sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
cb17d8468b7b360fe47501e6599d0ee3c56e1e39664cb3fc4dd988ca1eb829b2 | Shell | 1,876 | 74 | #!/bin/bash
#: Title : test_iftlist
#: Date : 2014-10-17
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../iftlist
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
ecda9cbba697816476007df4ad43f5689cac2359f46064aadc609edae345cc89 | Shell | 1,879 | 45 | #!/bin/bash
set -beEu -o pipefail
hgsql -N -hgenome-centdb -e 'select name from dbDb where active=1;' hgcentral \
| sort > rr.active.list
hgsql -N -e 'SELECT source,destination FROM asmEquivalent WHERE
sourceAuthority="ucsc" AND destinationAuthority="refseq" AND
matchCount=sourceCount;' hgFixed | sort -u > ucs... |
7578f0ecd44fbd1e82886f120d5dc490c117e2cbce4cecaf3ef9359455513cd0 | Shell | 1,880 | 17 | EXT=png
rm -rf ./manuscript/figures/simulation_*
# Constant generation time
cp ./results/simulated_mammals_no/inference_RevBayes.boxplot.is_nuc.${EXT} ./manuscript/figures/simulation_cstGT_phylogram_support.${EXT}
cp ./results/simulated_mammals_no/inference_RevBayes.boxplot.is_OU.${EXT} ./manuscript/figures/simulation_... |
948607793c2950c8858d77ef00f4e76e879943ca048399c2da975ed3fa8539de | Shell | 1,885 | 18 | source /data_/tardiflab/wenda/programs/micapipe-mod/scripts/init.sh
SUB=/data/tardiflab2/wenda/mwc/list
cat $SUB|while read line; do
antsApplyTransforms -d 3 -n NearestNeighbor -i /data/tardiflab2/wenda/mwc/splenium.nii.gz -r /data/tardiflab2/wenda/mwc/${line}/proc_struct/${line}_t1w_1.0mm_nativepro_brain.nii.g... |
b0039fe28a57ded85a5516237a4ed0a9e65a45063137588098e476100dbae591 | Shell | 1,885 | 94 | set -e
TIME=/usr/bin/time
bash get_gm12878.sh 1000000 22
bash get_gm12878.sh 100000 22
BEDPATH=hic_data/GM12878_combined_22_100kb.bed
#Chromosome3D
#create input
INPUT_PATH=Chromosome3D/input/GM12878_combined_22_100kb.txt
if [ ! -e $INPUT_PATH ]
then
python chromosome3d_input.py $BEDPATH $INPUT_PATH
fi
#run
$... |
053e4508a8907102322de1a9d6ba5b7de01e2e6dad4ca8accf58596e8937b3db | Shell | 1,894 | 47 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License... |
18514a6532f7adc9fdbe8c3f6c0ece9be39afa17316199a7cc2c88bf4c48b7dd | Shell | 1,894 | 63 | #!/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... |
67a398cb5875b76d677fb77d6a71eb674defa6075a5d6a027eb6ef72a6ad1dcd | Shell | 1,894 | 73 | #!/bin/bash
# Regression test for pointer argument forwarding under --inst-func.
# When a function takes a pointer argument and passes it to another function,
# getSizeOf used to enter infinite recursion.
set -eo pipefail
export VFC_BACKENDS_LOGGER=False
./clean.sh
# Bounded compilation: if the compiler hangs due t... |
35bfbc685503f96122828d5ab51abb74998ef87362a25f92f4b4c299f982ab4c | Shell | 1,896 | 21 | source ../setup.sh
model=/cluster/work/igc/kpaul/projects/small_molecule_multisolvent/MachineLearning/trained_models/ProductionRun_seed_1612_49_ckpt.pt
for solvent in water chloroform methanol dmso benzene thf acetonitrile pyridine acetone; do
sbatch --array=0-256 -n 2 --tmp=2000 --time=24:00:00 --mem-per-cpu=160... |
f2b167398bef4273f85d4aff0073dc0e6430584e5697582a1949c33963018316 | Shell | 1,904 | 85 | #!/bin/bash
debug=
cfgnam=exp
export DISPLAY=
if [[ $0 =~ ^\..+ ]]; then
wholecmdpath=${0/"."/$PWD}
elif [[ $0 =~ ^/ ]]; then
wholecmdpath=$0
else
wholecmdpath=$PWD/$0
fi
src=src
oldIFS=$IFS
IFS='/' read -r -a array <<< $wholecmdpath
array=(${array[@]}) #remove empty slots
IFS=$oldIFS
len=${#array[@]}
rootdir=${... |
7570d065af11e6195c02a88bdf465727e28c4fb23b3536de43e860016f33b4dc | Shell | 1,907 | 60 | #!/bin/sh
#
# Script for execution of deployed FieldTrip applications. It sets
# up the MCR environment for the current $ARCH and executes the
# specified command.
#
# Use as
# fieldtrip.sh <MATLABROOT> script.m
# fieldtrip.sh <MATLABROOT> script1.m script2.m ...
# fieldtrip.sh <MATLABROOT> jobfile.mat
#
# See al... |
3e644e7ecedf2b4925a2b8cc9b07337d6b77f3f3547e707ac1a7fb004fa03ee1 | Shell | 1,916 | 53 | #!/bin/bash
set -e
# Process sequencing data.
# Usage: bash process_sample.sh SOURCE DEST REF_GENOME EXONS
# SOURCE: The directory which contains all the fastq.gz files for a
# given sample
# DEST: The directory to save the processed data.
# REF_GENOME: The indexed genome for mapping (no extension)
# EXONS: The SA... |
9a5fedafcf93e1f0091d838bd0e6badec99bce24179cb50609745276d49df273 | Shell | 1,924 | 75 | #!/bin/bash
#: Title : test_tac2xml
#: Date : 2020-01-15
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
#: Note : Results not tested because reading output file not supported.
# Set the name of executable to test
PROGRAM=../../tac2xml
if [ ! -f $PROGRAM ]; then
if [ ! -f $... |
ff0b3c19068f25d39a0cbe87f69ee1991b4e27e19d2e46098fb03569d28e7302 | Shell | 1,934 | 71 | #!/bin/bash
#: Title : test_ana_lhdr
#: Date : 2026-09-03
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../ana_lhdr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
657dbe68cb775d65fff370d4128c5afd9d8b43a690a58250c62a7a806bcc168c | Shell | 1,944 | 75 | #!/bin/bash
# Copy per-subject BOLD and SC outputs into src/cubnm/data/hcp/
cd "$(dirname "$0")"
if [ -f ../../.env ]; then
source ../../.env
fi
SUBJECTS=(100206 100307)
CUBNM_DATA_DIR="${CUBNM_DATA_DIR:-$(cd ../../src/cubnm/data && pwd)}"
while [ $# -gt 0 ]; do
case "$1" in
--subjects)
... |
11cd513b67cb40a987bc2fc1698cc27eb1d5734da7f85b334e42149a6a3c00ec | Shell | 1,960 | 71 | #!/bin/bash
#: Title : test_pdoc2htm
#: Date : 2017-10-27
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../pdoc2htm
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
95eae27bd3f223f8182544762dc74abed747b1fd903b8309a242e0b96c04b572 | Shell | 1,961 | 64 | #!/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... |
ba39dc3d077939065bbad70b868bc1ba768c01164b6fd081512324df48921bbc | Shell | 1,973 | 73 | #!/bin/bash
#: Title : test_tacinv
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacinv
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
a5efc722ae1ee6535644841cb5ea22532e4d3838faa129d8f53e6e904a779952 | Shell | 1,980 | 76 | #!/usr/bin/env bash
set -eo pipefail
if [ "$#" -lt 1 ]; then
echo "Usage: profile command [args...]" >&2
exit 2
fi
# Launch the target command
"$@" &
ROOT=$!
#LOGFILE="profile-${ROOT}.log"
#echo "# timestamp_ms pid combined_VmHWM_kB" > "$LOGFILE"
# Function to recursively find all live PIDs in tree
get_tree_pids... |
76715050cfc398ad9ccbf3e850018556ced0b7bdcfc3061d294de9c468911cc4 | Shell | 1,998 | 69 | #!/bin/bash
# Replaying a profile that was dumped at full precision must not perturb the
# program: the result has to match the IEEE baseline in every instrumentation
# mode. See test.c for the mechanism.
set -eo pipefail
export VFC_BACKENDS_LOGGER=False
verificarlo-c test.c -o test --inst-func -lm
VFC_BACKENDS="l... |
8a50758f7528288c5702e5c9f8da5f5dd3b88a86edd32781c7899ff8a83edfaa | Shell | 1,999 | 57 | #!/bin/bash
DOCKERFILE=Dockerfile.mcalibmath
FUZZY_IMAGE_DEFAULT=verificarlo/fuzzy:v2.6.0-lapack
generate_docker() {
cat >${DOCKERFILE} <<HERE
# Base image
FROM ${1}
RUN mkdir -p /opt/mca-libmath/{fast,standard,quad,mpfr}
COPY --from=${2} /opt/mca-libmath/set-fuzzy-libmath.py /usr/local/bin/set-fuzzy-libmath
CO... |
6464aca3a36dce7dbd23ef2f02f2c239cb3e9ac03b3440700f84dcab84b390ff | Shell | 2,005 | 94 | #!/bin/bash
##uncomment to stop on error
set -e
##uncomment to show all commands executed by the script
#set -x
# Check the number of arguments
if [[ $# != 5 ]]; then
echo "Expected 5 arguments, $# given"
echo "Usage: script_name usecase absErr_min absErr_step nb_tests test"
exit 1
else
usecase=$1
abs_err_min=$2
... |
934aaf2c64469a1712051018c5d3c48deaf844a25e3e162c413ca08fe5f6a141 | Shell | 2,006 | 80 | #!/bin/bash
copyright=$(grep -m 1 "^# Copyright" plotting.py | sed -e "s/^# Copyright//")
author=$(echo $copyright | sed -e "s/^[0-9\-– ]*//")
project=scbiasnoise
heading=$(head -1 README.md | sed -e "s/^# //")
heading_underline=$(echo $heading | sed -e 's/./=/g')
url=https://codeberg.org/mahlzahn/$project
commit=$(gi... |
86cfbaac7f6c6e0969d00ef3f323de497d557cf931c3ad5f52d186c2af582fda | Shell | 2,013 | 77 | #!/bin/bash
cd ../..
source /fs1/software/modules/bashrc
module load loginnode
module load CUDA/11.2
module load cudnn/8.4.1-cuda11.x
export PYTHONUNBUFFERED=1
root_path="../../../.."
export PYTHONPATH="$(pwd)/$root_path/":$PYTHONPATH
export CUDA_VISIBLE_DEVICES=0,1,2,3,4,5,6
BATCH_SIZE=128
NUM_WORKERS=72
EPOCHS=1... |
60a4c563125453ccb0081f0567aeec190aceaedab0774d9a0f1658c230865ffe | Shell | 2,015 | 83 | #!/usr/bin/env bash
# =============================================================================
# 05_plot.sh — Visualization
# =============================================================================
# Generate plots from GWAS summary statistics.
# Available plot types: manhattan, qq, mqq, regional)
#
# Usage:... |
ab761db226e957d55a2294a1c98e6a17a11bb58b3c5fb04fdcaaf1cf8b6d45d6 | Shell | 2,021 | 53 | #!/bin/bash
# CPython, one build:
#
# recipes/python/build.sh <ieee|prism>
#
# Both builds are configured for the same prefix, $FUZZY_ROOT/python/<x.y>,
# with --enable-shared, so the floating-point code lives in
# libpython<x.y>.so.1.0 and in the extension modules of lib-dynload (math,
# cmath, _decimal, _statistics... |
a851c7631153e546678f8c5a34e0c384817543df10f44f2b6374d32f6d0af8fa | Shell | 2,029 | 57 | #!/bin/bash
# This script runs an infant brain morphometry pipeline using iBEATv2 and standard FreeSurfer (FS). The following pipeline assumes that iBEATv2 tissue segmentations have already been generated.
# 1. Run FS up to step 15 (https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#StepDescriptionSummaries)
# 2.... |
ae001c5d9fc0ea07cc5f1865521f15340a282ee6db8704e85d16ee334ba40851 | Shell | 2,032 | 79 | #!/bin/bash
#: Title : test_upet2sif
#: Date : 2017-02-12
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../upet2sif
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
65788d44767413d752f589f5723e168766c5bbdc3dfbb586c0952eeb88e6c00c | Shell | 2,033 | 39 | python launcher_scripts/run_from_config.py configs/iceberg/nist23/dag_gen_predict_train_nist23.yaml
# Assign intensities to prediction for next training run
python data_scripts/dag/add_dag_intens.py \
--pred-dag-path results/iceberg_nist23/split_1_rnd1/preds_train_100/tree_preds.hdf5 \
--true-dag-path data/spec_dat... |
4cd2e17c63b4ea9db6f3214a671a46fa5696e22dc829256a074ae0b880ec5c1f | Shell | 2,035 | 39 | python launcher_scripts/run_from_config.py configs/iceberg/nist20/dag_gen_predict_train_nist20.yaml
# Assign intensities to prediction for next training run
python data_scripts/dag/add_dag_intens.py \
--pred-dag-path results/iceberg_nist20/split_1_rnd1/preds_train_100/tree_preds.hdf5 \
--true-dag-path data/spec_dat... |
187f3284e69e3e141a0ce7bcd3e89df9fce6ac1d33e565cd1426fa6a0ddea8d2 | Shell | 2,046 | 71 | #!/bin/bash
#: Title : test_addtimes
#: Date : 2018-02-04
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../addtimes
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
9fffb48daa411f1b999dc81fc90fd6b20a5297e9e7bb3a1d0cdd310046d053ff | Shell | 2,051 | 55 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... |
49e8a9cf3783f7a27062a281081b5a190a6410f4993ad7e8370f81a1c1ed5cc8 | Shell | 2,093 | 73 | #!/bin/bash
# measureTrash.sh - write to log file measurements of /trash/ directory
# contents
# requires external script: /root/browserLogs/scripts/trashSizeMonitor.sh
#
# can be used as a cron job to record state of trash directory usage
# exit immediately on any command failure
set -beEu -o pip... |
54852239780f54976be6c4e81067383175bf15441cac32223c8f1127b031cb4a | Shell | 2,107 | 62 | #!/usr/bin/env bash
#--------------------------------------------------------------------------
#Set up the Path so that all aspects of the pipeline are invocable
#Setting the path within the pipeline instead of within the environment
#adds portability and prevents user error
#--------------------------------------... |
92d9cbfe3086e44ba4c93b8bf2bea95fb694a6d79089887944ccd8ec3b8a6879 | Shell | 2,115 | 88 | #!/bin/bash
# This script downloads a build of pandoc, and puts it in a portable directory
# 32 bit option is ignored
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# The Holy build box environment requ... |
76902699d6893517a536195f03522e36a12ba2154e8b130067a3bc9c7efce767 | Shell | 2,119 | 85 | #!/usr/bin/env bash
#-------------------------------------------------------------------------------
#
# Mesos executor for bds
#
#
# Pablo Cingolani 2015
#-------------------------------------------------------------------------------
#---
# Get BDS directories
#---
if [ "$USER" = "root" ]
then
# Use ... |
3c7e45def7b48715e4ae3a326bb18c1cbcf38281bf4f569ce6322f4211a713c4 | Shell | 2,124 | 66 | #!/bin/bash
#local_path=$1
Rscript -e 'cat(suppressWarnings(system.file("bash", "v1.1a_exonInclusion_CTspecific_case_control.sh", package = "scisorATAC")))' > path_to_casesVcontrols
casesVcontrols_path=$(<path_to_casesVcontrols)
caseList=$1
controlList=$2
chrom_file=$3
numThreads=$4
annotation_path=$5
#find "$(cd ... |
45ac030ef957f30564fad903ee5d437861dc27a21b280749877386de0463c96a | Shell | 2,126 | 76 | #!/bin/bash
#: Title : test_reslist
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../reslist
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
d0534afb842e2302a0559e8a0af074a651748f7880391c5a3071c0e9399e414b | Shell | 2,131 | 102 | #!/bin/bash
set -e
export VFC_BACKENDS_LOGGER_SILENT_LOAD=True
new_env() {
DIR=.$1
rm -rf $DIR
mkdir $DIR
cp -r *.c $DIR
cd $DIR
}
test1() {
new_env test1
rm -f *.ll
verificarlo-c -c test.c -emit-llvm --save-temps
if grep "fptrunc" test.*.2.ll; then
echo "[test1] cast o... |
c4b6cd7ecf54267739015319c03249c41fe01e378ddf286eafc6ad32e2b0ed56 | Shell | 2,134 | 89 | #!/bin/bash
set -e
source ../paths.sh
SAMPLES=100
SEED=$RANDOM
echo "Seed: $SEED"
declare -A options=([FLOAT]=--precision-binary32 [DOUBLE]=--precision-binary64)
declare -A precision=([FLOAT]=24 [DOUBLE]=53)
declare -A bitmask_modes=([IB]="ib" [OB]="ob" [FULL]="full")
declare -A mca_modes=([IB]="pb" [OB]="rr" [FULL... |
7ee7561da72be582ea9376328b5f6567e8235f17f1ee96d8c973d223852f5055 | Shell | 2,146 | 54 | #!/bin/bash
# Check if an argument is passed. If not, explain how to use it.
# First argument is the CUDA version.
# Second optional argument is the ubuntu version.
if [ $# -eq 0 ]; then
echo "Usage: $0 <CUDA_VERSION> [<OS_VERSION>]"
echo "Example: $0 10.2 18.04"
echo "If OS_VERSION is not provided, it de... |
5d36bcc7e6fd35b5d94f07b313dc43a46434df46202d16cd337a6311bee62130 | Shell | 2,149 | 74 | #!/bin/bash
#: Title : test_nii_lhdr
#: Date : 2014-10-24
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../nii_lhdr
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
5af78babb36663398cdded534c3d30f3e6cb427232eed60c624ec7c6af034a58 | Shell | 2,155 | 102 | #!/bin/bash
set -e
find_function_in_obj() {
nm test_${1}.o | grep loop_${1}
if [[ $? != 0 ]]; then
echo "Cannot find function loop_${1} in test_${1}.o"
exit 1
fi
}
find_function_in_ll() {
nl=$(grep "loop_${1}(" *.ll | wc -l)
# 4 = one declaration + one use for .1.ll and .2.ll
... |
7bbdc7bd6336a3a9d752abe172501f362710ccbeed505071e29b819092fec51e | Shell | 2,157 | 72 | #!/bin/bash
#: Title : test_sim_o2
#: Date : 2023-02-16
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../sim_o2
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
f382fbd21d4bf9d271c73163a9851589b8865b0fd82e2ac6677515ec1f5a287a | Shell | 2,164 | 69 | #!/bin/bash
#: Title : test_csv2ift
#: Date : 2014-10-21
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../csv2ift
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
3718d3c767abc3f6302aaef3c6db014193c3d1480197d9449dc0b4823b913bb6 | Shell | 2,181 | 58 | #!/bin/bash
# Check if a tag is provided
if [ -z "$1" ] || [ -z "$2" ] || [ -z "$3" ]; then
echo "Usage: $0 <username> <password> <image tag>"
exit 1
fi
# Assign the tag and image name to a variable
USER=$1
PASS=$2
TAG=$3
IMAGE_NAME="containers.repo.sciserver.org/ssec-snaptron/snapmine"
# Log in to Docker Hub
ec... |
816f441cd8a826e131eaea784fa020a7c3696d07b13562ac0a87a77d03163052 | Shell | 2,181 | 68 | #!/bin/bash
#: Title : test_fit_av
#: Date : 2019-02-25
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../fit_av
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
f85a24bd3cf6604407b706df4fe8c1f4db685a524a4334e48f4f31c3b87ae902 | Shell | 2,186 | 71 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# 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... |
9a5bdfa6e9055fc3384ad90dd51388c0ee9444fc560df22d21a60fbb2237a283 | Shell | 2,187 | 67 | #!/bin/bash
#
# A plug-in for the micapipe module 02_proc-func.sh that replaces the T1w-FUNC transform computation
# Uses a nonlinear SyN method with an initial translation step to align the images by their geometric center
#
# INPUTS:
# $1 : moving image
# $2 : fixed image 1
# $4 : prefix for output filen... |
5321b241b60bf0e2109b64215e56c2ffa4f7d5ec44025cbb484e73ec0dde8932 | Shell | 2,207 | 59 | #!/bin/bash
config=$1
echo $config
cd src/DeepExDC
echo "
# STEP 1 #
# Compartment score calculation
# select the best pc out of PC1 and PC2 for each chromosome
# by comparing each one against GC content and gene density through correlation
# input: scHi-C matrix files(.npy),ann... |
170dc6b261237c2bda56fc29e3635f6da3296fc2af6051fae06fca710beae5ef | Shell | 2,216 | 101 | set -e
bash get_gm12878.sh 1000000 22
bash get_gm12878.sh 100000 22
BEDPATH=hic_data/GM12878_combined_22_100kb.bed
#Chromosome3D
#create input
INPUT_PATH=Chromosome3D/input/GM12878_combined_22_100kb.txt
if [ ! -e $INPUT_PATH ]
then
python chromosome3d_input.py $BEDPATH $INPUT_PATH
fi
#run
perl Chromosome3D/chr... |
e5f9d7e9552d1c62b94d92e8ba5611bf0e4a2c2fe9e874ac559f5e2148115b62 | Shell | 2,246 | 55 | #!/bin/bash
# This script uses varKoder 1.0.0a
source $(conda info --base)/etc/profile.d/conda.sh
conda activate varKoder
export CUDA_VISIBLE_DEVICES=2,3
for infolder in datasets/*/;
do
INPUT_DATA=$(basename "$infolder")
for architecture in ig_resnext101_32x8d vit_large_patch32_224 fiannaca2018 arias2022;
... |
1d5e6097cf8ba2067f6be815f49fb9eda36b009d95b13760f852fceabc959b37 | Shell | 2,251 | 44 | #!/bin/bash
echo "creating e2e datasets..."
path=data/e2e
echo "train..."
python src/format_converting_e2e.py $path/train.txt $path/train_formatted.jsonl
python src/gpt2_encode.py --vocab vocab --input $path/train_formatted.jsonl --output $path/train.jsonl --add_bos --add_eos
echo "test..."
python src/format_convertin... |
7bd72a9b6d71faf416aa4e34d55cfd8ecc75f9049e08529a670908ba74a78dd4 | Shell | 2,256 | 76 | #!/bin/bash
#: Title : test_csvtrps
#: Date : 2020-06-17
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../csvtrps
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
ebc1446dd2c8d118336744f2426aa3a74fe657e7a187ae936c3d36dec246348d | Shell | 2,259 | 80 | #!/bin/bash
# modified from https://bedops.readthedocs.io/en/latest/content/usage-examples/master-list.html
beds=(plv.summits.bed
d2.summits.bed
w1.summits.bed
w2.summits.bed
w3.summits.bed
w4.summits.bed)
out=FOXA2_summmit_extend_merge.bed
tmpd=/tmp/tmp$$
mkdir -p $tmpd
## First, union all the peaks together into... |
2157ba59e37353f2164a037ab57288508f86afeff21125bc6d952795f0ea722d | Shell | 2,271 | 104 | #!/bin/bash
set -xe
export VFC_BACKENDS_LOGGER=False
./compile.sh
new_env() {
DIR=.$1
rm -rf $DIR
mkdir -p $DIR
cp -r compute_mpfr_rounding *.c *.py $DIR
cd $DIR
}
test1() {
new_env test1
## Denormal tests for range 2, precision 3
cat >input.txt <<EOF
0x1.a53a8b6373154p-1 0x1.cfa1850... |
8d42afab8f8c540b44a03a6f87310bb687ff3318a3738fb46843830bbf8ccbea | Shell | 2,273 | 47 | #!/usr/bin/bash
# ==============================================================================
# SCRIPT INFORMATION:
# ==============================================================================
# SCRIPT: RUN BIDS VALIDATOR COMMAND LINE TOOL THROUGH SINGULARITY
# PROJECT: SFGPI
# WRITTEN BY LENNART WITTKUHN 2020, ... |
9a8fb999a958ce38da65586960b5ab0e6eb17a679fd279795170b59a819bc7e1 | Shell | 2,282 | 55 | #!/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... |
aaaa3cbf6b32147a415135dd1f3b21e166c139e182930a2b20a5be7478a8742d | Shell | 2,305 | 85 | #!/bin/bash
#: Title : test_tacp2f
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacp2f
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"
... |
4478fa02340003bb730d2e15d74fdd0992f8037f1869317ad77f458d8230a424 | Shell | 2,307 | 55 | #!/bin/bash
set -e
# Make scripts executable
chmod +x clean.sh piecewise_search.py plot_results.py
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
if [ -z "$PYTHON" ]; then
if command -v uv >/dev/null 2>&1; then
PYTHON="uv run --no-sync python"
... |
6d470fc210153eca58ee95fc8b7d6fb73e7f28c35f6c6c7239363e17e1c43512 | Shell | 2,323 | 94 | #!/bin/bash
# This script builds the genomecomb extension using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build in (default ~/build/tcl$arch)
# -v|-tclversion|--tclversion: tcl version (default 8.5.19)
# -d|-debug|--debug:... |
93ee619e3854a2ae9f44ecfc74bb71822088b89d877166a98721a9cc4f6a7383 | Shell | 2,333 | 31 | # python SC_sim.py V1 ablation 0.0 1.0 2 50 21 freq_irflag_ccrate_jointfreq_phasediff 1
# python SC_sim.py V2a ablation 0.0 1.0 2 50 21 freq_irflag_ccrate_jointfreq 1
# python SC_sim.py V2b ablation 0.0 1.0 2 50 21 freq_irflag_ccrate_jointfreq_phasediff 1
# python SC_sim.py V2a_V1 ablation 0.0 1.0 2 50 21 freq_irflag_c... |
f8226fbc50e378a4fa1186953f6825f018bbd2d06ef664009c170988d443ca47 | Shell | 2,334 | 40 | export filesToRenameAndSave=( ${runName}_hp2000.ica/filtered_func_data.ica/stats/stats.log
${runName}_hp2000.ica/.fix_2b_predict.log
${runName}_hp2000.ica/.fix.log
${runName}_hp2000.ica/filtered_func_data.ica/eig... |
0fd9e56756147cbaaec709180d539c0fb7cd332f0b62ee218b9ab218697265f6 | Shell | 2,337 | 64 | #!/usr/bin/env bash
# =============================================================================
# 01_report.sh — Generate GWASLab QC report using tutorial_v4 test data
# =============================================================================
# Use the same dataset/reference files as test/test_tutorial_v4.py a... |
1ec0494a45730ee07d6578158e3a794c3612984932fa9a94f83e0d49c53dca2d | Shell | 2,349 | 58 | Rscript step1_fitNULLGLMM.R \
--plinkFile=./input/nfam_100_nindep_0_step1_includeMoreRareVariants_poly \
--phenoFile=./input/pheno_1000samples.txt_withdosages_withBothTraitTypes.txt \
--phenoCol=y_binary \
--covarColList=x1,x2 \
--sampleIDColinphenoFile=IID \
--traitT... |
2203e6ea3046cd14441b9e9b80d08b1eb892878872cf32017ab66dc55b27235c | Shell | 2,360 | 55 | #!/bin/bash
# NumPy wheel, one build:
#
# recipes/numpy/build.sh <ieee|prism>
#
# Needs the ieee CPython and LAPACK selected (`fuzzy use python=ieee
# lapack=ieee`): both builds compile against them, since the prism builds
# have the same ABI. Writes numpy-<version>+<build> to
# $FUZZY_ROOT/wheels/<build>. The prism ... |
8dbc6d6d2842ba2d83b00fce047768fe50641af2541ac391d4dce3e05f12dbb7 | Shell | 2,374 | 88 | #!/bin/bash -x
# WARNING: verify credentials are enabled "gcloud auth configure-docker"
# WARNING: verify credentials are enabled "gcloud auth application-default login"
#JOB_NAME="kubric_$(date +"%b%d_%H%M%S" | tr A-Z a-z)"
PROJECT_ID="kubric-xgcp"
REGION="us-central1" #< WARNING: match region of bucket!
run_mode=$... |
4ea480e033bbfb66d5928106c5dc5198163f378256f7005efc57a067d67060ef | Shell | 2,379 | 54 | #!/bin/sh
WGET="wget -N"
#---
# Download files
#---
# $WGET http://tritrypdb.org/common/downloads/release-8.1/TcruziCLBrenerEsmeraldo-like/gff/data/TriTrypDB-8.1_TcruziCLBrenerEsmeraldo-like.gff
# $WGET http://tritrypdb.org/common/downloads/release-8.1/TcruziCLBrenerEsmeraldo-like/fasta/data/TriTrypDB-8.1_TcruziCLBr... |
54739d1f176860b5096a04953f266def0f081a91fd54e0936bd292927963ec71 | Shell | 2,382 | 82 | #!/bin/sh
# Run at FMNH server
set +e
source /home/bdemedeiros/software/miniconda3/etc/profile.d/conda.sh
conda activate varKoder
export CUDA_VISIBLE_DEVICES=2,3
# Start by pretraining with single labels on the training set only, no validation metrics
#create validation set file
awk -F, '$5 == "True" {print $1}' t... |
9eeff54565963ce7fd5b7d54adebafa2fc5635e3dbde9797db98c567386120d4 | Shell | 2,383 | 60 | #!/bin/bash
set -e
# Regression test for the `uv` package manager integration
# (configure.ac UV detection + Makefile.am install-exec-hook).
#
# It does not run the full ./configure (LLVM detection, etc. make this
# slow and environment-dependent); instead it regenerates `configure`
# from configure.ac with `autoconf`... |
fe8e3b1e803bf98770eab7d89e5e0f49e5d91a379eab1e4a6df0030b68cace59 | Shell | 2,393 | 99 | #!/bin/bash
# This script builds portable nanopolish binaries using the Holy build box environment
# options:
# -b|-bits|--bits: 32 for 32 bits build (default 64)
# -d|-builddir|--builddir: top directory to build external software in (default ~/build/bin-$arch)
# -a|-all|--all: if 1 (default) all binaries are (re)buil... |
5ce45fa32bcb507cab67e5f3f3ffed7e0720c3c0dd27de18a117af994da3610f | Shell | 2,397 | 49 | #!/usr/bin/env bash
######################
# Full MassSpecGym ICEBERG CE-imputation pipeline.
#
# 1. Train ICEBERG on the MSG subset with collision energy labels
# 2. Use this model to impute intensities for those entries with missing collision energies
# 3. Create the complete dataset with imputed collision energy la... |
d3ddb75a44c575a79a30984ffd1888395692a124a75f4e771120f81bb5664795 | Shell | 2,411 | 59 | #!/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... |
957ee04b0d191d4d9004b4e3b998f0a28e3c32493ba013ede04adf17c92b1a7a | Shell | 2,416 | 79 | #!/bin/bash
#: Title : test_avgfract
#: Date : 2018-03-08
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../avgfract
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
1c5aa6b0c1c7be73726c9589106bea1215e11f4ebce3374aa9c9acaaa1c79012 | Shell | 2,422 | 72 | #!/bin/bash
#Need to create keys to pull out desired 1:1 orthologs
#will need to change path below or run line by line within folder, currently running with a line by line in terminal
#first move to the folder where you have your orthofinder results
cd ../data//0_refs/primary_transcripts/OrthoFinder/Results_Date/
#c... |
abfaf09e289a26615954ac3339d6d3bf7901d05d60dd8b34e5861e6773d6890a | Shell | 2,422 | 68 | #/bin/bash
MAINDHCPDIR="/mnt/HardDisk8TB/projects/neonatal_dhcp_ieee_access/data"
PROTOCOLS="/local/projects/scnn-investigation_haykel/protocols"
counter=1
for SUBJECT in ${MAINDHCPDIR}/*; do
for SESSION in ${SUBJECT}/ses-*; do
SUBJECID=${SUBJECT#${MAINDHCPDIR}/}
SESSIONID=${SESSION#${SUBJECT}/}
... |
68336c8806e4d9cb229cc88e0e4dfabe4a005a119954252e1ec720c9c61c9de7 | Shell | 2,427 | 100 | #!/bin/bash
# Compile the program with Verificarlo
function check_instrumentation() {
rm -f log
local type=$1
verificarlo test.c -DREAL=$type -o test_${type} --save-temps --verbose --inst-fma 2>log
# Check if the program was compiled successfully
if [ $? -ne 0 ]; then
echo "Compilation ... |
a4462f4be572f3a5bac50b640e1d2cc23fe5aa1b0bf156bb91b65a064f10ab6a | Shell | 2,432 | 75 | #!/bin/bash
#
# A plug-in for the micapipe module 02_proc-dwi.sh that replaces the T1w-DWI transform computation
# Uses a nonlinear SyN method with 2 equally weighted fixed images
#
# INPUTS:
# $1 : moving image
# $2 : fixed image 1
# $3 : fixed image 2
# $4 : prefix for output filenames
# $5 : log filen... |
027d4b84931ca4ba12baee10e14d646a6c1d59a55f605829d5387901e3ff734f | Shell | 2,433 | 76 | #!/bin/bash
#: Title : test_tacsort
#: Date : 2016-09-20
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacsort
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
32094536a9acc361b31eda68383764a773dee53d6814ea66b92ea83b2c751969 | Shell | 2,433 | 69 | #!/bin/bash
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=10G
#SBATCH --time=0-03:00
#SBATCH --account=def-barrett
#SBATCH --mail-type=ALL
#SBATCH --mail-user=janay.fox@mail.mcgill.ca
#######################################################
### Goal: Merge BAM files and run BS-SNPer
### Author: Janay Fox
############... |
5b9ddf83139377dc18662173665953d932565447f41757a5f02ed9d5de466dd9 | Shell | 2,436 | 102 | #!/bin/bash
usage() {
echo "Usage: $(basename "$0") [-j MAX_JOBS] [-r MAX_RETRIES]"
}
MAX_JOBS=${MAX_JOBS:-$(nproc 2>/dev/null || echo 4)}
MAX_RETRIES=${MAX_RETRIES:-3}
while getopts ":hj:r:" opt; do
case $opt in
h)
usage
exit 0
;;
j)
MAX_JOBS=$... |
752af493408fe4ac5b0b81c10dbc64e7c1ea1cdc32267c64e7d3c336f0a8db18 | Shell | 2,442 | 58 | #!/bin/bash
#SBATCH -A p20023
#SBATCH -p short
#SBATCH -N 1
#SBATCH -n 2
#SBATCH -t 04:00:00
#SBATCH --mem=20G
#SBATCH --mail-user=viriyakeo2023@u.northwestern.edu
#SBATCH --mail-type=END,FAIL
#SBATCH --job-name=z_apa
#SBATCH -o "%x.o%j"
source ~/.bashrc
conda activate peakachu
h="/projects/b1126/Viriya/hic/"
dir=... |
f3f1d163520dadcebc38eaf7c37c6fcaca4e97e21787b58c12293dc3301f41ff | Shell | 2,446 | 75 | #!/bin/bash
#
# A plug-in for the micapipe module 02_proc-dwi.sh that replaces the T1w-DWI transform computation
# Uses a nonlinear SyN method with 2 equally weighted fixed images
#
# INPUTS:
# $1 : moving image
# $2 : fixed image 1
# $3 : fixed image 2
# $4 : prefix for output filenames
# $5 : log filen... |
1cc7e3c7cfcb57dd7c5d07d8065207738a335c012748f954ef4469ceb787587c | Shell | 2,454 | 92 | #!/bin/bash -eu
set -o pipefail
PROGRAM_DIR=$(cd $(dirname $0); pwd -P)
# Reference
# https://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/109.20200815/
VER="GRCh38"
SUBVER="p13"
ASSEMBLY_ID="GCF_000001405.39"
RELEASE="109.20200815"
GENOME="$VER.$SUBVER.RefSeq"
# Path to scr... |
60c3066e0a3973f41ed744ecfe8f7e630e04263ed0a2fc74db13157e0bfaf2ea | Shell | 2,456 | 66 | #!/bin/bash
#
# Runs ANTs SyN registration for the whole cohort on the batch
#
#
# 2023 Mark C Nelson, McConnell Brain Imaging Centre, MNI, McGill
#------------------------------------------------------------------------------------------------------------------------------------
rootdir=/data_/tardiflab/mwc/bids/de... |
4ca796d4595badd68ec6f1d574cfe66870d5a696dac081e403d98c28a7263d4a | Shell | 2,460 | 107 | #!/bin/bash
# Generates uniclust30 all-against-all alignments on a SLURM cluster.
# Thanks to Milot Mirdita for help & feedback on this script.
set -e
if [[ $# != 3 ]]; then
echo "usage: ./run_uniclust30_search.sh <uniclust30_path> <scratch_dir> <out_dir>"
exit
fi
UNICLUST_PATH=$1
SCRATCH_DIR_BN=$2
OUT_DIR=... |
981f545dad3ac6db9e9693b61983f5e4d5afabb803004ba02c6296a17bc16c29 | Shell | 2,462 | 85 | #!/bin/bash
set -eux
BASE=6.0.0
service docker stop
mount -t tmpfs -o size=100% tmpfs /var/lib/docker
service docker start
gcloud auth configure-docker
if [ ${CHAINERX} -gt 0 ]; then
if [ ${GPU} -gt 0 ]; then
case ${CHAINER} in
stable)
DOCKER_IMAGE=asia.gcr.io/pfn-public-ci/ch... |
46312882c49e957237bb37bba9712a9acbfe6b68517de2ca6d4aba5c0b2caf96 | Shell | 2,473 | 92 | #!/bin/bash -eu
set -o pipefail
PROGRAM_DIR=$(cd $(dirname $0); pwd -P)
# Reference
# https://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/105.20190906/GCF_000001405.25_GRCh37.p13/
VER="GRCh37"
SUBVER="p13"
ASSEMBLY_ID="GCF_000001405.25"
RELEASE="105.20190906"
GENOME="$VER.$S... |
0fdf43ff3c80da646b6889472b73df0b2efad2c8d413659f88dba15a63239db8 | Shell | 2,479 | 93 | #!/bin/bash
# shellcheck disable=SC2206
#SBATCH --job-name=hyperopt_ms
#SBATCH --cpus-per-task=8
#SBATCH --output=logs/hyperopt_%j.log
#SBATCH --nodes=2
#SBATCH --gres=gpu:2
#SBATCH --nodelist=node[1236,1237]
#SBATCH --time=0-00:30:00
#SBATCH --partition=sched_mit_ccoley
##SBATCH --tasks-per-node=1
##SBATCH --mem-per-... |
1678aa53f0993a9cedd95283b97a49485f81fbe2aa589842758f52bdc2070ee8 | Shell | 2,479 | 81 | #!/bin/bash
#: Title : test_addvers
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../addvers
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
e5afc6cd7768c9be4f9d5c3171329fd7278d77cc093966ccec059b970eb98129 | Shell | 2,479 | 78 | #!/bin/bash
#: Title : test_parsort
#: Date : 2019-09-05
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../parsort
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
9ec94dfd471f80d9043ac9dfd206721933a66343cec236ef7eb0a25338d7bdf5 | Shell | 2,497 | 57 | Rscript step2_SPAtests.R \
--vcfFile=./input/genotype_10markers_chrX.vcf.gz \
--vcfFileIndex=./input/genotype_10markers_chrX.vcf.gz.tbi \
--vcfField=GT \
--chrom=chrX \
--sampleFile_male=./input/sampleid_males.txt \
--SAIGEOutputFile=./output/example_quantitative.SAIGE.vcf... |
4d0e92405d262b866b1e0f8cce6e60f371eb082d1554bf46c41b9ad3bbc6633b | Shell | 2,498 | 80 | ########conda
# conda install multiqc
# conda install trim-galore
# conda install RSeQC
# conda install subread
# conda install hisat2
# conda install samtools
conda activate rna
module load alignments/hisat2-2.1.0
module load utils/samtools-1.9
module load tools/stringtie-2.1.5
module load tools/subread-1.6.... |
ffd43dac6b636a2c69ffc1eddc605313b80e50b9ffa3ac7569257ef490695635 | Shell | 2,511 | 71 | #!/bin/bash
PathToDropSeqTools=/home/goodwintracking/Genomics/Software/Drop-seq_tools-2.1.0
PICARD=/home/goodwintracking/Genomics/Software/Drop-seq-master/lib/picard-2.18.14.jar
WorkingDirectory=/mnt/LocalData/Genomics/VNC/20190709_analysis
DataLocation1=/mnt/LocalData/Genomics/VNC/20190709_analysis/RawData/190109_K0... |
a2b5091030902756390b76896ebd78da65cf1fa7610b3c89491241ae15d5a01f | Shell | 2,514 | 88 | #!/bin/bash
#: Title : test_tacmidy
#: Date : 2019-09-02
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../tacmidy
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\n"... |
839157ba7636c3e0ce8e6722a00bbb7b3b54051ec704172b48dc5d1fefe3f07b | Shell | 2,544 | 90 | #!/bin/bash
#: Title : test_liverinp
#: Date : 2023-06-29
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../liverinp
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
e8386a2e997d4c57e25f89e4d0651ce09d41b0a1c5d3580d273481a16916e973 | Shell | 2,546 | 101 | #!/usr/bin/env bash
# =============================================================================
# 04_format_conversion.sh — Format Conversion
# =============================================================================
# Convert GWAS summary statistics between supported formats.
# Use 'gwaslab formatbook list' t... |
e8828e3ce9a03ed743e699046abac93f0c2429385f7ea46143a89116506caef7 | Shell | 2,557 | 89 | #!/bin/bash
#
# VPREC test orchestrator.
# For each (type, mode, range, precision) combination:
# 1. Set VFC_BACKENDS with appropriate VPREC parameters
# 2. Run compute_vprec_rounding against the pre-generated reference file
# 3. Run check_output to compare results
#
set -e
export VFC_BACKENDS_LOGGER=False
mode... |
796ea6df0c672072dec417381c3b92cade6d189e088950624342dd5973e21b2d | Shell | 2,565 | 101 | #!/bin/bash -eu
set -o pipefail
PROGRAM_DIR=$(cd $(dirname $0); pwd -P)
# Reference
# https://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/109.20200815/
VER="GRCh38"
# Latest version
SUBVER="p14"
ASSEMBLY_ID="GCF_000001405.40"
RELEASE="110"
# Previous version
SUBVER="p13"
A... |
1c7d1e25426a1e5911c6d45ebf38c6dc661c136e3bad86adefb4eef70ca30a1d | Shell | 2,590 | 94 | #!/bin/bash
#: Title : test_execlong
#: Date : 2017-10-03
#: Author : "Vesa Oikonen" <vesa.oikonen@utu.fi>
#: Options : None
# Set the name of executable to test
PROGRAM=../../execlong
if [ ! -f $PROGRAM ]; then
if [ ! -f $PROGRAM.exe ]; then
printf "Failed: executable $PROGRAM does not exist.\... |
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