sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
51c4facffbb10cd1a0f4626ebe62081a7b61512a8608b31bfbf80e5b0ccab9cc | Shell | 3,381 | 104 | #!/bin/bash
# Copyright 2017 The TensorFlow Authors. 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 required by... |
9b3d5075a5359c33fd8acc5ace47ca96939c9188fa9f6d7abac412836f92e45b | Shell | 3,382 | 104 | #!/bin/bash
# Copyright 2017 The TensorFlow Authors. 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 required by... |
e241efe81196e2fee5ebaf8dbd96e6e58a7970140f183e0d4474fe7663be249c | Shell | 3,397 | 117 | #!/bin/bash
# Test that the LLVM instrumentation pass emits ISA-specific vector wrapper
# calls when compiling with explicit architecture flags.
#
# For each ISA level the test:
# 1. Compiles test.c with the corresponding flag
# 2. Checks that the post-instrumentation IR (.2.ll) contains a call to the
# expect... |
adf8ee0b36d574e764aa8b490952d1bff3704f6840d7a98c57105eaac709235c | Shell | 3,439 | 117 | #!/bin/bash
#: Title : test_perfrat
#: Date : 2019-02-28
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../perfrat
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
affcc022fd8eb7a7a0c080ccc4e0107747d09f81c0aed563d41ee6dbbed494be | Shell | 3,447 | 67 | #/bin/bash
#
# initializes dependencies & paths necessary to run micapipe & related functions
#
#
# 2021 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#
# 2023 adapted to public version of micapipe & the BIDS organized MWC data by Mark Nelson
#---------------------------------------------------------------... |
b75abb7347ee80916bf23964c74c7ab0049762889d7a21a4d1b0ec3d153f3558 | Shell | 3,451 | 119 | #!/bin/bash
#: Title : test_mask2pxl
#: Date : 2017-08-30
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../mask2pxl
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
995e072e5bcb0b86ecaa19aee36b9dfa8033acec0cafefac0570a32292a6f00b | Shell | 3,454 | 63 | movfiletype=hcp
gmfile=inputdir/mysubj_graymatter.nii.gz
wmfile=inputdir/mysubj_whitematter.nii.gz
csffile=inputdir/mysubj_csf.nii.gz
erosionvoxels=1
filtname="hpf"
filtarg="--lowfreq 0.008"
skipvols="5"
gsrarg="--gsr"
connarg="--connmeasure covariance --shrinkage 0"
roiname=fs86
roifile=fs86.nii.gz
for scan in scan1... |
4b7c0c262ffe15729b03afece0735c8e6a3d32d1d802db319db90ab123db95b4 | Shell | 3,458 | 114 | #!/bin/bash
#: Title : test_dcftime
#: Date : 2018-05-27
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dcftime
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
771969c94efcd7389c0c28c709777b800cc3c26c0b2027ded13b1f2d014aa598 | Shell | 3,459 | 106 | #!/bin/bash
# Copyright 2017 The TensorFlow Authors. 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 require... |
95e8c45b46a0a85810168631ccdd9b1e0fa807037acd80773289727b64195e9f | Shell | 3,470 | 105 | #!/bin/bash
#: Title : test_niinan
#: Date : 2023-03-25
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../niinan
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
a66d2e24a5a6ff6a7374dc781bfc2302ac111aeeef1983df7f70132c04dff741 | Shell | 3,479 | 36 | #!/bin/sh
# GFF
# wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Macaca_fascicularis/GFF/ref_Macaca_fascicularis_5.0_top_level.gff3.gz
# Fasta
# wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Macaca_fascicularis/Assembled_chromosomes/seq/mfa_ref_Macaca_fascicularis_5.0_chr1.fa.gz
# wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Macaca_fa... |
7d72e4f22255e5a1af37a2abfaf2d751e347e670f9c528cb3d5bc3f86868a288 | Shell | 3,480 | 147 | #!/bin/bash
# This script builds portable hap.py binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, i... |
8d7f227e3f403b428fe75fdda6cc4d8671c2bbea3cd134e379bacf3d564d2500 | Shell | 3,483 | 111 | #!/bin/bash
{#-
# This is a template for generating a job script that will be run on an HPC
# cluster. It is written using the Jinja templating language (see
# https://jinja.palletsprojects.com for more information).
# All variables starting with the "NIPOPPY_" prefix are set internally by
# Nipoppy and cannot be cha... |
c6e89c6ab49b74581506976d569a5a188231aa8950b3033ad7cfacc4335b5d8d | Shell | 3,489 | 94 | #!/bin/sh -e
# Convert chromosome names for FASTA files
# zcat ORI/ref_Macaca_fascicularis_5.0_top_level.gff3.gz \
# | sed "s/NC_022272.1/chr1/" \
# | sed "s/NC_022273.1/chr2/" \
# | sed "s/NC_022274.1/chr3/" \
# | sed "s/NC_022275.1/chr4/" \
# | sed "s/NC_022276.1/chr5/" \
# | sed "s/NC_022277.1/chr6/" \
# | ... |
01fbe12ed3529dc8d22b34c37ba6a862a510d1a95b59d2d96443ba569d4e8223 | Shell | 3,491 | 119 | #!/bin/bash
#: Title : test_imginv
#: Date : 2018-05-31
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imginv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
f8a305ebfbccc41686eedcf54fafe764a1f4c0f61152e40b9cf446d6d3c8e15b | Shell | 3,495 | 116 | #!/bin/bash
#: Title : test_dcmlhdr
#: Date : 2019-05-02
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dcmlhdr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
2ca3dbe1a206576e9d832252634eadf5aa5c7bec4fa8b3459338ea773508b1d5 | Shell | 3,497 | 106 | #!/bin/bash
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... |
2ee241d94c906bc6e0f0d633d8c1819f979e733f4c9ea4160ab0d47b1e26bf6f | Shell | 3,503 | 86 | #!/bin/sh
#-------------------------------------------------------------------------------
#
# Command lines for SnpEff's manua (examples)
#
#
# Pablo Cingolani
#-------------------------------------------------------------------------------
genome="GRCh3... |
e4141781b63168ad9c4ef3e65062f1ae8eaf4c333ba603f35e1de668a88b3368 | Shell | 3,517 | 135 | #!/bin/bash
# This script downloads a build of modkit, and puts it in a portable directory
# 32 bit option is ignored
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# The Holy build box environment requ... |
c413ab5504dad402dd32cfbfa4594ee03ad1b877e9a6cb809ec1dfc6681296e1 | Shell | 3,524 | 115 | #!/bin/bash
##uncomment to stop on error
set -e
source "$(dirname "$0")/../paths.sh"
if [ -z "${LLVM_LIBDIR:-}" ] || [ ! -d "${LLVM_LIBDIR}" ]; then
echo "Error: LLVM_LIBDIR is not set to an existing directory: '${LLVM_LIBDIR:-}'" >&2
exit 1
fi
LLVM_OMP_DIR=""
for _cand in "${LLVM_LIBDIR}/aarch64-unknown-linux-gn... |
ab2d5bfc9511b5fe500d736277de42d7dc6f4d13592359b72cfdcba88f432ea4 | Shell | 3,543 | 144 | #!/bin/bash
print_banner() {
printf "\n\n\n\e[30m\e[42m$1\e[0m\n\n\n\n"
}
print_banner "Distributed status: $1"
echo $2
DATADIR=$2
if [ -n "$3" ]
then
USE_BASELINE=""
else
USE_BASELINE="--use_baseline"
fi
if [ "$1" == "single_gpu" ]
then
BASE_CMD="python main_amp.py -a resnet50 --b 128 --workers 4 --deter... |
07aa13fadc747a45bd16af8a3efa7ecb36725570490720dbe1b8fc65185b7e29 | Shell | 3,557 | 129 | #!/bin/bash
#: Title : test_maskconj
#: Date : 2017-08-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../maskconj
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
60680bbad4734c8c31a79a59a84600b9d5e8bc548c2596760284f2ad41287d70 | Shell | 3,567 | 99 | #!/bin/bash
# Copyright 2016 Google Inc. 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 required by applica... |
067b5e25b50a7c7c51bd69dc0fb79800a7ddebcca10febafe0e4c3e2f7f00da4 | Shell | 3,576 | 108 | #!/bin/bash
#: Title : test_tac2nii
#: Date : 2023-03-25
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tac2nii
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
5d9184fccc27d28aa2bbfd2bc0fb7d18d8df563ceb69f252040a7bc4fc9077c5 | Shell | 3,585 | 128 | #!/bin/bash
#: Title : test_e63to7
#: Date : 2016-11-02
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../e63to7
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
4dbf7707e6094a96a5e39bfa68a6c2de375bd117aaaed3c14e93e2daae5c4004 | Shell | 3,638 | 148 | #!/bin/bash
set -e
export SAMPLES=100
# check if variable static is set
: "${STATIC_DISPATCH:=0}"
if [[ $STATIC_DISPATCH -eq 1 ]]; then
DISPATCH="static=1"
else
DISPATCH=
fi
# check if variable march_native is equal to 1
# Ensure MARCH_NATIVE is set to either 1 or 0
: "${MARCH_NATIVE:=0}"
if [[ $MARCH_NAT... |
6345b11abea0d7cf55ab04704c9fe7feab64d776c8bdc423ef2052b60c709c98 | Shell | 3,658 | 120 | #!/bin/bash
# This script builds portable biobambam binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build... |
d3b4487d4f37ed63d726e400f229f59d5bb2bc455cee7808e37c2446938c8e32 | Shell | 3,679 | 109 | #!/bin/bash
# Copyright 2017 The TensorFlow Authors. 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 required by... |
27a81b8bf76678d751cd614be81ea8c5565157ac37fa3b67e895faef079b7317 | Shell | 3,692 | 141 | #!/bin/bash
# This script creates a portable nextflow appdir
# While it does not compile nextflow, Holy build box is still used to have same environment as other tools
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build... |
e27dab19e4b5c26feae6aeb42b1b8d25c09b041874c1ff85b852db1b157e7be8 | Shell | 3,694 | 71 | # Zeiss
# BEADS_DIR="/media/Data/smlm_z_data/20231121_nup_miguel_zeiss/stacks/";
# OUTDIR="/home/miguel/Projects/smlm_z/publication/VIT_Zeiss";
# OUTDIR='/home/miguel/Projects/smlm_z/autofocus/VIT_zeiss/out_resnet_fov-max_aug11'
# OUTDIR="/home/miguel/Projects/smlm_z/autofocus/VIT_zeiss_lowsnr_data/out_resnet_fov-max_a... |
e01b9100972af89f190f37da6dac74108d0cfd9159c0f78f319c30db10d67b3c | Shell | 3,717 | 101 | #!/bin/bash
TIMITROOT=$1
HTKTools=$2
mkdir -p data
MFCCCONF=conf/htk_mfcc.config
FBANKCONF=conf/htk_fbank.config
lower_case=0
upper_case=0
if [ -d $TIMITROOT/TIMIT/TRAIN -a -d $TIMITROOT/TIMIT/TEST ];
then
upper_case=1
TIMIT=$TIMITROOT/TIMIT
elif [ -d $TIMITROOT/timit/train -a -d $TIMITROOT/timit/test ];
t... |
d8a0fa256843729f17617b26276d81f027af0cc57c59988511c6ddd6063525de | Shell | 3,737 | 113 | #!/bin/bash
#: Title : test_fit_wcdf
#: Date : 2019-10-03
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_wcdf
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
d76305599ecdfa9f1dc0ded10507a0f46b6615537e810652c8498d2bdcebd50d | Shell | 3,756 | 138 | #!/bin/bash
OUTPUT_FILE=output
ERROR_FILE=error
VERIFICARLO=verificarlo-c
show_env() {
echo "VFC_BACKENDS_LOGGER=${VFC_BACKENDS_LOGGER}"
echo "VFC_BACKENDS_LOGGER_LEVEL=${VFC_BACKENDS_LOGGER_LEVEL}"
echo "VFC_BACKENDS_SILENT_LOAD=${VFC_BACKENDS_SILENT_LOAD}"
echo "VFC_BACKENDS_LOGFILE=${VFC_BACKENDS_L... |
4bce862150249726e156062cfd1db69dc9049c87fb2100e95a38e75353ae93e9 | Shell | 3,758 | 123 | #!/bin/bash
#: Title : test_e63mreg
#: Date : 2018-03-14
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../e63mreg
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
59668c16b4a3d038760d3d2998ee5648b16100024a348423d91c3e5fd3a013fb | Shell | 3,758 | 79 | #!/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... |
5e3359033bf2ea7e90bc8a2717050c78e5fafd5e6983f0870f40cb525986334c | Shell | 3,784 | 105 | #!/usr/bin/env bash
# =============================================================================
# 02_harmonize.sh — Harmonization
# =============================================================================
# Align GWAS summary statistics against a reference genome sequence.
# Harmonization fixes strand orientat... |
ab6b7e4a53bf30ab4a13f792620586cf6e254fda4fe8f57456cde570a4f994bc | Shell | 3,791 | 109 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: PARALELLIZE THE DECODING SCRIPT ON THE CLUSTER (TARDIS) AT THE
# MAX PLANCK INSTITUTE FOR HUMAN DEVE... |
55d916810abd9800b709310639a8a02af9d4e31983e8ac0f57dc1d0e497fb7a7 | Shell | 3,797 | 109 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: PARALELLIZE THE DECODING SCRIPT ON THE CLUSTER (TARDIS) AT THE
# MAX PLANCK INSTITUTE FOR HUMAN DEVE... |
77fbe9491102bb3cfdb867525ac712f0127fe35e66214f63015d564351673127 | Shell | 3,801 | 109 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: PARALELLIZE THE DECODING SCRIPT ON THE CLUSTER (TARDIS) AT THE
# MAX PLANCK INSTITUTE FOR HUMAN DEVE... |
8fb055dbdf7b03f11221b02241e63921728162cb587e9b55299a41dafd9ca82a | Shell | 3,801 | 109 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: PARALELLIZE THE DECODING SCRIPT ON THE CLUSTER (TARDIS) AT THE
# MAX PLANCK INSTITUTE FOR HUMAN DEVE... |
73fd3e88759e8918dbb2d347766fd016f15f5804b4956eff2fb18e7028a9411e | Shell | 3,807 | 138 | #!/bin/bash
#: Title : test_tacframe
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacframe
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
ca1e69a8bba193d74bbbc487d5373c95c093200bd189d2c69f1e8e107790bf17 | Shell | 3,822 | 120 | #!/bin/bash
# Regression test for the --inst-func crash on functions declaring a
# variable-length array. See test.c for the mechanism.
set -eo pipefail
export VFC_BACKENDS_LOGGER=False
rm -f ./*.ll
# 1. The program must simply run, whatever the backend.
#
# The compilations are bounded: when the pass regresses it... |
e8f00d9777c924d3a9aa3dbeba9cec1a69773fe207b7c8392816d790ef8ce00f | Shell | 3,827 | 56 | #!/bin/bash
# ---------------------------------------------------------------------
# SLURM script for a gpu job on a Compute Canada cluster.
# ---------------------------------------------------------------------
#SBATCH --account=dummy_group
#SBATCH --gres=gpu:1 # Request GPU "generic resources"
#SBATCH --cpu... |
e696bb713a60fabdef47020e6093ea4bc47c0766878bfd0094f6a9bddcd8aa60 | Shell | 3,841 | 124 | #!/bin/bash
#: Title : test_imgmatch
#: Date : 2019-11-19
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgmatch
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
c09ccaba62788212253911f57567d00c042ed0b8d705bb523267ddc729eb7a6d | Shell | 3,845 | 70 | #!/bin/bash
#SBATCH -N 1 # use 1 node
#SBATCH -n 1 # 1 task
#SBATCH --cpus-per-task 4 # cpu cores to use
#SBATCH -t 1-00:00:00 # 1 days, 0 hours, 0 minutes, 0 seconds
#SBATCH -p gpu_batch # use the gpu partition
#SBATCH -J RetroDiffusion # Job name... |
e3a64a14ace463bd9096c31b08c7678bccf91f2138c8599c1d128277628c8c8e | Shell | 3,851 | 56 | #!/bin/bash
# ---------------------------------------------------------------------
# SLURM script for a gpu job on a Compute Canada cluster.
# ---------------------------------------------------------------------
#SBATCH --account=dummy_group
#SBATCH --gres=gpu:1 # Request GPU "generic resources"
#SBATCH --cpu... |
222ddf2073645ae374d3dae442c0222b9cd94205e7d0f4cc70c160c6923b4fe9 | Shell | 3,863 | 158 | #!/bin/bash
# This script builds portable flye binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, if ... |
8edcc3faccdc1ae9f4bc8e6ede5e060ae3ec09410f3593325b9cacd4aa98170b | Shell | 3,866 | 160 | #!/bin/bash
# This script builds portable cuteSV 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... |
2f559110e92bf22b8f8c6b8dc566810803547971114546b5ba5fa50fd36a82bc | Shell | 3,881 | 102 | #!/bin/bash
#
# Assesses T1w to FUNC 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
#
# See $ MeasureImageSimilarity --help for more info
#
# Inputs:
# $1 :
# $2 :
# **... |
6cd82c433608b0d916b1c28d1488600cd2190613ada40034d6575ea799d0a00b | Shell | 3,892 | 153 | #!/bin/bash
set -e
export SAMPLES=100
# check if variable static is set
: "${STATIC_DISPATCH:=0}"
if [[ $STATIC_DISPATCH -eq 1 ]]; then
DISPATCH="static=1"
else
DISPATCH=
fi
# check if variable march_native is equal to 1
# Ensure MARCH_NATIVE is set to either 1 or 0
: "${MARCH_NATIVE:=0}"
if [[ $MARCH_NAT... |
a9c17f39e7bf27f138636268fa093217335d20d92733332ab9936c1641461777 | Shell | 3,895 | 103 | #!/bin/bash
# Copyright 2016 Google Inc. 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 required by applica... |
f51b48674f32668eca559d390fbaedf5914104bbdca08bb30f76369133160300 | Shell | 3,910 | 40 | #! /bin/bash
# ONTraC Installation
conda create -y -n ONTraC python=3.11
conda activate ONTraC
pip install git+https://github.com/gyuanlab/ONTraC.git@V2
# Running ONTraC
mkdir -p data log analysis_output
## without kernel method (meta input only)
ONTraC --meta-input data/merfish_meta.csv --preprocessing-dir data/... |
ae1c28be002294a12d2e4c6761177e86ad2c3c5e40e35b86c2a4acfbdeeb877f | Shell | 3,937 | 117 | #!/bin/bash
#02_constants.sh
TESTDIR=Bembidion
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 $(mktemp -u -t tmp.XXXXXXXXXX))
f... |
c10cd9fcc20c8d9ce3af18e452938bcf558cc7038706fda1898c38eb9385de39 | Shell | 3,954 | 117 | #!/bin/bash
# trashSizeMonitor.sh - quickly measure size and age of files in /trash/
#
# returns: path name to a two column file with last access time and file name
# for each file in the /trash/ directory.
#
# requires external scripts: fileStatsFromFind.pl and dirStatsFromFind.pl
#
# this script is used... |
721e090d35b388a6c173b415c2e6ee985de63cefeb14d1b2b11cf56801e56a2b | Shell | 3,958 | 106 | #!/bin/bash
# A runtime precision or rounding-mode change must reach the threads running
# instrumented arithmetic.
#
# Validates:
# 1. interflop_call(INTERFLOP_SET_PRECISION_BINARY32, 8) changes what the
# calling thread computes, after that thread has already rounded.
# 2. The same change, made inside an Ope... |
6539f13f4cc96724a2ba8d306d9e22f657ef76fd154eb95605fd04b7c3cd9356 | Shell | 3,964 | 158 | #!/bin/bash
# This script builds portable raven binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, if... |
1133762b596df5597f3bc25760841054c5c40913de614a56f20ad73221ee68b8 | Shell | 3,980 | 129 | #!/bin/bash
#
# BIDSifies the MWC data by:
# 1. Using a single subject's config file (sub-06) as a template to generate config files for all other subs
# 2. Runs dcm2bids on all subjects
# 3. Performs the following manual editing of the BIDS file structure
# a. Keeps a single T1w scan from those with repeats ... |
e1831f54a94c6301c1c4837ed5750ad18eeb5684eb8f404e382028fe60f2288c | Shell | 4,007 | 132 | #!/bin/bash
#: Title : test_imgfrdif
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgfrdif
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
4898cf09795e49549a8cfb4cbb47866546c3388747b969cf502c3e0566de79cb | Shell | 4,013 | 112 | #!/bin/bash
# This script makes a portable java
# using the Holy build box environment to create the portable binaries.
# The build directory contains a (patched) tcc that will find out from which dir it is run, and use the included
# musl library for compiling portable, statically linked executables.
# The tcc-syst... |
6a4fa56f28bfa086145f411d67c099cb36e70df703f0dbd016294126ee3e7352 | Shell | 4,015 | 121 | #!/bin/bash
#: Title : test_bpr2cpr
#: Date : 2014-10-19
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../bpr2cpr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
61ce6612a36c04f6c2c79fe335e01de55f8e4515963337eaf3ad6552279aca99 | Shell | 4,020 | 157 | #!/bin/bash
# This script builds portable longshot binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build,... |
6ef9b7d9af3ac4ff5d8ac57bf3eaaee9cb5338de68135832cc1e58b03e907b9b | Shell | 4,020 | 137 | #!/bin/bash
#: Title : test_taclkup
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../taclkup
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
2ef3f7d6242f4bc4b4d18ec2fca57e59fbc4d1c48111eafb7330f33a8f281ef9 | Shell | 4,023 | 32 | #!/bin/bash
#SBATCH --cpus-per-task=32
#SBATCH --time=24:00:00
module load bowtie2
module load samtools
module load bedtools
module load dimelo
cd /data1/czhao/xiaodong/FOXA2_D2_H3k4me1_dual/result/pass
dimelo-plot-enrichment-profile -f FOXA2_D2_H3k4me1_dual_sorted.bam -s q4 q3 q2 q1 -b FOXA2_ChIP_peak_4w_only_peak_... |
dd889e0429ae4b3733c99ef04863e75df52d0cbb83885fe5efe6415f04f799f4 | Shell | 4,024 | 121 | #!/bin/bash
#: Title : test_img2scn
#: Date : 2016-10-05
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../img2scn
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
d6680b876c7f23397f6abfdf9ac4b75e48e172f99c49c3314fa98c4f9a86401f | Shell | 4,034 | 135 | #!/bin/bash
projdir=`pwd`
bindir=$projdir/src/scaff-bin/
mkdir -p $bindir
mkdir -p $projdir/src/log/
errs=0
##### Download and install BWA ######
echo "Downloading and installing BWA"
if [[ ! -s $bindir/bwa ]]; then
if [[ ! -d $projdir/src/bwa ]]; then
cd $projdir/src/
git clone https://github.com/lh3/bwa.... |
d7dd6d157d0dcfd89d6cdd0ff19dbba67d2f75730d23ae2c424179a0d492c075 | Shell | 4,035 | 96 | #/bin/bash
##################################
### Set variables beneath this ###
##################################
# Save OLD PATH
export OLD_PATH=$PATH
#------------------------------------------------------------------------------#
# SOFTWARE CONFIGURATION for MICAPIPE
#-------------------------------------------... |
85b7dec156323578de952e65b6e7cac93af272f7e5a89d538f9030425aac3186 | Shell | 4,036 | 136 | #!/bin/bash
#: Title : test_convsurg
#: Date : 2019-02-15
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../convsurg
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
ab89b438c43ce27a07f83bd27b97a3c688a2a3e2b6068e9697cfec286ec654fb | Shell | 4,040 | 104 | #!/bin/bash
#
# Compares methods for T1w to FUNC 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 ... |
924225093925797887ca0d049fa18abaf5cad438602036b944f2b09a14bb38d7 | Shell | 4,041 | 139 | #!/bin/bash
#: Title : test_atnmake
#: Date : 2016-10-22
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../atnmake
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
58b2bb38464b28b21653e6bab4bd9e3b4d3cf481b86df75714a3faaf3629296a | Shell | 4,082 | 145 | #!/usr/bin/env bash
# =============================================================================
# 09_variant_filters.sh — PLINK-style filters and optional fix_* steps
# =============================================================================
# Demonstrates:
# --fix-chr-pos, --extract / --exclude (ID lists), ... |
4a5d595f692a15a6624e55c82e95d77b07350d7ec2d72b717b21cad05df43a48 | Shell | 4,090 | 90 | #!/bin/bash
#
# Shell wrapper for running the original COMMIT implementation (regularization: commit.solvers.non_negative)
# IC weights obtained for streamlines will be used to compute connectome edge weights
#
# Inputs:
# $1 : subject (i.e. 01, 02, ... , 50)
# $2 : function id (DEPRECATED)
#
# * * Requir... |
fd08c16864b11d4651ba4c40f349d860bccd619fb13fa0cf0c3d8738ead640fc | Shell | 4,093 | 116 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: PARALELLIZE THE DECODING SCRIPT ON THE CLUSTER (TARDIS) AT THE
# MAX PLANCK INSTITUTE FOR HUMAN DEVE... |
9beead3a13b14bda40b3469add1ab274880eec7873bdfa7c04c292f5d92136f1 | Shell | 4,097 | 119 | #!/bin/bash
#: Title : test_imglhk2d
#: Date : 2021-12-16
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imglhk2d
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
bfb644c2f4e8eb4666789e80c7aea02f0d06c94b487cfa572d5696a743e5dd29 | Shell | 4,124 | 75 | #!/bin/bash
# Modified by Ravi Mill for CPRO2_learning 03/16/18. Modified by Carrisa Cocuzza 2023 for Yale HPC (Milgram cluster) and TCP dataset.
# NOTE: This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here
# Change this: this is the base directo... |
569120abdf4a3def341612e8db38336c213af373fc35966a3012dcdeb667f2c7 | Shell | 4,138 | 116 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: PARALELLIZE THE DECODING SCRIPT ON THE CLUSTER (TARDIS) AT THE
# MAX PLANCK INSTITUTE FOR HUMAN DEVE... |
6ed6838df9f7100ae43e854e8930f0241c6f0857c46bbbcf026325f6db177bed | Shell | 4,150 | 124 | #!/bin/bash
#: Title : test_e7emhdr
#: Date : 2014-09-04
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../e7emhdr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
80def42dc2ac2b0e5edbb26c71eafc240207e0ae7b7c35569571e8bd3e23a3ca | Shell | 4,155 | 144 | #!/bin/bash
#: Title : test_parai
#: Date : 2019-02-27
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../parai
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
9edae32d674f32c4a868981266fc34b6ef9913e6b0e591e484e1bcbd3cfa8609 | Shell | 4,158 | 163 | #!/bin/bash
# This script builds portable sniffles2 binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build... |
c8acedb86e810b5e2ff436ae3fcd9da4116b68159b9f1f58704d9f904728b9b2 | Shell | 4,158 | 117 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: PARALELLIZE THE DECODING SCRIPT ON THE CLUSTER (TARDIS) AT THE
# MAX PLANCK INSTITUTE FOR HUMAN DEVE... |
803f27d531c22b06e9dfff1c7414b729d1014ae731d1aa4ee1dc199905144b3f | Shell | 4,187 | 151 | #!/bin/sh
# the next line restarts using tclsh \
exec cg source "$0" "$@"
# Script to download and prepare all reference databases (including genome) for mm10
# call using
# makedbs_mm10.sh ?options? ?dest? ?webcache?
# where
# * dest: the directory where the reference databases will be installed (default /complgen/r... |
572bd85fc77fb07e2a41f6765ba53ad6085307b33aba48fbd74731b229c66c6e | Shell | 4,202 | 168 | #!/bin/bash
# This script builds portable ont_fast5 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... |
1a38a7bcff816ceaa7cf179b926202e961ca4a327664a450243eb9d274c17961 | Shell | 4,207 | 157 | #!/bin/bash
#: Title : test_imgweigh
#: Date : 2016-08-16
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgweigh
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
a9b7ae23b1cb335d9682cfee182f101a89add85c2aa424579d93562cc89420d4 | Shell | 4,209 | 172 | #!/bin/bash
# This script builds portable manta binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, if... |
60d0872bb485c5512ffbfc0cd48eecf2c10c09b1093ca35af7ac1b7ed32fc418 | Shell | 4,225 | 110 | #!/bin/bash
label_type=$1 # "lesion" or "sc"
# check if the label_type is provided
if [ -z $label_type ]; then
echo "Please provide the label type: 'lesion' or 'sc'"
exit 1
fi
if [ $label_type == "lesion" ]; then
echo "Separating region-based masks into lesions only"
threshold=1
metrics_to_compu... |
235b528098474a1f824bb6ce596dcab67f8ede25f9cc32fa3c625594fdcb9907 | Shell | 4,228 | 107 | #!/bin/bash
#
# Compute geodesic distance along cortical mesh:
#
# Generates geodesic distance matrices along native cortical surface using specified parcellations
#
# This workflow makes use of wb_command and custom python scripts
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micapipe/tree... |
12e36e68d04698ecbbf5c3b0cc339983fc5f03f38b42776406b930ae7bcf3f9b | Shell | 4,253 | 133 | #!/bin/bash
#
# Computes a brian mask using a few different methods:
# 1. mri_synthstrip from freesurfer
# 2. FSL BET with default params
# 3. FSL BET with lower value for -f (mor liberal fractional intensity threshold, larger brain outline estimates)
# 4. ANTs antsBrainExtraction.sh (maybe not intended for func da... |
c8be150311f4a8ae29ce089f2f201af13ac74d37310c9b99f6422f4cd7a2ae11 | Shell | 4,254 | 168 | #!/bin/bash
# This script builds portable hisat2 binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)build, i... |
18fa6d551365fd586993853aa61a8f9845c97198982db14f9e87b10a37f69340 | Shell | 4,255 | 149 | #!/bin/bash
#: Title : test_tacjoin
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacjoin
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
cc743b2be1f6b88d6d173c0a5b3b660a7aab1efc3a5342fbe0b63775045ca34e | Shell | 4,257 | 127 | #!/bin/bash
#: Title : test_imgssegm
#: Date : 2019-03-16
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../imgssegm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
6cbedf6102dd4ca90c9358e2b189ab0a0a90d52284b646ab15a981654341667c | Shell | 4,269 | 141 | #!/bin/bash
#: Title : test_e63mdel
#: Date : 2018-03-13
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../e63mdel
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
e3e6b60e6fbddcef494dd0f3a9a9d0df23c1e9ecbeedb4a561a969842032c93b | Shell | 4,291 | 142 | #!/bin/bash
#: Title : test_nii_ehdr
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../nii_ehdr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
eaa37a6a65dcc1f1ec23efc5df04006273111d921559d3432848cf57822872fc | Shell | 4,318 | 105 | #!/bin/bash
# Tests that PRISM SR virtual precision produces results at the correct bit
# position for +, *, fma, and / on scalar float, scalar double, float4,
# and double2.
#
# For each (type, op, precision) triple, verifies:
# BRACKETS: exactly 2 distinct SR values, differing by 1 ULP at precision p.
# STOCHAS... |
4efefaab73a090e6d0e6401446e7c2ee2c9a26eb97bde5336f27c1158ba47a3c | Shell | 4,362 | 144 | #!/bin/bash
#: Title : test_dcmxform
#: Date : 2018-11-11
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
LC_NUMERIC=C
export WSLENV=LC_NUMERIC/w
# Set the name of executable to test
PROGRAM=../../dcmxform
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Fai... |
c91817c39db4bafc3bd961a7ff35cf778ceac63dd9303daf9bf1b2cc75124b09 | Shell | 4,379 | 125 | # pick the utterance
TIMITROOT=$1
HTKTools=$2
mkdir -p vis_greasy
FBANKCONF=conf/htk_fbank.config
lower_case=0
upper_case=0
if [ -d $TIMITROOT/TIMIT/TRAIN -a -d $TIMITROOT/TIMIT/TEST ];
then
upper_case=1
TIMIT=$TIMITROOT/TIMIT
elif [ -d $TIMITROOT/timit/train -a -d $TIMITROOT/timit/test ];
then
lower_c... |
7e41f7a6869e19246b67166af6452061028c6599dc0948e1e03e1b98c4cffc67 | Shell | 4,381 | 132 | #!/bin/bash
#: Title : test_dftcbv
#: Date : 2014-11-05
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../dftcbv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
578b5f2ca428550f955b3f55ceb3d7110e4248b4bfb20b70b2f9a032ece04eb2 | Shell | 4,401 | 137 | #!/bin/sh
set -x
# Script arguments
INPUT_FILE=$1
OUTPUT_FOLDER=$2
SIGNATURE_FILE=$3
DATA_FOLDER=$4
CORES=$5
# Enviroment variables
HYPERMUT=1000
SCRIPTS_FOLDER="/hotmaps/scripts"
DATASETS_FOLDER=$INTOGEN_DATASETS/hotmaps
# Preprocess
input_folder=$(dirname "${INPUT_FILE}")
input_name=$(basename "${INPUT_FILE}... |
d6ded42aa5325919448427310f29d93917953b1d99b6e15c3a1cebb8705323dc | Shell | 4,405 | 79 | # Zeiss
# BEADS_DIR="/media/Data/smlm_z_data/20231121_nup_miguel_zeiss/stacks/";
# OUTDIR="/home/miguel/Projects/smlm_z/publication/VIT_Zeiss";
# OUTDIR='/home/miguel/Projects/smlm_z/autofocus/VIT_zeiss/out_resnet_fov-max_aug11'
# OUTDIR="/home/miguel/Projects/smlm_z/autofocus/VIT_zeiss_lowsnr_data/out_resnet_fov-max_a... |
1f70ffbaef39e194060266f9ce5e2ff8515dcbdb8339fd9a2af7dc88bb008fa8 | Shell | 4,409 | 67 | #!/bin/bash
script="$(readlink -f "$0")"
dir="$(dirname "$script")"
dir="$(dirname "$dir")"
echo "Making debug versions of bins in $dir (fast, using tcc)"
cd $dir/src
CC=tcc
COPT="-g -DDEBUG"
CFLAGS="$COPT -D_FILE_OFFSET_BITS=64 -Wall -I$dir/src -I$dir/src/external"
GZTOOLS_C="../src/gztools.c ../src/lz4.c ../src/lz... |
471af944fd3a90bdab69b28ce0a57b8e62adb3697752f7ca0a74d47637e3791d | Shell | 4,412 | 170 | #!/bin/bash
# This script builds a distributable directory contained version of python3 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)... |
4ad9bbd11228a8093a0aa6f05a24022d2f639db8efe8d8fd0ee6cc5828ec7aed | Shell | 4,415 | 146 | #!/bin/bash
#: Title : test_csvrmcol
#: Date : 2020-04-27
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../csvrmcol
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
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