sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
25b1015f2bbb8f2d1042b1c196c4565669de83af3c38c5618e82299d422e28c6 | Shell | 697 | 30 | #!/bin/bash
# The working directory for this script will be "tests/scripts"
. /opt/conda/etc/profile.d/conda.sh
conda activate pytorch-ci
TUTORIAL_ROOT="./tutorials"
function fail {
echo FAIL: $@
exit -1
}
export MPLBACKEND=Agg
export DGLBACKEND=pytorch
export DGL_LIBRARY_PATH=${PWD}/build
export PYTHONPATH=... |
cf404b20c9907f039b4f02e43a6f41ea3a5ec7a566dd624e0747e71f455efe5a | Shell | 703 | 17 | TF_CFLAGS=( $(python -c 'import tensorflow as tf; print(" ".join(tf.sysconfig.get_compile_flags()))') )
TF_LFLAGS=( $(python -c 'import tensorflow as tf; print(" ".join(tf.sysconfig.get_link_flags()))') )
g++ -std=c++14 -shared alphagrad_2body.cc -o ../bin/alphagrad_2body.so -fPIC ${TF_CFLAGS[@]} ${TF_LFLAGS[@]} ... |
4cde62c6eb4d8f8dd473a581bdfba3ec73211ea2c3e285480d9c1ed9638353d5 | Shell | 706 | 6 | nohup env CUDA_VISIBLE_DEVICES=0 python -u train.py --prop 6 --save_model tmp_model.pt --title > train_1.log 2>&1 &
#nohup env CUDA_VISIBLE_DEVICES=2 python -u train.py --prop 6 --save_model tmp_model1.pt --title > train_2.log 2>&1 &
#nohup env CUDA_VISIBLE_DEVICES=3 python -u train.py --prop 6 --save_model tmp_model2.... |
0f8177beb0861476cf8bf11966f007c68d330fa69a4fd8b9fca251d9df4ae212 | Shell | 716 | 16 | #!/bin/bash
# Enters into docker container and then starts running do_data run for DeepDraw models
# Kai Sandbrink, 2020.11.09
# idea: https://stackoverflow.com/questions/35547966/how-to-write-a-bash-script-which-automate-entering-docker-container-and-doing
docker start kai_dlcdocker_data_tf15
docker exec --user kai... |
fdc2ae0a1d80fa55c0ff589d29f4435af63ddec47a033d96a1fd5ff7d22c3d1c | Shell | 731 | 23 | #!/bin/bash
# warning: this test is useful to check if training fails, and what speed you can achieve
# the toy datasets are too small to obtain useful translation results,
# and hyperparameters are chosen for speed, not for quality.
# For a setup that preprocesses and trains a larger data set,
# check https://github.... |
004b8fbf2a0573444015b7b780efccb2d4293a2eb07adc0359995d16f411a0b9 | Shell | 734 | 31 | #!/usr/bin/env bash
module load afni
module load fsl
module load matlab/R2021B
# args: 1=TB_PATH, 2=SRC_DIR, 3=OUTPUT_DIR, 4=SUB, 5=SES,
# 6=NUMBER_OF_ECHOS, 7=DONORDIC, 8=DOTSNR, 9=FORCE, 10=NUM_WORKERS, 11=script_dir
unset $SUB
unset $SES
TB_PATH="$1"
SRC_DIR="$2"
OUTPUT_DIR="$3"
SUB="$4"
SES="$5"
NUMBER_OF_ECH... |
ab7164bf8a9dc7939427b7ae59c9b4c7be880996ea8d8357ebe6863a6f797f92 | Shell | 745 | 13 | #!/bin/sh
actual_path=$(pwd)
sed -i 's@root_path=.*@root_path='"\'$actual_path\'"'@' source_routine/physics_layer_mod.py
sed -i 's@root_path=.*@root_path='"\'$actual_path\'"'@' source_routine/force_layer_mod.py
sed -i 's@root_path=.*@root_path='"\'$actual_path\'"'@' gradient_utility/grad_threebody_par.py
sed -i 's@roo... |
1b21f156904dec04a9d4212ddd369ce584be584e38b7d5a8fb50f922a4a2a0f0 | Shell | 748 | 25 | #!/usr/bin/env bash
## install.sh: run during an AppVeyor build to install the conda environment
## and the optional Pandoc spellcheck dependencies.
# Set options for extra caution & debugging
set -o errexit \
-o pipefail
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge-pypy3-$(un... |
d83193e28b1cc636395e7906578b65ab857b17d583fd5e77da1410c49908b172 | Shell | 748 | 40 | #!/bin/bash
# Add slice timing information to epi files
abids_loc=$(which abids_tool.py)
if [[ $abids_loc =~ "not found" ]]
then
echo "Cannot find abids_tool.py on path."
echo "Is AFNI properly installed?"
exit 1
fi
# for i in {1..30}
# do
# epi=$($QC_CODE_ROOT/rawloc.sh $i epi)
# abids_tool.py ... |
0004bc210455528a1e691ed325d74f965066cbe42e4dcce90dd223d637e9ec13 | Shell | 752 | 24 | #!/bin/bash
# warning: this test is useful to check if training fails, and what speed you can achieve
# the toy datasets are too small to obtain useful translation results,
# and hyperparameters are chosen for speed, not for quality.
# For a setup that preprocesses and trains a larger data set,
# check https://github.... |
f148692df15b285ee27a18bef761d5e26f0f63e4e63759c6a86563cca5fdd210 | Shell | 756 | 29 | #!/bin/bash
P=$1
# source language (example: fr)
S=$2
# target language (example: en)
T=$3
# path to nematus/data
P1=$4
# path to subword NMT scripts (can be downloaded from https://github.com/rsennrich/subword-nmt)
P2=$5
# tokenize
perl $P1/tokenizer.perl -threads 5 -l $S < {P}.${S} > {P}.${S}.tok
perl $P1/tokeni... |
4e001ea2c2850a11aa249c95518bfa428a035c002e5d9a122a89cb15cb9786ac | Shell | 761 | 31 | #!/bin/bash
# Helper script to build tensor adapter libraries for PyTorch
set -e
mkdir -p build
mkdir -p $BINDIR/tensoradapter/pytorch
cd build
if [ $(uname) = 'Darwin' ]; then
CPSOURCE=*.dylib
else
CPSOURCE=*.so
fi
CMAKE_FLAGS="-DCUDA_TOOLKIT_ROOT_DIR=$CUDA_TOOLKIT_ROOT_DIR -DTORCH_CUDA_ARCH_LIST=$TORCH_CUDA_ARCH... |
42c5fc9d1dfc347acbd2a812d2bd329b0fb0c9a37254a4dbc02fab5068de22bc | Shell | 762 | 24 | #!/bin/bash
# warning: this test is useful to check if training fails, and what speed you can achieve
# the toy datasets are too small to obtain useful translation results,
# and hyperparameters are chosen for speed, not for quality.
# For a setup that preprocesses and trains a larger data set,
# check https://github.... |
c20a273993d273ed68ad3ddf041475703e6b9987ec966dee95d4a63a3b4ce735 | Shell | 767 | 24 | #!/bin/bash
# warning: this test is useful to check if training fails, and what speed you can achieve
# the toy datasets are too small to obtain useful translation results,
# and hyperparameters are chosen for speed, not for quality.
# For a setup that preprocesses and trains a larger data set,
# check https://github.... |
b42729421643deb433bf39081c4041cd14f5c9501de11d0bb05f3346bdde7ea3 | Shell | 773 | 13 | #!/bin/sh
actual_path=$(pwd)
perl -i -pe's@root_path=.*@root_path='"\'$actual_path\'"'@' source_routine/physics_layer_mod.py
perl -i -pe's@root_path=.*@root_path='"\'$actual_path\'"'@' source_routine/force_layer_mod.py
perl -i -pe's@root_path=.*@root_path='"\'$actual_path\'"'@' gradient_utility/grad_threebody_par.py
pe... |
d3cb823ea82d6f46dc0bedbe2c8c1e38af4f7620d6f9a147ec8c55ea8b2939a6 | Shell | 773 | 24 |
# 1. cd to BIDS dir sub/ses/func
ls *ret*
for i in *ret* ; do mv $i ${i//retFF/retfixFF} ; done
for i in *ret* ; do mv $i ${i//retCB/retfixRWblock} ; done
for i in *ret* ; do mv $i ${i//retRW/retfixRW} ; done
or we can do
for i in *ret* ; do mv $i ${i//ret/retfix} ; done
for i in *ret* ; do mv $i ${i//retfixCB/retf... |
1083c79cce797008fdf7f0ff1b530a2d5cdf8e311ba82876c3e49ffc09bae8eb | Shell | 778 | 27 | #!/bin/bash
# Rewrites bare-basename dylib deps in $1 to absolute paths and re-signs.
# Needed because some deal.II-candi / OpenCASCADE libs have bare-basename
# install names, which dyld cannot find on macOS without DYLD_LIBRARY_PATH.
set -e
target="$1"
if [ -z "$target" ] || [ ! -f "$target" ]; then
echo "fix_dylib... |
53a30410bf657201ce9ace7504dea99463fd0a1873f98ed15dd3a0a1b857918d | Shell | 779 | 15 | TF_CFLAGS=( $(python -c 'import tensorflow as tf; print(" ".join(tf.sysconfig.get_compile_flags()))') )
TF_LFLAGS=( $(python -c 'import tensorflow as tf; print(" ".join(tf.sysconfig.get_link_flags()))') )
g++ -std=c++14 -shared proj3bodyonbasis_2alpha1betaNODEN.cc -o ../bin/proj3bodyonbasis_2alpha1betaNODEN.so -fP... |
a37cf4255c0fbc234998d7c68b94fc55844af499325745b16f955a3d5b46edf3 | Shell | 781 | 25 | #!/bin/bash
#
# ALIGNMENT OF Y-CHROMOSOME READS
#
# IT ASSUMES THAT THE FOLLOWING FASTQ FILES EXIST (FOR INPUT):
# o_fw_pr.fq o_rv_pr.fq o_fw_unpr.fq o_rv_unpr.fq
#
# $1 -> REFERENCE FASTA FILE
# $2 -> ORGAN
# $3 -> NUMBER OF THREADS
# $4 -> HIGH_SENSITIVITY = 1 ?
#
rm -f cy_index_file* cy_aligned_sorted-$2.bam.bai
bo... |
2f2435215a0f1fc646f602537f83b0ef97797ad946553ff22f6008e865b3eea6 | Shell | 782 | 23 | #!/usr/bin/env bash
# Input python command to be submitted as a job
#SBATCH --array=0-29
#SBATCH --output=logs/%j-rsa.out
#SBATCH --job-name RSA
#SBATCH -p psych_week
#SBATCH --mem-per-cpu 25G -t 100:00:00 --mail-type ALL -n 1 -c 1 -N 1
# Set up the environment
module load miniconda
module load OpenMPI
# Source cond... |
c86e07464d11a8d0e6092af3c2a2bd23064d92b9872edd0a48357930047f80a9 | Shell | 786 | 25 | #!/bin/bash
# warning: this test is useful to check if training fails, and what speed you can achieve
# the toy datasets are too small to obtain useful translation results,
# and hyperparameters are chosen for speed, not for quality.
# For a setup that preprocesses and trains a larger data set,
# check https://github.... |
c08a9ee9bcff83f182035225c82ad86fb4b52ad6dc8dfd6b70997408ba7ec44b | Shell | 790 | 25 | #!/usr/bin/env bash
set -euo pipefail
LATEST_WORKING_DIR="$(find . -maxdepth 1 -type d -name 'working-*' -printf '%T@ %P\n' | sort -nr | awk 'NR==1 {print $2}')"
if [[ -z "${LATEST_WORKING_DIR}" ]]; then
echo "No working-* directory found" >&2
exit 1
fi
require_match() {
local description="$1"
local find_arg... |
45c0d111887f9ab576003481a212f4102c34a062dc3a88fd79ea3cb9af98da5b | Shell | 795 | 34 | #!/bin/bash
#
# RUNNING SPECIFIC REFERENCE FOR MULTIPLE INDIVIDUALS AND SEQUENCED SAMPLES
#
declare -a INDIVIDUALS1=('I1' 'I3' 'I6' 'I7' 'I8' 'I14' 'I15' 'I16' 'I18')
declare -a INDIVIDUALS2=('I23' 'I24' 'I25' 'I26' 'I27' 'I28' 'I36' 'I40' 'I46' 'I47' 'I54')
#
# HISEQ
echo "Running hiSeq ..."
cd hiseq/tracespipe/src/
.... |
aee0361b18320f25607e72cccef38522c89356296be3a9eaf8c1c0d3ea477bd3 | Shell | 798 | 23 | #!/bin/bash
#
efetch -db nucleotide -format fasta -id NC_012920.1 > MT.fa
#
gto_fasta_extract_read_by_pattern -p "AY386330.1" < VDB.fa > B19.fa
gto_fasta_extract_read_by_pattern -p "MG921180.1" < VDB.fa > HPV.fa
gto_genomic_gen_random_dna -n 5000 | gto_fasta_from_seq -n "Synthetic-GTO-5k" > SYN.fa
#
gto_fasta_mutate -s... |
2adb9e0590bd11a52fe21612db8683bcc2d350bec39a090c3dc9b857056276e1 | Shell | 826 | 26 | #!/bin/bash
# warning: this test is useful to check if training fails, and what speed you can achieve
# the toy datasets are too small to obtain useful translation results,
# and hyperparameters are chosen for speed, not for quality.
# For a setup that preprocesses and trains a larger data set,
# check https://github.... |
e75c1ceaa5420c57b5664867d964b307ef1bd1e6c478d7a46d9e853725c73f73 | Shell | 826 | 37 | #!/bin/bash
#
# TRACES_project_coordinates.sh positions_files max_coverage
#
if [ ! -f "$1" ]; then
echo "ERROR: Input file $1 does not exists!";
exit;
fi
#
mapfile -t POSITIONS < $1
#
for read in "${POSITIONS[@]}" #
do
#
IPOS=`echo $read | awk '{ print $2 }'`;
EPOS=`echo $read | awk '{ print $3 }'`;
COVE... |
7d8037c1dc102eec935dbbc7822efa010b9973681a5c93d0dcf092d8f8e7572f | Shell | 829 | 21 | #!/bin/bash
# Compare main with venv-factorize, a copy whose run_harmony encodes the batch
# labels with pd.factorize(..., sort=True) instead of np.unique (same codes,
# so the same results). The two alternate, three repeats per dataset, into
# results-factorize.jsonl. Waits for run.sh to release the lock first.
set -u... |
8286b8c109279cc2b8cf92515f76c340c19ff1fd96d47678220e066efc7dae86 | Shell | 831 | 17 | #!/bin/bash
#
ORGAN="$1";
#
TOTAL_COVERAGE=`awk '{sum += (($3-$2)*$4)} END {print sum}' ../output_data/TRACES_cy_bed/cy-coverage-$ORGAN.bed `;
TOTAL_SIZE=`tail -n 1 ../output_data/TRACES_cy_bed/cy-coverage-$ORGAN.bed | awk '{ print $3}'`;
NORMALIZED_COVERAGE=`echo "scale=4; $TOTAL_COVERAGE / $TOTAL_SIZE" | bc -l`;
prin... |
8e6411a7dc093f53abde067a4043d5ee217253bae70826f4a1a006211da84926 | Shell | 832 | 39 | #!/bin/bash
# Translate "task" or "rest" to the correct directory in this environment
# Usage: pass "task" or "rest" to this script to get back a directory
subj=$1
valid_ids="Valid task IDs range [001-030], valid rest IDs range [101-120]."
if [[ ! $subj ]]
then
echo "You must supply a valid subject ID."
echo... |
c710afa6773275ec51a41627c9e110028bdaf61ce07a1949294404f87bdc5e19 | Shell | 832 | 37 | #!/bin/bash
#
# TRACES_project_coordinates.sh positions_files max_coverage
#
if [ ! -f "$1" ]; then
echo "ERROR: Input file $1 does not exists!";
exit;
fi
#
mapfile -t POSITIONS < $1
#
for read in "${POSITIONS[@]}" #
do
#
IPOS=`echo $read | awk '{ print $2 }'`;
EPOS=`echo $read | awk '{ print $3 }'`;
COVE... |
e76d98cf13765acedc72a40c73dec763820e8c9694f567c7bc3474077f62548b | Shell | 846 | 17 | #!/bin/bash
#
ORGAN="$1";
#
TOTAL_COVERAGE=`awk '{sum += (($3-$2)*$4)} END {print sum}' ../output_data/TRACES_mtdna_bed/mt-coverage-$ORGAN.bed `;
TOTAL_SIZE=`tail -n 1 ../output_data/TRACES_mtdna_bed/mt-coverage-$ORGAN.bed | awk '{ print $3}'`;
NORMALIZED_COVERAGE=`echo "scale=4; $TOTAL_COVERAGE / $TOTAL_SIZE" | bc -l`... |
310c5d44adba53e7c3966c955e43ea00895ef6fbd08fb938109668c0187881ae | Shell | 859 | 49 | #!/bin/bash
# Script to get specific raw files loaded
# Pass subject and filetype
subj=$1
ftype=$2
valid_ftypes="Valid ftypes are 'T1w', 'epi'"
subjloc=$($QC_CODE_ROOT/subj2loc.sh $subj)
# Need to get more stuff for rest sets, which have longer names
if [[ $((10#$subj)) -ge 101 ]]
then
anat_addendum="_ses-01_r... |
9598d52c7027c2a0712b3c01ae6795ab9c1a80f40079e4a59ab725d8ec313122 | Shell | 865 | 28 | #!/bin/bash
#
# ASSEMBLE
if [ "$#" -lt 8 ]; then
>&2 echo "YourCall: $0 $*"
>&2 echo -e "Usage: $(basename "$0") Organ nThread bResume memLimit o_fw_pr.fq o_rv_pr.fq o_fw_unpr.fq o_rv_unpr.fq\n";
exit 1;
fi
Organ=$1; shift
nThread=$1; shift
BResume=$1; shift
memLimit=$1; shift
fq1p=$1; shift
fq2p=$1; shif... |
7128369de85179fc8f80335027f7741af787970ae3a760f5aa3ce5b0480114cd | Shell | 876 | 38 | #
CHECK_INPUT () {
FILE=$1
if [ -f "$FILE" ];
then
echo "Input filename: $FILE"
else
echo -e "\e[31mERROR: input file not found ($FILE)!\e[0m";
SHOW_MENU;
exit;
fi
}
#
INPUT_FILE="latest_list.txt"
CHECK_INPUT "$INPUT_FILE";
#
mapfile -t INT_DATA < $INPUT_FILE;
for dint in "${INT_DATA[@... |
9aa0e4c7d6ca425f8ab248380f58e9c188fd0ff6b30b85dfae2d5335c040adb8 | Shell | 885 | 27 | #!/bin/bash
#
# NO HPV77!
declare -a VIRUSES=("B19V" "BuV" "CuV" "HBoV" "AAV" "BKPyV" "JCPyV" "KIPyV"
"WUPyV" "MCPyV" "HPyV6" "HPyV7" "TSPyV" "HPyV9" "MWPyV"
"STLPyV" "HPyV12" "NJPyV" "LIPyV" "SV40" "TTV" "TTVmid"
"TTVmin" "HAV" "HBV" "HCV" "HDV" "HEV" "SENV" ... |
1fb8bad83d5cfe2c83c3caba48f6051ae2f6c0c33644280d554153154875426e | Shell | 898 | 25 |
## download eQTL v8
## eGene and significant variant-gene associations based on permutations.
## The archive contains a *.egenes.txt.gz and *.signif_variant_gene_pairs.txt.gz file for each tissue.
# Note that the *.egenes.txt.gz files contain data for all genes tested; to obtain the list of eGenes, select the rows ... |
477b053a71ac5018675236e8b3b0097ef603c2a2b5dec1dabf6cac8f0ef88e60 | Shell | 898 | 25 | #!/bin/bash
if [ "$#" -lt 1 ]; then
>&2 echo "Usage: $(basename "$0") seqs.fna > maskedSeqs.fna";
exit 1;
fi
#Use sdust to identify low complexity regions in the provided DNA sequences
#This creates a bed file which bedtools can use to hardmask (replace with N's)
#the lcr regions. Note: falcon ignores non-can... |
c571ad7b197d101b1193a25f155796c5df79385094df28a47e50d172d2e89dfb | Shell | 900 | 33 | #!/usr/bin/env bash
# Push HTML files to gh-pages automatically.
# Fill this out with the correct org/repo
ORG="WhitakerLab"
REPO="scona"
# This probably should match an email for one of your users.
EMAIL="kw401@cam.ac.uk"
set -e
# Clone the gh-pages branch outside of the repo and cd into it.
cd ..
git clone -b gh-p... |
4881face5b3e09d8a22b42b9086e04c105fcb688db6e9a6d6b40413f56dbf3cc | Shell | 904 | 26 | #!/bin/bash
#
declare -a INDIVIDUALS1=('I1' 'I3' 'I4' 'I6' 'I7' 'I8' 'I12' 'I14' 'I15' 'I16' 'I18' 'I19' 'I29' 'I30')
declare -a INDIVIDUALS2=('I1' 'I2' 'I3' 'I4' 'I5' 'I6' 'I7' 'I8' 'I9' 'I10' 'I11' 'I12' 'I13' 'I14' 'I15' 'I16' 'I17' 'I18' 'I19' 'I20' 'I21' 'I22' 'I23' 'I24' 'I25' 'I26' 'I27' 'I28' 'I29' 'I30' 'I31' ... |
6e2097cf1c4d6305f358ebe45896f64356e5e905d647824541a336dcd0d72137 | Shell | 906 | 39 | #!/usr/bin/env bash
set -euo pipefail
ADDR="${SM_CI_BB_ADDR:-127.0.0.1:8080}"
LOG_DIR="ci-artifacts"
LOG_FILE="${LOG_DIR}/bb.log"
PID_FILE="${LOG_DIR}/bb.pid"
mkdir -p "${LOG_DIR}"
if curl -fsS "http://${ADDR}/len" >/dev/null 2>&1; then
echo "Blackboard already reachable at ${ADDR}"
exit 0
fi
if [[ "${ADDR}" !=... |
3a00aa739fe8b74b210ab7414ab72c0f54c960658c73ee2a17cc1e46ab1c8495 | Shell | 913 | 27 | #!/usr/bin/env bash
set -euo pipefail
cd /raid/mbrown/simplemind
SMCORE_BIN="/raid/mbrown/.micromamba/envs/smcore/bin"
CORE_BIN="/home/mbrown/go/bin/core"
export PATH="$SMCORE_BIN:/home/mbrown/go/bin:$PATH"
ARTIFACT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
BB_ADDR="${BB_ADDR:-127.0.0.1:18082}"
PAYLOAD_HOST... |
9a5272dd9ce4eed54f0c12734485a0861cf74b864ce0be9adc85e48306f9299f | Shell | 913 | 25 | #!/usr/bin/env bash
# Input python command to be submitted as a job
#SBATCH --array=0-29
#SBATCH --output=logs/%j-rsa.out
#SBATCH --job-name RSA
#SBATCH -p psych_week
#SBATCH --mem-per-cpu 25G -t 100:00:00 --mail-type ALL -n 1 -c 1 -N 1
# Set up the environment
module load miniconda
module load OpenMPI
module load dSQ... |
c114e753cc791b91818b266ce3102df8f4fae9f7a6031e85e3bbd005de0fdc25 | Shell | 916 | 18 | #!/bin/bash
#
PATTERN="$1";
ORGAN="$2";
#
TOTAL_COVERAGE=`awk '{sum += (($3-$2)*$4)} END {print sum}' ../output_data/TRACES_specific_bed/$PATTERN-coverage-$ORGAN.bed `;
TOTAL_SIZE=`tail -n 1 ../output_data/TRACES_specific_bed/$PATTERN-coverage-$ORGAN.bed | awk '{ print $3}'`;
NORMALIZED_COVERAGE=`echo "scale=4; $TOTAL_... |
1648ea2c081ebf2f4aea34e38b343e30c21c5f158b166f330f0c781eeccb33a1 | Shell | 917 | 26 | mkdir Fastq
### SRR11442505.1;Public1NOSN
mkdir Fastq/Public1NOSN
mv Public1NOSN/SRR11442505.1_1.mod.fastq.gz Fastq/Public1NOSN/Public1NOSN_S8_L001_R1_001.fastq.gz
mv Public1NOSN/SRR11442505.1_2.mod.fastq.gz Fastq/Public1NOSN/Public1NOSN_S8_L001_R3_001.fastq.gz
mv Public1NOSN/SRR11442505.1_3.mod.fastq.gz Fastq/Publ... |
7a4f0fa5ccc1e5e2e4dc9c4731fcf9ab02f276cdb365373397f7c8cd6fab187e | Shell | 922 | 28 | # bash /mnt/c/Users/s/Documents/Github/Rapidtide-task-rest/MSI_Create_Maps.sh
# <input_file> the imaging data that is your 'REST' portion (not detrended)
input_dir='/mnt/c/Users/s/OneDriveNU/Data/fMRI'
# <output_file>
output_dir='/mnt/c/Users/s/OneDriveNU/Data/Tmean'
subject_list=("01" "02" "03" "04" "06" "07" "08" "0... |
441370ce53a4a40ab8eed60f1e45495fd33545bfab0352d4f2dd9c0970dec95f | Shell | 928 | 39 | #!/bin/bash
# Check if a path is provided as an argument
if [ -z "$1" ]; then
echo "Usage: $0 <path>"
exit 1
fi
# Get the provided path
input_path=$1
# Check if the provided path is a valid directory
if [ ! -d "$input_path" ]; then
echo "Error: $input_path is not a valid directory"
exit 1
fi
# Iterate over ... |
98b15abd1aad86293fe022dff43e0a834d2b45c7469bf29fdd0e92adc52077a5 | Shell | 939 | 27 | #!/bin/sh
if [ $1 -le $2 ]; then
echo "running simulation for trial $1 out of $2"
rm -r ./of
rm report_det.dat
python update_random_seed.py $1 # Changing random seed for each trial
python create_dirs.py # Create the data directory
python update_music_file.py # Make sure... |
51675220c33bfdd7a4b65991de1ae532c565e1b2e70231e9650799735e3ef004 | Shell | 946 | 23 | #!/usr/bin/env bash
# Input python command to be submitted as a job
#SBATCH --array=0-29
#SBATCH --output=logs/%j-sim-cv-mr.out
#SBATCH --job-name SIM_CV_MR
#SBATCH -p psych_week
#SBATCH --mem-per-cpu 25G -t 100:00:00 --mail-type ALL -n 1 -c 1 -N 1
# Set up the environment
module load miniconda
module load OpenMPI
# ... |
1c819404c31361db6f64afb39a1de57c4f724eb6f0205e9d5dcdec3e76c929de | Shell | 952 | 26 | #!/bin/bash
#
declare -a INDIVIDUALS1=('I1' 'I3' 'I4' 'I6' 'I7' 'I8' 'I12' 'I14' 'I15' 'I16' 'I18' 'I19' 'I29' 'I30')
declare -a INDIVIDUALS2=('I1' 'I2' 'I3' 'I4' 'I5' 'I6' 'I7' 'I8' 'I9' 'I10' 'I11' 'I12' 'I13' 'I14' 'I15' 'I16' 'I17' 'I18' 'I19' 'I20' 'I21' 'I22' 'I23' 'I24' 'I25' 'I26' 'I27' 'I28' 'I29' 'I30' 'I31' ... |
005cb6afa1cae86ac9d521f9e626f978e1de0a3afc3385c5bb3e9fc12dfcb92d | Shell | 953 | 10 | #!/usr/bin/bash
java -cp `ls target/*-fatjar.jar` io.anserini.reproduce.RunMsMarco -collection msmarco-v1-passage >& logs/log.msmarco-v1-passage
java -cp `ls target/*-fatjar.jar` io.anserini.reproduce.RunMsMarco -collection msmarco-v1-doc >& logs/log.msmarco-v1-doc
java -cp `ls target/*-fatjar.jar` io.anserini.reprodu... |
f82a3c111fcc8bfc3214b9fe7765b7c0cbbafe51f040cc5e0eb00c6079feea8b | Shell | 962 | 27 | #!/usr/bin/env bash
set -euo pipefail
LATEST_WORKING_DIR="$(find . -maxdepth 1 -type d -name 'working-*' -printf '%T@ %P\n' | sort -nr | awk 'NR==1 {print $2}')"
if [[ -z "${LATEST_WORKING_DIR}" ]]; then
echo "No working-* directory found" >&2
exit 1
fi
require_match() {
local description="$1"
local find_arg... |
a712aa691eb2cd3a55d900b196420b144d9cd684031d374ca858017192351501 | Shell | 973 | 47 | #!/bin/bash
. /opt/conda/etc/profile.d/conda.sh
conda activate pytorch-ci
GCN_EXAMPLE_DIR="./examples/pytorch/"
function fail {
echo FAIL: $@
exit -1
}
function usage {
echo "Usage: $0 [cpu|gpu]"
}
# check arguments
if [ $# -ne 1 ]; then
usage
fail "Error: must specify device"
fi
if [ "$1" == "... |
4a7fceeac8ac80c21e3cfd166e3e445dffc583eebf6210812da7da7c8a6602af | Shell | 975 | 18 | cellranger mkgtf $1 $2 \
--attribute=gene_biotype:protein_coding \
--attribute=gene_biotype:lincRNA \
--attribute=gene_biotype:antisense \
--attribute=gene_biotype:IG_LV_gene \
--attribute=gene_biotype:IG_V_gene \
--at... |
d7dde19eec9aa19c2be063d576b72808a9ccb32795bf31fdf4f2bca83a87c259 | Shell | 982 | 34 | #!/bin/bash
# Helper script to build dgl sparse libraries for PyTorch
set -e
mkdir -p build
mkdir -p $BINDIR/dgl_sparse
cd build
if [ $(uname) = 'Darwin' ]; then
CPSOURCE=*.dylib
else
CPSOURCE=*.so
fi
CMAKE_FLAGS="-DCUDA_TOOLKIT_ROOT_DIR=$CUDA_TOOLKIT_ROOT_DIR -DTORCH_CUDA_ARCH_LIST=$TORCH_CUDA_ARCH_LIST -DUSE_CUD... |
b72275c6a539142c33393d048de7f577621cb9cafbfbc9fc46a8c540885d4b18 | Shell | 986 | 44 | #!/bin/sh
set -x
#echo "Inserisci il nome dell'archivio FSDA da analizzare : "
#read what
what=`cygpath -a $1`
if [ ! -d "$what" ]
then
echo "ERRORE :" $what " non esiste !!!!"
exit 1
fi
mkdir $2/EXAMPLES_test
if [ $? != 0 ]
then
echo "ERRORE : EXAMPLES_test esiste !!!!"
exit 1
fi
EXCL_FILES="! -... |
f48b33373bcb2f2a5c91a5dfa421f09ef433d718a1477d0abf46cada2cbee6ff | Shell | 1,021 | 43 | #!/bin/bash
# Usage: ./Reads_extract2.sh --SiteFile site.bed --BamPath /absolute/path/to/nanopore.sam --Fast5Dir /absolute/path/to/nanopore_reads --Output /absolute/path/to/extracted_reads.txt
while [[ $# -gt 0 ]];do
key=${1}
case ${key} in
--SiteFile)
Site=${2}
shift 2
;;
--BamPath)
... |
1fa2456e4661fc9f5691fe602ee434c3b324bfb1f551ffc20d5cbc3fe6c44c5f | Shell | 1,026 | 12 | #!/bin/bash
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V25_* .
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V26_* .
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V27_* .
#scp dpratas@atlas.... |
9acb0a88e88a6673cd7e68ea43071b9663f5f3360a438da5355c9cb625fce46f | Shell | 1,027 | 61 | #!/bin/bash
makespec_loc=$(which @SUMA_Make_Spec_FS)
if [[ $? != 0 ]]
then
echo "SUMA not found, is AFNI installed?"
exit 1
fi
reconall_loc=$(which recon-all)
if [[ $? != 0 ]]
then
echo "recon-all not found, is freesurfer installed and setup?"
exit 1
fi
subject=$1
if [[ ! $subject ]]
then
echo... |
562409b1a46110fb8faaf0a9812d40d2800381df54f99db9f72906ede1762c19 | Shell | 1,028 | 13 | #!/bin/bash
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V32_* .
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V33_* .
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V34_* .
#scp dpratas@atlas.... |
dc18905ca688c502d4fed7f3510a4c35c4ad3534d9831481e845ab6bb74d7205 | Shell | 1,033 | 27 | #!/bin/bash
CURRENT_DIR=$(dirname "$0")
PARAM_FOLDER="parameter_sets"
CURRENT_PARAMS="$PARAM_FOLDER/current_parameter"
if [ "$#" -ne 1 ]; then
echo "Error: change_parameters.sh requires exactly one parameter."
echo "Usage: $0 <parameter>"
exit 1
fi
PARAM_SET="$PARAM_FOLDER/$1"
if [ "$1" = "original_para... |
2b9aab344e6021e75b508a2297027a80f9cdca88aaf19aa6ebc60cd6cd736fe4 | Shell | 1,050 | 36 | #!/bin/bash
# Job name:
#SBATCH --job-name=best_weights
#
# Account:
#SBATCH --account=fc_cerebellum
#
# Partition:
#SBATCH --partition=savio2
# Quality of Service:
#SBATCH --qos=savio_normal
#
# Wall clock limit:
#SBATCH --time=01:00:00
#
## Command(s) to run:
module load python/3.7
source ~/.bash_profile
source $(pi... |
57cb404b087a23e567391e9bbcb070a866161594ec7c4378f019e10e04af1d2e | Shell | 1,054 | 25 | #!/bin/bash
#
# ./TRACES_ivar.sh ../output_data/TRACES_viral_alignments/H_N-HV6B.fa ../output_data/TRACES_viral_alignments/viral_aligned_sorted-H_N-HV6B.bam H_N HV6B 0.2
#
Reference=$1; # EXAMPLE: TTV.fa
Alignments=$2; # EXAMPLE: ttv_aligned_sorted-heart.bam
Organ=$3; # Example: heart
Label=$4; #... |
f341cc5ed44b706abd7cca3bc65a8c7513ae7ac5b974cd469f8538ece7fd0463 | Shell | 1,072 | 29 | basedir=/export/home/glerma/public/Exchange/LMC_DWI_course
sing_path=${basedir}/containers
#sub=$(cat $basedir/subSesList.txt | awk 'NR >1 {print $(1)}' | tr ',\n' ' ')
# define an array of subjects
sub=("BHpilot_IT")
#cmd="ls ${basedir}/dicom/${subj}"
#echo $cmd
#eval $cmd
module load apptainer/latest
for sub in "$... |
16874cb5168a579c74f27bf6cecfc7b01fa7cc56411442751927773300371ffc | Shell | 1,073 | 54 | #!/bin/bash
# unlink_all_symlinks.sh
# Removes all symbolic links in a directory and its subdirectories
if [ $# -ne 1 ]; then
echo "Usage: $0 <directory>"
echo "Example: $0 /DATASETS/VOTCLOC/BIDS"
exit 1
fi
DIR="$1"
if [ ! -d "$DIR" ]; then
echo "Error: Directory not found: $DIR"
exit 1
fi
echo ... |
00e553a200cb2ee8647730b540d1b862dfb496cf16d103a46b48106af4e37a87 | Shell | 1,074 | 29 | #!/bin/bash
#SBATCH --time=30:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=16384M # memory per CPU core
#SBATCH --mail-user=petemade@isu.edu
#SBATCH --mail-type=END
# Compatibility variables for PBS. Delete if not needed.... |
1e7a080caf7926ffe97bfef4b562b6cc9dd81711c40614104559a487420aa1b3 | Shell | 1,075 | 24 | basedir=/export/home/glerma/public/Exchange/LMC_DWI_course
sing_path=${basedir}/containers
#sub=$(cat $basedir/subSesList.txt | awk 'NR >1 {print $(1)}' | tr ',\n' ' ')
sub=("BHpilot_IT")
ses=001
module load apptainer/latest
cmd="apptainer run \
--bind ${basedir}:/base \
${sin... |
bd497b90f638b44c1b56b5c86b234e22993a1bd93bc0033645d87f7d746be4c8 | Shell | 1,086 | 35 | #!/bin/bash
#
# ./TRACES_blastn_n_db.sh query.fa
#
# ==============================================================================
#
SPATH="../system_files/blast_dbs/nt";
QUERY="$1";
DBASE="nt";
#
# http://www.metagenomics.wiki/tools/blast/blastn-output-format-6
#
#STYLE="6 qacc sacc pident mismatch btop";
#
# qseqid... |
e2c8058521e1f917348299b321bd2fce621065c69939bc85fcf500c299f95b83 | Shell | 1,092 | 39 | #!/bin/bash
cat ../meta_data/meta_info.txt | tr ':' '\t' | awk '{ print $1}' > names_tmp_TRACES.tmp
mapfile -t NAMES < names_tmp_TRACES.tmp
#
rm -f names2_tmp_TRACES.tmp
#
printf "\t" > names3_tmp_TRACES.tmp;
#
for name in "${NAMES[@]}" #
do
printf "$name\t\t" >> names3_tmp_TRACES.tmp;
done
printf "\n" >> names3_... |
60c9f65309211d3cc6bcc0272e949eaee568458264c26bfb26b9edb4a5dcd60c | Shell | 1,095 | 37 | #!/bin/bash
# Verificar si se proporcionó el nombre del archivo Dockerfile como argumento
if [ $# -ne 1 ]; then
echo "Uso: $0 <nombre-del-archivo-dockerfile>"
exit 1
fi
DOCKERFILE="$1"
# Buscar las líneas LABEL en el archivo Dockerfile
LABEL_LINES=$(grep "^LABEL" "$DOCKERFILE")
# Extraer el valor de la etiqueta... |
616d265e44a918a2e44463fee2c5216756634ffd4bd8655853f7ddcd2c8e607d | Shell | 1,096 | 35 | #!/usr/bin/env bash
set -euo pipefail
repository_root="$(git rev-parse --show-toplevel)"
example_root="${repository_root}/contrib/lit/examples/he"
run_root="${JAQMC_LIT_RUN_ROOT:-${repository_root}/runs/he_lit}"
raw_path="${run_root}/lit/lit_spectrum.npz"
post_dir="${run_root}/post"
jaqmc_command="${repository_root}/.... |
1af72ae399bc86b5373ee8a734a942ac5b4b13ffd296d91053e3920e2510f4ff | Shell | 1,102 | 39 | #!/bin/bash
if [[ ! $QC_CODE_ROOT ]]
then
echo "QC_CODE_ROOT not set."
echo "Please set it manually or source an environment template."
exit 1
fi
$QC_CODE_ROOT/check_env.sh
if [[ $? != 0 ]]
then
echo "Environment not set up correctly; see above."
exit 1
fi
sid=$1
SUB_LABEL=$(printf sub-%3.3d $si... |
0bc0c33a23f7eebe796b8d20298627e2b376aca27f35485939a56251b2253327 | Shell | 1,104 | 13 | #!/bin/sh
# Smoke test: fail the image build immediately if a later `pip install` replaced or broke the pinned CUDA torch stack
# (e.g. a dep that drags in a different torch/CUDA/NCCL -- which surfaces as `undefined symbol: ncclCommResume` at
# `import torch`; see run 28991812987). We import torch (which eagerly loads ... |
8857d233dd313386a14f82e086e504443ff8fa86ecbb48fec67c2ce84cea5a5d | Shell | 1,104 | 34 | #!/bin/bash
# Job name:
#SBATCH --job-name=connect_train
#
# Account:
#SBATCH --account=fc_cerebellum
#
# Partition:
#SBATCH --partition=savio2
# Quality of Service:
#SBATCH --qos=savio_normal
#
# Wall clock limit:
#SBATCH --time=60:00:00
#
## Command(s) to run:
module load python/3.7
source ~/.bash_profile
source $(p... |
930c0bd616d53f265e219de90970874a5ee8a3a12f7600951ec66a8e30ce364a | Shell | 1,121 | 29 |
# bash run.layer.sh <layer> <the number of kernels> <threads> <optional: the number of flexible motifs> &> .layer<layer>.log
#<layer> the layer number
#<the number of kernels> the number of kernels in the layer
#<threads> the number of neuron can be demixed at the same time
#<optional: the number of hard-syntax mot... |
cf4ae12aec304a33cb7dbc6a665d0b671c2ac5f98f2313721a188f2a4e97082d | Shell | 1,121 | 43 | #!/bin/bash
#
declare -a INDIVIDUALS=('I1' 'I3' 'I4' 'I6' 'I7' 'I8' 'I12' 'I14' 'I15' 'I16' 'I18' 'I19' 'I24' 'I29' 'I30');
#
#
./TRACESPipe.sh --gen-adapters
./TRACESPipe.sh --get-phix
./TRACESPipe.sh --get-mito
./TRACESPipe.sh --get-y-chromo
#./TRACESPipe.sh --build-viral
#./TRACESPipe.sh --build-unviral
#
for x in "... |
6c458dba7dea39283d34c9ee41e815d58f1f94e71922cfa7f00f9dc78c693c29 | Shell | 1,125 | 13 | #!/bin/bash
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V9_* .
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V10_* .
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V11_* .
#scp dpratas@atlas.fi... |
031efdef600f9f2a716378f8d2ea8f4a0748d421b097fe8daac08b8a432473ba | Shell | 1,126 | 12 | #!/bin/bash
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V39_* .
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V40_* .
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V41_* .
#scp dpratas@atlas.... |
2dd8c444212d8f92484f2404107a6cd6c984d22fbb33c3c4a5f3b0f262286274 | Shell | 1,128 | 13 | #!/bin/bash
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V17_* .
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V18_* .
#scp dpratas@atlas.fimm.fi:/fas/NGS/pipes/fastq/fimm_ngs_mtoppinen/autopsy_NGS_novaseq1/V19_* .
#scp dpratas@atlas.... |
da10bfc86c53fefc019916cd851541659171a416a0d63a1ccba98e47d0156c45 | Shell | 1,130 | 66 | # BUILD MODE
BUILD=RELEASE
# Source directory of BeatIt. Use full Path
BeatIt_SOURCE_DIR=
# Install directory
PREFIX=$BeatIt_SOURCE_DIR/../install
# MPI
MPICC=mpicc
MPICXX=mpicxx
# If you have one, this can be useful
# TPL Base Folder
# Example
# TPL=~/TPL
TPL=
# petsc
# Example:
# PETSC=$TPL/petsc/3.7.4/opt/
PET... |
485fd03a644d50ee107b17ac744a86dea97fe3f62b7fe7ff08071dd5418b98b4 | Shell | 1,135 | 37 | #!/bin/bash
function fail {
echo FAIL: $@
exit -1
}
echo $PWD
export DGLBACKEND=pytorch
export DGL_LIBRARY_PATH=${PWD}/build
export PYTHONPATH=${PWD}/tests:${PWD}/python:$PYTHONPATH
export LD_LIBRARY_PATH=${PWD}/build:$LD_LIBRARY_PATH
export DIST_DGL_TEST_CPP_BIN_DIR=${PWD}/build
export DIST_DGL_TEST_IP_CONFIG... |
ee315c5c005a990348941a32e0d8b471c8820fcebd4e853383b364d7834ba6d9 | Shell | 1,136 | 45 | #!/bin/bash
cur_dir=$(pwd)
host_count=`cat hostfile | wc -l`
graph_name="order"
perhost_part=2
current_host=`ifconfig | grep -Eo 'inet (addr:)?([0-9]*\.){3}[0-9]*' | grep -Eo '([0-9]*\.){3}[0-9]*' | grep -v '127.0.0.1'`
echo "metis creation start"
##Nodes
`python3 metis_creation.py -n ${graph_name}`
echo "metis c... |
f69f6ccaa73ad642189c366d1aaec7deb5a459c42dadc691b1d3481817af3ff2 | Shell | 1,141 | 36 | #!/bin/bash
# warning: this test is useful to check if training fails, and what speed you can achieve
# the toy datasets are too small to obtain useful translation results,
# and hyperparameters are chosen for speed, not for quality.
# For a setup that preprocesses and trains a larger data set,
# check https://github.... |
e4d6fb6c1accd2fc2ed24b12795baf9f0de09a3c5feca4350906ed605353d82d | Shell | 1,169 | 54 | #!/bin/bash
# Run freesurfer for one subject
reconloc=$(which recon-all)
if [[ $reconloc =~ "not found" ]] || [[ $reconloc =~ "no recon-all" ]]
then
echo "Cannot find recon-all, is freesurfer loaded?"
exit 1
fi
nuloc=$(which nu_correct)
if [[ $reconloc =~ "not found" ]] || [[ $reconloc =~ "no recon-all" ]] ... |
c52f756c79c219f035893f195e8781492b3ee9611a10997525825a14967c68b0 | Shell | 1,174 | 37 | #!/bin/bash
#SBATCH --time=00:30:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=15360M # memory per CPU core
#SBATCH -J "preproc1" # job name
# Compatibility variables for PBS. Delete if not needed.
export PBS_NODEFILE=`/fs... |
2dc58571e08c4bf4d8541c5fbb0b48681ee1ef454faaf439a7eb6f8b3c8f9483 | Shell | 1,177 | 52 | #!/bin/bash
echo "----------------------------"
echo "Compile gendata"
cd gendata
make clean; make
echo "----------------------------"
echo "Compile uTR"
cd ../uTR
make clean; make
cd ..
echo "----------------------------"
echo "Calculate compression ratio"
gen_units=gendata/gen
uTR=uTR/uTR
num_TRs=1000
min_unit_oc... |
3f00155d33090e4356f1eb9569dcd22f20abc33b1132c72fb3c3cb4de2207a68 | Shell | 1,179 | 45 | #!/bin/bash
. /opt/conda/etc/profile.d/conda.sh
function fail {
echo FAIL: $@
exit -1
}
function usage {
echo "Usage: $0 backend device"
}
if [ $# -ne 2 ]; then
usage
fail "Error: must specify backend and device"
fi
export DGLBACKEND=$1
export DGLTESTDEV=$2
export DGL_LIBRARY_PATH=${PWD}/build
... |
b5ea4ddd628bd5f393a31294eda09cae7e13d534db44fdfc949506b6f6be0069 | Shell | 1,179 | 41 | #!/bin/bash
. /opt/conda/etc/profile.d/conda.sh
function fail {
echo FAIL: $@
exit -1
}
function usage {
echo "Usage: $0 backend device"
}
if [ $# -ne 2 ]; then
usage
fail "Error: must specify backend and device"
fi
[ $1 == "pytorch" ] || fail "Distrbuted tests run on pytorch backend only."
[ $... |
6b7490de70f2abcb381e625bb89b8dd051433b53f42c3cd64dd4300e2254cfa4 | Shell | 1,196 | 40 | #!/usr/bin/env bash
set -euo pipefail
repository_root="$(git rev-parse --show-toplevel)"
example_root="${repository_root}/contrib/lit/examples/he"
run_root="${JAQMC_LIT_RUN_ROOT:-${repository_root}/runs/he_lit}"
ground_dir="${run_root}/ground"
lit_dir="${run_root}/lit"
jaqmc_command="${repository_root}/.venv/bin/jaqmc... |
f2f55512eed434df429deb89e16bd0979760fe2e0b6e2aa7ae96f730430c34f7 | Shell | 1,199 | 55 | #!/usr/bin/bash
function secure_file {
if test -f $1.orig; then
rm $1
cp $1.orig $1
else
cp $1 $1.orig
fi
}
pacman -S --needed ntp
FILE=/etc/ntp.conf
secure_file $FILE
rm $FILE
echo "
# Please consider joining the pool:
#
# http://www.pool.ntp.org/join.html
#
# For additional ... |
5abda95b0e17354abc0c14f5a9eb698d8bf38a8bdc978d49bf41f8d2afa3a3a7 | Shell | 1,201 | 45 | #!/bin/bash
# Job name:
#SBATCH --job-name=connect_train_evalute
#
# Account:
#SBATCH --account=fc_cerebellum
#
# Partition:
#SBATCH --partition=savio2
# Quality of Service:
#SBATCH --qos=savio_normal
#
# Wall clock limit:
#SBATCH --time=50:00:00
## Command(s) to run:
module load python/3.7
source ~/.bash_profile
sou... |
c0fc6e8bc841801e3b1c19804678e795d77b513c24d4eaaf26a609f032689116 | Shell | 1,206 | 35 | #!/bin/sh
# NEST is installed here. When you relocate NEST, change this variable.
export NEST_INSTALL_DIR=<root>/nest-simulator-2.20.0_install
# NEST finds standard *.sli files $NEST_DATA_DIR/sli
export NEST_DATA_DIR=$NEST_INSTALL_DIR/share/nest
# NEST finds help files $NEST_DOC_DIR/help
export NEST_DOC_DIR=$NEST_IN... |
eb8f82656bc43ea8534d27b1f092fd07ee07e253f3f73fba8cbad13f4dc0f49e | Shell | 1,214 | 39 | #!/bin/bash
#SBATCH --mem-per-cpu 32G -n 2 -c 1 -N 1
#SBATCH --time 10:00:00
#SBATCH --partition=psych_day
#SBATCH --job-name randomise
#SBATCH --output=logs/%j-randomise.out
# Initialise FSL properly
source "$FSLDIR/etc/fslconf/fsl.sh"
module load FSL
export FSLOUTPUTTYPE=NIFTI_GZ
# Move to the right directory
# $3 ... |
506e56b8967d0f5f9cec42150b804c5b1d973f075f38236bdd8b219d431653bf | Shell | 1,217 | 69 | #!/usr/bin/bash
pacman -S --needed hostapd dnsmasq dhcpcd
systemctl enable hostapd dnsmasq dhcpcd
systemctl start hostapd dnsmasq dhcpcd
SSID=OpenBCI-Stream
PASSPHRASE=raspberrypi
function secure_file {
if test -f $1.orig; then
rm $1
cp $1.orig $1
else
cp $1 $1.orig
fi
}
FILE=/et... |
bdfa6a704d867b82a30a8f8097984dcd22eab629d930d14dc80e1ee87f207465 | Shell | 1,224 | 58 | #!/bin/sh
echo
echo "+------------------------------+"
echo "| FicTrac install script |"
echo "+------------------------------+"
echo
# Get Ubuntu version
ver="$(lsb_release -sr)"
echo "Found Ubuntu version $ver"
if [ "$ver" = "22.04" ] || [ "$ver" = "20.04" ]; then
echo
echo "+-- Installing dependencies --... |
dba9caf533133c5b4f4a8a0fdfd10d3a6ae12ad170f666e16304bd92e8876486 | Shell | 1,231 | 39 | #!/bin/bash
#
THREADS="$1";
OUTPUT="../output_data/TRACES_mtdna_authentication";
#
# ==============================================================================
#
CHECK_FILE () {
if [ ! -f $1 ];
then
echo -e "\e[31mERROR: file $1 not found!\e[0m"
echo "For addition information, see the instructions at ... |
81c5485f1f9399f64b110947627a6062374bb0c62c99505c6dd3d90e545aa21c | Shell | 1,233 | 31 | #!/bin/bash
#SBATCH -J cobel # A single job name for the array
#SBATCH -n 1 # Number of cores
#SBATCH -N 1 # All cores on one Node
#SBATCH --mem 20000 # Memory request
#SBATCH -t 1-00:00 # Maximum execution time (D-HH:MM)
#SBATCH -o cobel_%A_%a.out # Standard output
#SBATCH -e cobel_%A_%a.err # Standard error
module re... |
ae90efb93a59e763725fd8b647384ee77b15a693af5652ad8f32906fe6053872 | Shell | 1,238 | 63 | #!/bin/bash
sswarper_loc=$(which @SSwarper)
if [[ $? != 0 ]]
then
echo "SUMA not found, is AFNI installed?"
exit 1
fi
subject=$1
if [[ ! $subject ]]
then
echo "You must provide a subject number."
exit 1
fi
sid=$(printf "%3.3d" $subject)
if [[ ! $QC_CODE_ROOT ]]
then
echo "QC_CODE_ROOT is not s... |
951e38891d5c6d3e4cd30ddd6260ca9c086227a91ea138c648de89a9b8eac40a | Shell | 1,262 | 23 | #!/bin/bash
#
echo -e "\e[34m[TRACESPipe]\e[32m Simulation of human ref VDB.fa and experimental samples (organ=sample_blood) ... \e[0m";
#
efetch -db nucleotide -format fasta -id "MT682520" > sample_B19.fa 2>> ../logs/Log-stderr-sample_blood.txt
efetch -db nucleotide -format fasta -id "NC_007605" > sample_EBV.fa 2>> ..... |
79761976d5a68a41c950774755736f3c390bf248f7b3a59f4b76426cb444e05e | Shell | 1,275 | 35 | #!/bin/bash
function main {
if [ "$#" -lt 6 ]; then
>&2 echo "Usage: $(basename $0) threads outDir adapterFile prefix 1.fq 2.fq [bDedup = 0]";
exit 1;
fi
nThread=$1; shift
outDir=$1; shift
adapterFile=$1; shift
prefix=$1; shift
in1=$1; shift
in2=$1; shift
bDedup=$1; ... |
705906cf42b1ea9a7d47773437e9603fbd3721b98decbb82b6b6eea80760b5dd | Shell | 1,293 | 43 | #!/bin/bash
corrected_args=()
docker_args=()
mounts=0
for var in "$@"
do
if [ -d "${var}" ]; then
echo "$var is a directory" >&2
var=$(realpath "${var}")
host_dir=$(dirname "${var}")
((mounts+=1))
container_dir="/data/mount_${mounts}"
docker_args+=("-v ${host_dir}:${cont... |
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