207d63eb30514554bb37233f4 | Shell | 12,529 | 264 | #!/bin/bash
#
# Registers T1w <--> FUNC space using a nonlinear SyN method for a given SUBJECT & SES
#
# # INPUTS:
# $1 : id = num in (01..30)
# $2 : SES = num in 1, 2
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#---------------------------------------------------------------------------... |
e865ceaf055a0050af2893e2cd96c4568b344fbfb44e0295a19c446d136be026 | Shell | 12,577 | 385 | #!/bin/bash
#: Title : test_sim_rtcm
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../sim_rtcm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
79dcf4c1bf11d57aa265678e96f7d994ee889d10832b70b2377fafa9c5aaee97 | Shell | 12,579 | 369 |
# Revision 1 for Sims bash script
# assumes PRS_GX_functions_v2 loaded in, and PRS_GXE_sims.sh already performed.
# repeats analysis with adding an additive+epistatic scenario
# screen -r -D 3115212.pts-202.login-q-1
#####################
source ~/pytorch-env113/bin/activate
########
# take the _smallcases geno... |
f2c9381edaa1ff442e1a124903048bdd063dc7901822bd2639a866c4264e7e7c | Shell | 12,619 | 393 | #!/bin/bash
#: Title : test_imgmtrap
#: Date : 2023-03-15
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgmtrap
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
0d82097e43d53d5a0ae3fa0f531bc783367b93fdcb5a9e007f48fd3f11a329a1 | Shell | 12,621 | 395 | #!/bin/bash
#: Title : test_abssbkg
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../abssbkg
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
df84d2eca7998ab716c5d5abbdc838f90ae8ba0d130c3067af687b5e88330295 | Shell | 12,824 | 382 | #!/bin/bash
#: Title : test_tacren
#: Date : 2019-08-26
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacren
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
3c88fcc9820d168be2e61f59ff05cd1c79bb5e78e0bd3c3c7673d7c8fab69284 | Shell | 12,842 | 501 | #!/bin/bash
#: Title : test_tacmsamp
#: Date : 2019-06-20
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacmsamp
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
4f198685084ccca966f1b89914474617ac829dc1351b21b73fe4dfbfbbe17b48 | Shell | 12,993 | 394 | #!/bin/bash
#: Title : test_masksize
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../masksize
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
b8cbd393895ac660a075518041ffb5a13cce783a9cc1add9ba659094d74d66f8 | Shell | 13,009 | 334 | #!/bin/bash
#: Title : test_fit_wcbf
#: Date : 2026-11-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_wcbf
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
da0e8cc1179cca9e40ca67328c5f0739fee8da29097c8efb8d4164f2629493d4 | Shell | 13,024 | 384 | #!/bin/bash
#: Title : test_dftcat
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dftcat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
e500f2f4a63fe9116a762a7adcf635d8aac298021c90711f740f1be4c6bc1cee | Shell | 13,282 | 237 | #!/bin/bash
# C. Cocuzza, 2023-2024. Running HCP processing pipelines on Transdiagnostic Connectome Project (TCP) data.
# This script is specifically for post-fix QA (visualizing scenes) on select participants.
# Based on HCP-provided example PostFixBatch.sh
# NOTE: set up of environment, compilers, paths, etc. are... |
0df8e84c88ae8433d8f67c037506a0cbbf877607817f873ab23e162272fdf63d | Shell | 13,332 | 395 | #!/bin/bash
#: Title : test_convexpf
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../convexpf
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
9ee3a15a1280078075b87084573203b91b13571fb7b259754d3b72ec07cd8dba | Shell | 13,559 | 396 | #!/bin/bash
#: Title : test_simimyoc
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../simimyoc
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
9ab54ac3e66e40b6daff101a5f20e99a580de10ed62fefd0629db2ec232a7b45 | Shell | 13,562 | 351 | #!/bin/bash
#: Title : test_pxl2tac
#: Date : 2016-06-13
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../pxl2tac
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
5c9b4c35aaf083ea4cd03de16008aa0ed58ab0ed4d42abb8cdd9769369ba754e | Shell | 13,710 | 446 | #!/bin/bash
#: Title : test_tacformat
#: Date : 2023-02-13
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacformat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist... |
3437eee544469e685ca401039f4158d16529e583c5f81a5964b55272fe612402 | Shell | 13,798 | 367 | #!/bin/bash
#
# Compare the CSA of soft GT thresholded at different values on spine-generic test dataset.
#
# Adapted from: https://github.com/ivadomed/model_seg_sci/blob/main/baselines/comparison_with_other_methods_sc.sh
#
# Usage:
# sct_run_batch -config config.json
#
# Example of config.json:
# {
# "path_data"... |
f50e8c1529618e7c8a681042f05563abd7eca08d7069cba5d4f205ac69966d42 | Shell | 13,919 | 387 | #!/bin/bash
#: Title : test_fitdt
#: Date : 2026-04-08
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fitdt
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
e0318df6deb2dee50b6d84262f2c57d593e0c7a5b2ce11aa5621668acbe9ab6a | Shell | 14,047 | 424 | #!/bin/bash
#: Title : test_b2t_mo2
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../b2t_mo2
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
6faf119256a9d4fb6429681619d72f62953647a5a707d0ca5bc16a0b29159d3e | Shell | 14,137 | 398 | #!/bin/bash
#: Title : test_ecatmrp
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../ecatmrp
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
aa4a534608125238633b1403827a328a362ed819cb12ee8e6f028f885c297ef0 | Shell | 14,174 | 399 | #!/bin/bash
#: Title : test_bfmh2o
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../bfmh2o
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
430b08ac9ac9e637433522e4e73b6ffff6697c704c668a66ca85355612b0c6ca | Shell | 14,385 | 400 | #!/bin/bash
#: Title : test_sim_av
#: Date : 2019-01-24
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../sim_av
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
21f160a8b21d56956bb3acaa9f8846c858b561572b7098e22457967f39b99fcb | Shell | 14,502 | 349 | #!/bin/bash
#: Title : test_dftinteg
#: Date : 2014-10-02
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dftinteg
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
8b0ff25c5fc79b5992516040cabf3e816a9eae72833e80fd19cd29e93ab40a0a | Shell | 14,557 | 433 | #!/bin/bash
#: Title : test_imgbox
#: Date : 2016-06-14
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgbox
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
4c270a23214ae544cb41945553aa29fea2c3c2a8681e7cedbc03162c48c58dfc | Shell | 14,568 | 432 | #!/bin/bash
# This script builds external tools which are by default distributed with genomecomb using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 ... |
e996859424ad416acf46043514bbdae3352864727ae7f72f4de6f235fb31e2a6 | Shell | 14,623 | 434 | #!/bin/bash
#: Title : test_imgprofi
#: Date : 2018-02-13
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgprofi
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
414de7bbc93118465a7ac4aa0c968523725067abb8534e52087245a5122f6ef4 | Shell | 14,710 | 446 | #!/bin/bash
#: Title : test_rescoll
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../rescoll
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
d23b2c68e9e13fe8badb53cccd79419b2740acf9e802af65c4b3dce2292cd68c | Shell | 14,812 | 424 | #!/bin/bash
#: Title : test_ecatfbp
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../ecatfbp
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
0c1d45fbbe3c71c195dc0d0cf961577c7bf0b38a77d01774e037eb56bbfbccd8 | Shell | 14,866 | 444 | #!/bin/bash
#: Title : test_fitmbf
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fitmbf
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
f6a9ecc2e944a14a948d53eff769c3cf3064bc90276eec46319f2d0634c21876 | Shell | 14,979 | 351 | #!/bin/sh
# the next line restarts using tclsh \
exec cg source "$0" "$@"
set build hg18
set mirbasegenome hsa
set mirbaserelease 20
logverbose 2
if {![info exists argv]} {set argv {}}
set argv [job_init {*}$argv]
foreach {dest webcache} $argv break
if {![info exists dest]} {set dest /complgen/refseqnew}
if {![info ... |
c6d154ea9807a60e720a252552d23bb208dee155b0e1aea72747acbc8beabf86 | Shell | 15,011 | 376 | #!/bin/bash
#: Title : test_taccbv
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../taccbv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
bd7bbaad984be904b764994444d5026b1175df47963f6deff7e7ba5e5b4fe346 | Shell | 15,044 | 491 | #!/bin/bash
#: Title : test_imgcutof
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgcutof
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
002a0c907006ac6b4aced0ce754bbff2b98fd42063701babcddec42739898ed4 | Shell | 15,058 | 172 | #!/bin/bash
#SBATCH -o logs/2024.12.12.
#SBATCH -J pert_seq
#SBATCH --time=5-00:00:00
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=150G
#SBATCH --cpus-per-task=20
#SBATCH --nodes=1
#SBATCH --gres=gpu:1
#SBATCH --partition=gpu
#--partition=gpu or defq
echo " "
echo " Nodelist:= " $SLURM_JOB_NODELIST
ech... |
c081a0c6248a7994cc79c07cc9e8abc75a1e1bdb048207fa6254fb59229371de | Shell | 15,230 | 467 | #!/bin/bash
#: Title : test_imgledif
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgledif
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
4a96cc8cac8c3b48d93873bf67b3ff626d83a658b3ee9858fae233cb34649138 | Shell | 15,288 | 493 | #!/bin/bash
#: Title : test_imgflip
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgflip
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
0f42605d8db4fe10deacd04cbf35e93792aad21c04aad43bb42670ad6d2646fa | Shell | 15,302 | 426 | #!/bin/bash
#: Title : test_fit_bpr
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_bpr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
6609ddad8f97daab358c3ca091fd0a803beac6db2d314f6df3cc0b2f3bf2b65f | Shell | 15,473 | 489 | #!/bin/bash
#: Title : test_injdifft
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../injdifft
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
2669c58c32f79a88c7b46ae05fc1f25f91d2222a6d5db17fc066b11868519131 | Shell | 15,501 | 341 | #!/bin/bash
#: Title : test_maskcloak
#: Date : 2022-02-17
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../maskcloak
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist... |
ab310ff93daeb8d3e971905564ea2309fd25c3096ffaa25810090e730ac2214d | Shell | 15,638 | 507 | #!/bin/bash
#: Title : test_fit_fexp
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_fexp
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
2c567f13b0a3f8ec7a77a72e705472858d7fe2f476e409cee37070e388184945 | Shell | 15,659 | 469 | #!/bin/bash
#: Title : test_imglhbdv
#: Date : 2019-06-19
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
#: Todo : Error situations
# Set the name of executable to test
PROGRAM=../../imglhbdv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: exe... |
998f1c1ce0de9718fafa9099007b8603df95c78286af72d5e6c97a0157f3264b | Shell | 15,660 | 416 | #!/bin/bash
# 03_test_installation.sh
source 02_constants.sh
# Initialize arrays to track successful commands and profiling data
successful_commands=()
# Check if bash version supports associative arrays
if [[ "${BASH_VERSINFO[0]}" -ge 4 ]]; then
declare -A command_exit_codes
declare -A command_wall_times
... |
79d467f667a4c61b5b8c6d484131d9d0f202527b8351458c782c99f48724de44 | Shell | 15,736 | 281 | library(tidyr)
#I want to look at the distributions of ortho tpms by species
#hypothalamus
#Lets start by looking at fuk
orthhypfuk <- read.table("/Users/bill/project_Adult_EVE/data/step1_transcripts2genes/orthotpms/hypot/ortho.fuk.hypot.tpm.tsv", header=FALSE)
as_tibble(orthhypfuk) %>%
pivot_longer(names_to = "sampl... |
4328763af08be05db63b4d6700c5da90b60c522d38fed90c00fd608e0d816863 | Shell | 15,798 | 483 | #!/bin/bash
#: Title : test_fit_hiad
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_hiad
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
23d379401ed6eb5124cd0ceed89cf5a7e0a7e151378af9e2f805cd74c845262b | Shell | 15,804 | 475 | #!/bin/bash
#: Title : test_img2flat
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../img2flat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
63ac6c4a696539488f5fb5923b36e7a405e0b29f676c6168f75232bc2b74f3b6 | Shell | 15,890 | 453 | #!/bin/bash
#: Title : test_dftsuv
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dftsuv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
ba5d270c4226394b6c3292108f6f7865bbb6f1a648a85e4606d0429098b8d98c | Shell | 16,174 | 490 | #!/bin/bash
#: Title : test_imgdelfr
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgdelfr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
5b9deeb0f95472e8e203a4e09add59db5c57d3933f8d067d7eb93939aa931cf3 | Shell | 16,197 | 310 | #!/bin/bash
#
# Generates structural connectivity matrices using the following parameters:
#
# (1) Parcellations: ("aparc-a2009s" "aparc" "economo" "glasser-360" "vosdewael-100" "vosdewael-200" "vosdewael-300" "vosdewael-400" "schaefer-100" ...
# "schaefer-200" "schaefer-300" "schaefer-400" "schaefer-500" "scha... |
8e85070c182f47eeea9c35632c1477aada51eb212d0e9493f64edd871260b9de | Shell | 16,230 | 471 | #!/bin/bash
#: Title : test_fit_gvar
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_gvar
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
cdb426d6c3f66a5f4b6ed1ae2476e64cd677b152d6c93991ec0607b3586eb024 | Shell | 16,438 | 390 | #!/bin/bash
#
# exit on any error at any time
set -beEu -o pipefail
# all files should be permissions 'rw-' for 'user' 'group' 'other'
umask 0
# debugging trace all commands, uncomment this set -x statement:
#set -x
#
# trashCleaner.bash - script to save session user data into a special
# area outside of trash, and ... |
7e113cceec551d2b83ce7458d8f4531ab6123b03b7b496fd71d0d6817aecb980 | Shell | 16,572 | 467 | #!/bin/bash
#: Title : test_convttm
#: Date : 2020-01-19
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../convttm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
5e1268a221a1fa1645b6fd5aebc39f040abae11781d448ce07ac54f8415db83b | Shell | 16,766 | 531 | #!/bin/bash
#: Title : test_dftmax
#: Date : 2018-03-08
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dftmax
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
3c2dafaad1bb41096760e962ed13cebe82e64a9c6da998805b03ce0491a50da8 | Shell | 17,116 | 515 | #!/bin/bash
#: Title : test_imglhdv
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imglhdv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
aeb0906c934d9dd0059ae350cd2f1ba592b54a928fed3bfa95dda471fef7829f | Shell | 17,217 | 552 | #!/bin/bash
#: Title : test_tacdecay
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacdecay
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
346ada8aede373ddf87bb8270016bcf47c0494a279283e7b3de274df03b7bbc9 | Shell | 17,309 | 369 | #!/bin/bash
#
# Registers T1w & dwi images using multiple methods / parameter combinations in ANTs (flirt also compared)
#
# # INPUTS:
# $1 : id = num in (01..30)
# $2 : SES = num in 1, 2
#
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#---------------------------------------------------... |
2449f57e0408360dc365b0e60ce91b36322e1ca8c718f9e1cf8326f253d0fc7b | Shell | 17,367 | 477 | #!/bin/bash
#: Title : test_dftratio
#: Date : 2022-05-09
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dftratio
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
5f868c79bd753f1b2cfafb61539ba583b9bd330ca486bf4ffb30a42ee846732f | Shell | 17,814 | 468 | #!/bin/bash
#: Title : test_fitdelay
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fitdelay
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
bdca3d3445b1b6f2a4a6cb1ab27f2c04a31fd9fed8ca1ae27c01589c970e0cef | Shell | 17,919 | 498 | #!/bin/bash
#: Title : test_imglhk3
#: Date : 2018-03-22
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imglhk3
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
e22a0e79317ca42b7cb5b48ec9a939979bbacce44ea5ee68d3893930f98ed67a | Shell | 18,054 | 430 | #!/bin/bash
#: Title : test_ecat2nii
#: Date : 2016-11-30
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../ecat2nii
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
9486cc7c9658bc5da298d632992f16e1f25f01bad9647eb178596bf31c1f7017 | Shell | 18,144 | 522 | #!/bin/bash
#: Title : test_heartcor
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../heartcor
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
28c88b931764770f8bb2facf02929e5c822f395149a565fab943bf2aff057428 | Shell | 18,246 | 552 | #!/bin/bash
#: Title : test_parformat
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../parformat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist... |
33b9f39fa3f6c643cddf99376be695d932fb22b083bc46bb3ee9062cb971ed75 | Shell | 18,295 | 588 | #!/bin/bash
#: Title : test_eframe
#: Date : 2019-06-18
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../eframe
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
173d7d66b70b063117d22d9b1385a1e0074c50fb5be5fe72d537584d362e236b | Shell | 18,458 | 443 | #!/bin/bash
set -e
set -x
do_preproc=1
do_connmeasure=0
do_concat=0
#set these after determining if its HCP or not first
#bpfarg="--lowfreq 0.008 --highfreq 0.09"
#hpfarg="--lowfreq 0.008"
#bpfarg="--lowfreq 0.01 --highfreq 0.15"
#hpfarg="--lowfreq 0.01"
#skipvolarg="--skipvols 10"
#connarg="--connmeasure precisi... |
9d7cb42070918fd8ace06d25ae147da11fb50f658e4267eac4edfe627905c61c | Shell | 18,483 | 557 | #!/bin/bash
#: Title : test_b2t_h2o
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../b2t_h2o
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
867451b0f8a351535011edb96fb21ab61a5ef8b4cbcd204bf802f119c8d8e2f5 | Shell | 18,505 | 532 | #!/bin/bash
#: Title : test_tactime
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tactime
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
275da29070591f36ca320aac4da814f13c3f90677639ae5af0485e15b12574fb | Shell | 18,883 | 555 | #!/bin/bash
#: Title : test_simcmdk
#: Date : 2023-04-06
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../simcmdk
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
26048cc1f51cbaa8ff578bbb4885239e0645b6669adb8e733cdf602c1773f3e8 | Shell | 18,954 | 590 | #!/bin/bash
#: Title : test_imgthrs
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgthrs
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
e7bf17d8a4150478194e3e805841982942d51410482a23e87ee4895fa523cea8 | Shell | 19,017 | 377 | #!/bin/bash
#
# Process data.
#
# Usage:
# ./process_data.sh <SUBJECT>
#
# Manual segmentations or labels should be located under:
# PATH_DATA/derivatives/labels/SUBJECT/<CONTRAST>/
#
# Authors: Julien Cohen-Adad
# The following global variables are retrieved from the caller sct_run_batch
# but could be overwritten ... |
393380ed4f244915a5b5011bb95f66033816db96f8aac3e6795c51bccb815628 | Shell | 19,090 | 645 | #! /bin/bash
# Copyright (c) MONAI Consortium
# 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 required by applicable law or agreed to ... |
29b71d052cd73a590a070602416ddd13725cfa8203661ff1b0c8be1e48272303 | Shell | 19,178 | 502 | #!/bin/bash
#: Title : test_eabaort
#: Date : 2023-06-30
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../eabaort
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
042739ea25bb359487b16d11adf7dfb33b6c4cd2c148504d8c41695efb66f78d | Shell | 19,267 | 558 | #!/bin/bash
#: Title : test_tacweigh
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacweigh
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
430e67e91382766639990db7ce2edffc457019f87e01584ab67e4029a1a1ba3c | Shell | 19,658 | 572 | #!/bin/bash
#: Title : test_imgbfk3
#: Date : 2018-03-20
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgbfk3
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
beb6bdfa8cf89461ce54125a61034daa77b2de969c0fb4ee8173ef51e835dbf9 | Shell | 19,773 | 674 | #!/bin/bash
#: Title : test_ana2ecat
#: Date : 2026-09-11
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../ana2ecat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
7b62621d2b1c91a5fc0354d45e83e414ab23ea4130603027ecdd4437206769e2 | Shell | 20,074 | 532 | #!/bin/bash
#: Title : test_imgki
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgki
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
9f813b9afc41d70d6ce21ffd889fbf9a77c031cd09affb38d779cae35e0ec0de | Shell | 20,146 | 554 | #!/bin/bash
#: Title : test_pardiff
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../pardiff
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
4735b7923095111d5efa2d78521189c6214e5e8c10a2e6ce571741022006db9d | Shell | 20,234 | 555 | #!/bin/bash
#: Title : test_fit_pbr
#: Date : 2023-05-23
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_pbr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
7e9a43f6943637c061662503c08d8a379d6500327cbcb579d1d1d16502c6fe11 | Shell | 20,379 | 83 | #!/bin/tcsh -efx
cp inDir/wgEncodeHudsonalphaChipSeqPeaksA549Gr.broadPeak.gz outDir/wgEncodeHudsonalphaChipSeqPeaksA549Gr.broadPeak.gz
encodeMergeReplicates -add -maxMin -uniqueName inDir/wgEncodeHudsonalphaChipSeqPeaksRep1A549CtcfPcr1xDexa.broadPeak.gz inDir/wgEncodeHudsonalphaChipSeqPeaksRep2A549CtcfPcr1xDexa.broadP... |
3bf4698183562cb954d2fea8f5d91fb631e0e0e73439d093f3f52511ec2d81d3 | Shell | 20,704 | 627 | #!/bin/bash
#: Title : test_imgsuv
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgsuv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
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