sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
1c748e96f3190ad818caa7b5f7961f4383eef86f091aa59bd366b6129bd20b78 | Shell | 1,392 | 36 | #!/bin/bash
#SBATCH --mem=16G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=6:0:0
#SBATCH --gpus-per-node=1
cd $project/moralization_temporal
module purge
module load python/3.10 scipy-stack StdEnv/2023 gentoo/2023
source ~/venv2/bin/activate
for p in "previous_link" "polarity"
do
for i in {0.... |
23a902e4d749a4479c8f2506772b563ef503335a9166d36b1ddbacc46988e914 | Shell | 1,393 | 28 | ############### ToRORd ##############################
MODEL_FILE_CPU="ToRORd_fkatp_endo.c"
MODEL_FILE_GPU="ToRORd_fkatp_endo.cu"
COMMON_HEADERS="ToRORd_fkatp_endo.h"
#
COMPILE_MODEL_LIB "ToRORd_fkatp_endo" "$MODEL_FILE_CPU" "$MODEL_FILE_GPU" "$COMMON_HEADERS"
############## ToRORd fkatp Mixed ENDO_MID_EPI ############... |
7cc5259b74dca87791dab01ac9fe2b9750e6f041fd09cec30f1e0e45852e36b0 | Shell | 1,395 | 54 | #!/bin/bash -l
#SBATCH -J eiann_gpu_mnist_ray
#SBATCH -o /scratch2/11358/yashchennawar5555/logs/EIANN/eiann_gpu_mnist_ray.%j.o
#SBATCH -e /scratch2/11358/yashchennawar5555/logs/EIANN/eiann_gpu_mnist_ray.%j.e
#SBATCH --requeue
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --partition=rtx
#SBATCH --mem=80G
#SBATCH --cpus-... |
afd10d3e8dda4861433dc0b005f1580dbaca87aa39f5dae9f9c2019a05305a01 | Shell | 1,395 | 44 | #!/bin/bash
#
# Collects the pull-requests since the latest release and
# aranges them in the CHANGES.rst.txt file.
#
# This is a script to be run before releasing a new version.
#
# Usage /bin/bash update_changes.sh 1.0.1
#
# This script was originally developed by the nipreps developers.
# For the full LICENSE and te... |
d6c0810bd01bc0f3a08cd4e68bb80f039c7e2c46b259cd8047936c1f194ddb76 | Shell | 1,396 | 86 | #!/bin/bash
set -e
set -x # Enable shell tracing
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
nP=$3
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}/cli.log"
mkdir -p "$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}"... |
e8a1951a6210157963c31179f1e1d0ba99583767f6ff7fbd3daff5a10b00c6fe | Shell | 1,399 | 30 | # examples/twom_example.sh
#!/bin/bash
echo "=== TWOM Example Analysis ==="
echo "Running TWOM on example subjects (language mapping data)..."
echo ""
echo "Key analysis modes:"
echo " 1. Relevant voxels (default): Group-consistent activations only"
echo " 2. All voxels: Includes single-subject effects"
echo ""
# ... |
37a9e6b04744f2229b6167d2241da6db4562b7ffa367610cce33224cd729b753 | Shell | 1,405 | 30 | #!/bin/bash
#SBATCH --mem=64G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=10:0:0
#SBATCH --mail-type=ALL
#SBATCH --gpus-per-node=1
# Define project directory
#project=/path/to/your/project
cd $project/moralization_temporal
module purge
module load python/3.10 scipy-stack
source ~/venv2/bin/activate... |
679e25d11a3bc63a8a1880e5f8975868cc57f5e9b6df8e84d1d1a261f0a54f63 | Shell | 1,405 | 49 | #!/usr/bin/env bash
#####################################################################
# Example script for running Sei deep learning model sequence
# prediction with Selene
# Usage:
# sh 1_sequence_prediction.sh <input-file> <genome> <output-dir> --cuda
# Please only specify hg38 or hg19 as input for <genome> if... |
aaae6539f10404c7045fefa81b335f4b95c8774443c5d614afec7b160123530f | Shell | 1,406 | 56 | #! /bin/bash
#
# This is a shell script to register GRE image to T1w image
#
# Dependencies: (1)ANTs
#
# Creator: Kwok-shing Chan @DCCN
# kwokshing.chan@donders.ru.nl
# Date created: 6 October 2022
# Date edit:
############################################################
script_dir=`readlink -f "$0"`
SEPIA_HOME=`dirna... |
05aa7eb6ee209b3c3c8f65cab268ea984d955e8f9307037845f5c40b264b5964 | Shell | 1,420 | 43 | #!/usr/bin/env bash
# Runs all Python examples
set -Eeuox pipefail
if [[ "$#" -gt 1 ]]; then
echo "usage: run_python_examples.sh <prefix>"
exit 1
fi
PREFIX=${1:-}
$PREFIX python3 -m pip install -r python/example/example_requirements.txt -U
runpyex () {
echo "=== Executing $1 =============================... |
1d476ecb8e2df93020c5f2652b9251eb3dad28dca32cbb53d6b84e88b7eeefe9 | Shell | 1,436 | 38 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=01:00:00
#SBATCH --job-name=maxfilter_batch
#SBATCH --output=/imaging/hauk/rl05/fake_diamond/scripts/preprocessing/meg/job_log/job_output.log
#SBATCH --error=/imaging/hauk/rl05/fake_diamond/scripts/preprocessing/meg/job_log/job_error.log
# read... |
537f99936d4025ca68b684dd9a4d78446ffbb9d87c77c1399ce889fe6b2f76f3 | Shell | 1,445 | 42 | #!/bin/bash
#
# Jaclyn Taroni for ALSF CCDL 2020
#
# This shell script runs the analysis module for molecularly subtyping embryonal
# tumors.
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "... |
4247a9cc433f388635015a02d303a1625fa566f2c0aa1a1af391b554363283c2 | Shell | 1,446 | 70 | #!/bin/bash
set -e # Exit on error
# Usage: Run this script from your input directory:
# cd /path/to/your/images
# bash run_template_building.sh /path/to/ANTs/bin/
if [ $# -lt 1 ]; then
echo "Usage: $0 /path/to/ANTs/bin/"
exit 1
fi
export ANTSPATH="$1"
# Set number of threads for ITK
export ITK_GLOBAL_DEFA... |
f1898a891408417e7f0fcd3e4643fadf4b3964969a50eb8d2b369d38d7148c4a | Shell | 1,449 | 39 |
#!/bin/bash
source /cbica/projects/luo_wm_dev/miniconda3/etc/profile.d/conda.sh
conda activate babs
########################
# PNC - act-hsvs
########################
cd /cbica/projects/luo_wm_dev/input/PNC/derivatives/babs_qsirecon_pyafq_act_v2
babs-status --project-root $PWD # check status - must be in root of bab... |
223c58a93a0cdf35ed44bab75b76658e65bc0e5c5082acc02f173074c7c285f1 | Shell | 1,451 | 41 | #!/bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the Apache License, Version 2.0 (the "Lice... |
63ca225eeea5a9a434c5c33dd4069a3ad1c67d3bf8db982190e63af7830c62d3 | Shell | 1,451 | 40 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=01:00:00
#SBATCH --output=/dev/null # suppress default output file
#SBATCH --error=/dev/null # suppress default error file
######################
# setup for ... |
c8e83a3cda4add22e9c5b63aded01bdd62add3dfd9cb311253180ab400b1cc86 | Shell | 1,452 | 59 | #!/bin/bash
set -euo pipefail
REMOTE_ROOT="$1"
RELAY_SCRIPT="$2"
RELAY_HOST_FILE="$3"
RELAY_PID_FILE="$4"
RELAY_LOG_FILE="$5"
RELAY_PORT="$6"
REVERSE_PORT="$7"
RELAY_PYTHON="$8"
cd "${REMOTE_ROOT}"
UAN_HOST="$(hostname -f)"
printf '%s\n' "${UAN_HOST}" > "${RELAY_HOST_FILE}"
if [ -f "${RELAY_PID_FILE}" ]; then
OLD_... |
83070cd4cb400528640f3b1cf2a91bba891c2cb915b7f6d16a83c554e6fc8a6c | Shell | 1,453 | 23 | #!/bin/bash
#SBATCH -J humann2_regrouprenorm
#SBATCH -A b1057
#SBATCH --mail-type=ALL
#SBATCH --mail-user=elizabeth.mallott@northwestern.edu
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --mem=12G
#SBATCH -t 12:00:00
#SBATCH --output=/home/ekm9460/humann2_regrouprenorm.out
#SBATCH --error=/home/ekm9460/humann2_regrouprenorm.err
#... |
c9de5ab36211149ab4ce1329918748369754c4261509987cdec5cd759e497679 | Shell | 1,453 | 46 | #!/usr/bin/env bash
set -euo pipefail
repository_root="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
cd "$repository_root"
conda_executable=""
if command -v conda >/dev/null 2>&1; then
conda_executable="$(command -v conda)"
else
for candidate in \
"$HOME/miniforge3/bin/conda" \
"$HOME/mini... |
102cde8e3dffac9b5f059b4357a49f087356bcd2ae4c1033b338fb127f83adf6 | Shell | 1,455 | 48 | #!/bin/bash
#
# importruns_vaso-split_reverse.sh <basename> <TR> <run1_file> <run2_file>
#
# - imports functional vaso runs into current directory and splits them into nulled and
# non-nulled, ASSUMING NOTNULLED TO BE FIRST!
# - sets the TR
# - overwrites 1st two volumes of each
# - writes list of imported base file ... |
795c596586a97a29f060a1da9787b1103b4a1440b27f0223c838ce0ee2200354 | Shell | 1,455 | 42 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=02:00:00
#SBATCH --output=/dev/null # suppress default output file
#SBATCH --error=/dev/null # suppress default error file
######################
# setup for ... |
df0bea7c9e8a7e5c74fcb4f59c54c361f749ab318d9b8eea471dddbc0b295dd9 | Shell | 1,455 | 39 | #!/bin/bash
#SBATCH -p gidbkb
#SBATCH --nodes=1
#SBATCH --gpus-per-node=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-gpu=8
#SBATCH --mem=100G
#SBATCH -o /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/slurm_stdout/%j.out
#SBATCH -e /pollard/data/projects/sdrusinsky/enformer_fine_tuning/logs/train/... |
edecae4f40ee7204ee9407c8e336d804f02d9ba9ccec616ed7c607ba8de0b9b7 | Shell | 1,457 | 17 | python3 generate_ogbl_dataset.py --dataset BALBc_no2 --splitting_strategy spatial
python3 generate_ogbl_dataset.py --dataset BALBc_no2 --splitting_strategy spatial --no_edge_attr
python3 generate_ogbl_dataset.py --dataset BALBc_no3 --splitting_strategy spatial
python3 generate_ogbl_dataset.py --dataset BALBc_no3 --spli... |
b1f8256840bbfe6a1bac7e869e4ec084f5ca426f47e679a84d1b70c92553c6b0 | Shell | 1,459 | 38 | #!/bin/bash
pop="$1"
task="$2"
method="$3"
eval="$4"
START=$(pwd)
OUT="$(mktemp -d /tmp/merge.XXXXX)"
cp "../bids_dataset/derivatives/rsa/sub-average/figures/pop-${pop}_task-${task}_method-${method}_eval-${eval}_slice_model-"*.png $OUT
cd "$OUT"
to_merge=""
for model in "symbolic" "IT" "both"; do
convert "pop-${... |
2fb4586fdb5d8031b5ee0afcc82dd253732dbd407f5fba188dc91d3248e11c75 | Shell | 1,460 | 21 | #!/bin/zsh
#Set paths for template, input and output files
set template_dir = /your/path/to/marmoset/brain/template
set input_dir = /your/path/to/tSNR/and/Probability/maps
set out_dir = /your/path/to/surfaces/directory
#Set workbewnch directory as current directory
cd /Users/az/abin/workbench/bin_macosx64
# Map the... |
dc79c486fad08e6b112d9a805a8af5ced7723df85cec1c619593be5073e6460e | Shell | 1,464 | 22 | #!/bin/sh
OPTS="-W -Wall -Wwrite-strings -Wstrict-prototypes -Wmissing-prototypes -Wold-style-definition -Wmissing-format-attribute -Wcast-qual -g -O2"
gcc48 -I. -funwind-tables $OPTS -c atomic.c -o atomic.o
gcc48 -I. -funwind-tables $OPTS -c dwarf.c -o dwarf.o
gcc48 -I. -funwind-tables $OPTS -c fileline.c ... |
bbdd4fecacf61a10a2da22efd4ae952769e6dfc1b7560cd088643cb13895d648 | Shell | 1,466 | 59 | # ===== SET UP =====
set -ueo pipefail
if [ $# -ne 1 ]; then
echo -e "Usage: $0 <input_data_and_params>"
exit 1
fi
echo -e "#=====================\n#"
echo -e "# $(basename "$0") \n#"
echo -e "#=====================\n#"
# Read input config
neda=$(dirname $(dirname "$0"))
source $neda/scripts/process_input.sh... |
c48f06fb30dea7ff7dcb3b2849ff5f6dafac94583872e2655b541c8c06b4829d | Shell | 1,466 | 89 | #!/bin/sh
#
# Builds an index from UMD Freeze 3.0 of the Bos Taurus (cow) genome.
#
BASE_CHRS="\
Chr1 \
Chr2 \
Chr3 \
Chr4 \
Chr5 \
Chr6 \
Chr7 \
Chr8 \
Chr9 \
Chr10 \
Chr11 \
Chr12 \
Chr13 \
Chr14 \
Chr15 \
Chr16 \
Chr17 \
Chr18 \
Chr19 \
Chr20 \
Chr21 \
Chr22 \
Chr23 \
Chr24 \
Chr25 \
Chr26 \
Chr27 \
Chr28 \
Chr29 ... |
c7f94522a363caa830fa880e87af80c9a46f2da89cf652d6231a38d8fad4a964 | Shell | 1,469 | 47 | #!/bin/bash
# Bethell and Taroni for CCDL 2019
# Run the dimension reduction plotting pipeline specifically in CI
set -e
set -o pipefail
# This script should always run as if it were being called from
# the directory it lives in.
script_directory="$(perl -e 'use File::Basename;
use Cwd "abs_path";
print dirname(... |
f767205315640369223912c3bf571044b1b38e659eb0f9030950d2a40b5bbb50 | Shell | 1,474 | 64 | #!/usr/bin/env bash
set -euo pipefail
BUILD_DIR="build"
BIN_DIR="src/bin"
if [[ "${1:-}" == "--clean" ]]; then
echo "[INFO] Cleaning build..."
rm -rf "${BUILD_DIR}" "${BIN_DIR}"
fi
mkdir -p "${BIN_DIR}"
for cmd in cmake hatch python; do
if ! command -v "${cmd}" >/dev/null; then
echo "[ERROR] ${c... |
e14b0e4c4919727f723bcc6c540d3bba337c364e21b5cbe27ed2e9e7e7b0db2f | Shell | 1,478 | 47 | #!/usr/bin/env bash
set -euo pipefail # Will fail on error
# ==============
# How to run this script
# 1) Load the input data
# https://scilpy.readthedocs.io/en/latest/documentation/getting_started.html
# 2) Call this script with
# ---> bash streamlines_math.sh path/to/your/data path/to/save/output... |
d2ef927a9bccd3ca5230bfd5433a45e4635a08f32bc0c9d650ee8dea4d70a5c5 | Shell | 1,479 | 45 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=02:00:00
#SBATCH --output=/dev/null # suppress default output file
#SBATCH --error=/dev/null # suppress default error file
######################
# setup for ... |
064e2d047af52b45f6e9bbad23f9b9468719fe9acb197e8e70f45f4c08d7499e | Shell | 1,480 | 41 | #!/bin/bash
datasets=("HCPD" "HBN")
# submit this with ./submit_noddi_tractprofiles.sh
for dataset in "${datasets[@]}"; do
config_file="/cbica/projects/luo_wm_dev/two_axes/code/config/config_${dataset}.json"
# where to save output and error logs
logs_dir="/cbica/projects/luo_wm_dev/two_axes/code... |
fcd18fec34bdc6ada6f8448fc038c368628d655a7b016fe815c6b70cc1b3994c | Shell | 1,480 | 54 | #!/usr/bin/env bash
set -e
t1w_file=$1 # skull-stripped, bias-corrected T1w image
synthseg_file=$2 # SynthSeg output file
wmh_file=$3 # optional, if not provided, a pseudo WMH (all=0) will be created
output_dir=$4
pvs_probmap_filename=$5 # pvs_probmap.nii.gz
pvs_binary_filename=$6 # thr_pvs_seg.nii.gz
threshold=$7 # ... |
7fa198ecfcebc91a2a97e9d529a838a63864ead5a0dd436f9f78fe4a0011dcb9 | Shell | 1,485 | 66 | #!/bin/bash
# Fail if anything not planed to go wrong, goes wrong
set -eu
sw=mricron
source ../vers.inc
ver=$kVers
arch=amd64
#set widgetset set for default(QT5)
wigetset=
sw=${sw}${wigetset}
pkg=${sw}_${ver}_${arch}
#deb=${pkg}.deb
exePath=${pkg}/usr/bin/
appPath=${pkg}/usr/share/applications/
docPath=${pkg}/usr/shar... |
8a9677fedc27ca3109949c0fb0a5d2eba60f4f6f99578dfb3fd598206e236c6b | Shell | 1,487 | 41 | #!/bin/bash
datasets=("HCPD" "HBN")
# submit this with ./submit_mapmri_tractprofiles.sh
for dataset in "${datasets[@]}"; do
config_file="/cbica/projects/luo_wm_dev/two_axes/code/config/config_${dataset}.json"
# where to save output and error logs
logs_dir="/cbica/projects/luo_wm_dev/two_axes/co... |
caf624c8c869e49d3d497def16cd934b0e92786f3c04afce62a41d8a42b0a361 | Shell | 1,490 | 45 | #!/usr/bin/env bash
set -euo pipefail # Will fail on error
# ==============
# How to run this script
# 1) Load the input data
# https://scilpy.readthedocs.io/en/latest/documentation/getting_started.html
# 2) Call this script with
# ---> bash btensor_scripts.sh path/to/your/data path/to/save/outputs... |
e0016b7763a5dd34ae1bab3747b35d8f13e677f4298a82319dc0f3c047471db9 | Shell | 1,492 | 47 | #!/bin/bash
# raw data
rawFQ_dir='/path/folder'
n_cell=5000 # set expected cells
outdir='out_trackerbarcodes'
mkdir -p $outdir
fastqR1=$outdir/TrackerSeq.merged.R1.fastq.gz
fastqR2=$outdir/TrackerSeq.merged.R2.fastq.gz
cat $rawFQ_dir/*_R1_001.fastq.gz > $fastqR1
cat $rawFQ_dir/*_R2_001.fastq.gz > $fastqR2
## ... |
0db325f77ab3757b210a9e14e1ec7cea313df80405cab54af0c81224c8226f70 | Shell | 1,498 | 41 | #!/usr/bin/bash
#SBATCH --job-name=Run_Deseq2_v12 # Job Name
#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=shuklas1@chop.edu # Where to send mail
#SBATCH -a 1-5500 # number of threads you want to be run simultaneously, for v12 ... |
680349ad79e8f905df7eff8ff66717e2661520a1f132151762efc9334971e7df | Shell | 1,499 | 51 |
#!/bin/bash
source /cbica/projects/luo_wm_dev/miniconda3/etc/profile.d/conda.sh
conda activate babs
########################
# PNC - act-hsvs
########################
cd /cbica/projects/luo_wm_dev/input/PNC/derivatives/babs_qsirecon_pyafq_act_v2
babs-merge --project-root $PWD
#cd /cbica/projects/luo_wm_dev/input/PN... |
59c96fa3d29b8002bce4d8c268527d6e4fe7020f8a8c5f5034640c3c11f90588 | Shell | 1,500 | 33 | #!/bin/bash
export SUBJECTS_DIR=/media/miplab-nas2/Data/Karolis/huppi_high_res_resting/derivatives/freesurfer/
# export SUBJECTS_DIR=/media/miplab-nas2/Data/Karolis/high_res_resting/derivatives/freesurfer/
subject=sub-LAM026
refAnatDir=/media/miplab-nas2/Data/Karolis/huppi_high_res_resting/derivatives/ref_anat/${subj... |
de8d4d89837887726a60a4cfc2d37aeac492f19439672af55baa077266928748 | Shell | 1,501 | 69 | #!/bin/bash
set -e
while getopts "sb:" opt; do
case $opt in
s) use_sra=1 ;;
b) branch="$OPTARG" ;;
*) echo "Usage: $0 [-s] [-b <branch_name>]" && exit 1
esac
done
shift $(($OPTIND - 1))
if [ "$branch" == "" ] ; then
branch="master"
fi
set -x
dnf config-manager --set-enabled devel... |
02b3411f6b689759c6140f5e58647cfbddf3d0a40b72e47b65a413c7f64074f1 | Shell | 1,502 | 51 | #!/bin/bash -l
#SBATCH -J eiann_gpu_mnist
#SBATCH -o /ocean/projects/bio240068p/chennawa/logs/EIANN/eiann_gpu_mnist.%j.o
#SBATCH -e /ocean/projects/bio240068p/chennawa/logs/EIANN/eiann_gpu_mnist.%j.e
#SBATCH --requeue
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --partition=GPU-shared
#SBATCH --gres=gpu:v100-32:1
#SBAT... |
56e5c682bdfbb82f8c7403f40ac215eb98ade59f8203b1a7d070f2820164b84e | Shell | 1,507 | 58 | #!/usr/bin/env bash
# Usage: ./sfari-make-metadata.sh ssc_name:sex:family:member path/to/lra
ssc_name=$(echo $1 | cut -f1 -d':')
# Check if directory exists
if [ ! -d "./raw_data/${ssc_name}/" ]
then
echo "${ssc_name} does not exist- skipping." 1>&2
exit 1
fi
sex=$(echo $1 | cut -f2 -d':')
family=$(echo $1 | cut... |
db56267dc221bbcb6380d0216b4f9449b35f298c85db73f42cbb7eb8dc84e3b6 | Shell | 1,508 | 47 | #! /bin/sh
cd tests
. ./compat.sh
sort -k2,2 > ${pref}.md5sum <<EOF
9251799dd5dbd3f617124aa2ff72112a ${pref}.histo
9251799dd5dbd3f617124aa2ff72112a ${pref}_filtered.histo
EOF
cat > ${pref}_commands <<EOF
gunzip -c seq1m_0.fa.gz
gunzip -c seq1m_0.fa.gz
EOF
$JF bc -t $nCPUs -o ${pref}.bc -s 1M -C -m 40 --timing ${pref... |
3b6d9fbd32411a1fccbbd93ebadc5c86a3f9aa8989bbb026f80c258662ec17b3 | Shell | 1,509 | 31 | #!/bin/bash
# ============================================================================
# Developing brain Region Annotation With Expectation-Maximization (Draw-EM)
#
# Copyright 2013-2020 Imperial College London
# Copyright 2013-2020 Antonios Makropoulos
#
# Licensed under the Apache License, Version 2.0 (the "Lice... |
d3037afaae3d28d537a10b07056269b920c20ca48b1b5b63dc90a083104e33cb | Shell | 1,513 | 23 | #!/bin/bash
prefix=/People/alexbui/workspace/proteins/ab_affinity
data_prefix=/Arontier_1/Projects/AbAg_decoy/dataset/generated_graphs
output_prefix=/Arontier_1/Privates/alexbui/projects/ab_affinity
DATASETS="ab_chai1_fullgraph,nb_chai1_fullgraph,tcr_pmhc_chai1_fullgraph,ab_boltz2_fullgraph,nb_boltz2_fullgraph,tcr_pmh... |
016e0490f629380c8f0dd0bc31c48626ad9f45361faed4814cb5c2c04d57b2c9 | Shell | 1,515 | 51 | #!/usr/bin/env bash
set -euo pipefail # Will fail on error
# ==============
# How to run this script
# 1) Load the input data
# https://scilpy.readthedocs.io/en/latest/documentation/getting_started.html
# 2) Call this script with
# ---> bash btensor_scripts.sh $in_dir/your/data $in_dir/save/outputs... |
7a7b8b11d535de1573ae4bf088e61ea5a046e23cd39045abf4a8ef4ae4901982 | Shell | 1,516 | 54 | #!/bin/bash
#
# [description]
# Rerun specified workflow for given pull request.
#
# [usage]
# rerun-workflow.sh <WORKFLOW_ID> <PR_BRANCH>
#
# WORKFLOW_ID: Identifier (config name of ID) of a workflow to be rerun.
#
# PR_BRANCH: Name of pull request's branch.
set -e -E -u -o pipefail
if [ -z "$GITHUB_ACTIONS"... |
af300275ce6199326a65b3c607fe1a51c58cafaae7ed766751dff82e557e3c8d | Shell | 1,520 | 38 | #!/bin/sh
# create roi mask
name_mask=LOC #harvardoxford_cortical_prob_Temporal_Fusiform_Cortex_anterior_division
roi=LOC #TemporalFusiform #
name_results=tStat_visual_sameStructSameStimMinusSameStructDiffStim # tStat_hexSameMinusSameStim #tStat_hexStrMinusNothing # tStat_projSameStr_allOthers #tStat_hexStrMinusNothing... |
df583e16f01982c7f2ae5ce5740366953f0373d80ce69669e995733ec1a4f41c | Shell | 1,522 | 56 | # ===== SET UP =====
set -ueo pipefail
if [ $# -ne 1 ]; then
echo -e "Usage: $0 <input_data_and_params>"
exit 1
fi
echo -e "#=====================\n#"
echo -e "# $(basename "$0") \n#"
echo -e "#=====================\n#"
# Read input config
neda=$(dirname $(dirname "$0"))
source $neda/scripts/process_input.sh... |
f3074ddafd38877f3eec90cde3d2b95b3bf752a4724cd6b244b09bb8883567d3 | Shell | 1,522 | 30 | #!/bin/bash
# A script that can be ran in the PyPA manywheel containers if you want to produce uploadable wheels for PyPI.
# Steps:
# 1. Prepare a (temporary) working directory (referred to as $LOCAL_WORK_DIR).
# 2. Have the version of Arbor you want to build manylinux compliant wheels for available at $LOCAL_WORK_DIR... |
19ed5517d675f7f9a106fb493aa3afb00b036ba30fdf7be5377666d69435c412 | Shell | 1,525 | 60 | #!/bin/bash
# PNC
json_content='{
"Acknowledgements": "",
"Authors": [],
"BIDSVersion": "1.0.2",
"DatasetDOI": "",
"Funding": [],
"HowToAcknowledge": "",
"License": "",
"Name": "RBC_PNC",
"ReferencesAndLinks": [],
"template": "project"
}'
PNC_json="/cbica/projects/luo_wm_dev/... |
1b1a50a224d37b4dbcd8f4e632b48b0f2ba42537f4dcc066d5352c893f320e3b | Shell | 1,530 | 51 | #!/bin/bash
set -e
set -o pipefail
# download methylation files from the OpenPedCan data v13 data release s3 bucket
URL="https://d3b-openaccess-us-east-1-prd-pbta.s3.amazonaws.com/open-targets"
RELEASE="v14"
# Set the working directory to the directory of this file
cd "$(dirname "${BASH_SOURCE[0]}")"
# If RUN_LOCA... |
c21ece53db3d2b35cc0b35fae524e8f040d2d8dbb9e8a917743d781e3a4094a9 | Shell | 1,531 | 43 | #!/bin/bash
#
# register_fs-to-vasoT1_no-manual.sh <vaso_T1_file> <fs_dir>
#
# - converts FS T1 to nifti
# - if initial_matrix.txt does not exist: starts ITK-SNAP in order to perform semi-automatic rigid-body registration in ITK-SNAP and save transformation matrix as initial_matrix.txt
# - runs non-linear registration ... |
0982ade0f398b420cb065b10563e38eaf9c7dd10d02e4daf9dbea0f4bcb20099 | Shell | 1,532 | 50 | #!/bin/bash
# List of subjects
subjects=()
# Directories
data_nii_dir="nifti data directory"
data_bids_dir="bids data directory"
data_phase_dir="phase data directory"
data_pre_dir="preprocessed data directory"
data_work_dir="working directory"
fmriprep_license_dir="fmriprep licence directory"
# Clean out working dir... |
138236a8b76e5739e2242f6971d196fb26dc995443521ac988df6ddea737d996 | Shell | 1,536 | 56 | #!/bin/env bash
#Change PROT depending on your system
#Calculates PC projections
PROT=cTEMPPROT
DNAME=pc1_pc2_pc3
ndx=../../dpca.ndx
gro=../../dpca.gro
vec=../covar/eigenvec.trr
[[ ! -e $DNAME ]] && mkdir $DNAME
function project_all () {
local dname=$1
xtc=../../dihed_traj/all.trr
out1=$dname/all_1.xvg
out... |
feaf373c031c7a5ad93f78e0ab4ee4d5f2b01b11e045b21ea47bb0cdf92b8dd9 | Shell | 1,538 | 34 | #!/bin/bash
#SBATCH --job-name=datalad_get_freesurfer_HBN
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=5G
#SBATCH --time=12:00:00
#SBATCH --propagate=NONE
#SBATCH --output=/cbica/projects/luo_wm_dev/two_axes/code/logs/datalad/HBN/freesurfer_%j.out
#SBATCH --error=/cbica/projects/luo_wm_dev/two_axes/code/l... |
6db685342b39ab70e7d5e6adfe013a81f6135b732fc4f4d91e559e9327404e4e | Shell | 1,539 | 26 | #!/bin/bash
prefix=/People/alexbui/workspace/proteins/ab_affinity
output_prefix=/Arontier_1/Projects/AbAg_decoy/dataset
python $prefix/src/make_graph_rcsb.py -o $output_prefix/generated_graphs/tcr_agnb_fullgraph \
-f $output_prefix/structures_chai1-single/cross/tcr-ag_nb/rank0_pdbqts \
-m seq -hn "B" -hi 9999 ... |
966fa69ef1487d109f1fea458c50cbe4a4431db19d2f5d139c7dba86ef71087c | Shell | 1,539 | 58 | #!/bin/bash
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --job-name=gnn_bd_training_start
#SBATCH --output=logs/gnn_bd_training_start-%j.log
#SBATCH --mem=500MB
#SBATCH --partition=short
ml Python/3.8.16-GCCcore-11.2.0
source $HOME/venvs/eve/bin/activate
# Function to submit job
submit_job() {... |
28078ade2cbe2bf6f0a18b0736e1d9778a89839423843a9ad102dec1148e3e8a | Shell | 1,544 | 43 | #!/bin/bash
# run_acmefdfd.sh
#
# Copyright (c) 2025, 2026, Constantine Sideris (sideris@stanford.edu) and Jui-Hung Sun
# (juihungs@usc.edu)
#
# This program is free software: you can redistribute it and/or modify it under the terms
# of the GNU Affero General Public License as published by the Free Software Foundat... |
bcebd673c886e758b48eb65ea1045acf2ef352e3451acbdaa029f04b4993f517 | Shell | 1,544 | 42 | #!/bin/bash
datasets=("HCPD" "HBN")
# submit this with ./submit_datalad_trks.sh
for dataset in "${datasets[@]}"; do
config_file="/cbica/projects/luo_wm_dev/two_axes/code/config/config_${dataset}.json"
# where to save output and error logs
logs_dir="/cbica/projects/luo_wm_dev/two_axes/code/logs/... |
97c22f1d3746aab17073f7926bde475929f495bfe080859cacdad3abfc972ec4 | Shell | 1,553 | 59 | #!/bin/bash
set -e # Exit immediately if a command exits with a non-zero status
mypython=$1
echo "Python is $mypython"
# MARINE environment variable must be set from main marine directory:
# export MARINE=$(pwd)
echo "Running bulk tests..."
tests_folder="strandedness_tests/"
echo "Bulk tests scripts"
ls -lh... |
df41e82d30fee45c7ac3ff43be6784f3b0a80d0d4a5e3c8979a3a3930774db50 | Shell | 1,554 | 51 | #!/bin/bash
# [description]
#
# Look for the last run of a given GitHub Actions workflow on a given branch.
# If there's never been one (as might be the case with optional workflows like valgrind),
# exit with 0.
#
# Otherwise, check the status of that latest run.
# If it wasn't successful, exit with a non-0... |
46c69cbfabdc4ca94d1e82335599d22e39d2a82eaf321a134febdfae7ad488d4 | Shell | 1,556 | 100 | #!/bin/bash
set -e
set -x # Enable shell tracing
cd ../..
if [ $# -eq 0 ]; then
echo "$0 experimental_date animal_id ?"
exit 1
else
ED=$1
ID=$2
nP=$3
fi
OUTPUT="e:/data/user/yu-ting/analysis/phys"
OUTPUT_FILE="$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}/cli.log"
mkdir -p "$OUTPUT/${ED}_${ID}__2P_YW/plane${nP}"... |
b8a73a577e7461cc676213695868817f2268fdd18e4c21110ddc1344553dd704 | Shell | 1,558 | 41 | VERSION=$1 #git describe --tags
echo "Current version (full): $VERSION"
#VER=`echo $VERSION | cut -d '.' -f 1,2` # major.minor only
VER=`echo $VERSION | awk -F'[.-]' '{print $1 "." $2 "." $3}'`
echo "Current version (major.minor.patch): $VER"
V=`echo $VERSION | awk -F'[.]' '{print $1 "." $2}'`
echo "Current version (ma... |
61845bb4fa0e53e18b3e66bd6ef265d6b414beee17eae9367d00b355e663fd84 | Shell | 1,570 | 43 | # trains distilled DeepSTARR models that predict epistemic uncertainty (stdev) and mean
DATA_DIR=../data/DeepSTARR_ensemble_over_size
CONFIG=../config/DeepSTARR.yaml
PROJECT_NAME=DeepSTARR_ensemble_size
# N_ARR=( 2 3 4 5 10 15 20 25 )
N_ARR=( 4 5 10 15 20 25 )
NMODS=10
### boolean vars (toggle true/false)
# # train... |
da2006ec037f26d285301e475406fc11348e746600b3ce1799d2910e627112e2 | Shell | 1,572 | 45 | #!/bin/bash -l
export DATE=$(date +%Y%m%d_%H%M%S)
export JOB_NAME=export_optimized_EIANN_mnist_"$DATE"
sbatch <<EOT
#!/bin/bash -l
#SBATCH -J $JOB_NAME
#SBATCH -o /ocean/projects/bio250022p/chennawa/logs/EIANN/$JOB_NAME.%j.o
#SBATCH -e /ocean/projects/bio250022p/chennawa/logs/EIANN/$JOB_NAME.%j.e
#SBATCH -p RM-512
#SBA... |
38f2318c136853768b54d88fea922d30a568f57c990429510961003268e24cc4 | Shell | 1,583 | 56 | # run through all plotting functions
# activate environment
source ~/.zshrc
conda activate phys
# export env variables for R
export R_HOME="/Library/Frameworks/R.framework/Resources"
export DYLD_LIBRARY_PATH="/Library/Frameworks/R.framework/Resources/lib:$DYLD_LIBRARY_PATH"
# set the demo variable to true by default... |
4d728e97e4bcf33f210e2a51ab9394b675374d7a204b3129cb0f1eba501de1c9 | Shell | 1,584 | 68 | #!/bin/bash -e
wf_name="sharp"
version="0.1.1"
files="submit-hashtag.sh submit-citeseq.sh submit-asapseq.sh submit-cellplex.sh Sharp.deps.zip Hashtag.wdl CiteSeq.wdl AsapSeq.wdl Sharp.options.aws.json configs/*.json"
dest="$HOME/scing/bin"
usage()
{
cat << EOF
USAGE: `basename $0` [options]
-d destination (e.g. ... |
3143c32118a0414e4df6a23e83d5003a5ceb2cd4d93cfa8c360aaf2534c10377 | Shell | 1,589 | 58 | #!/bin/bash
declare -a SVG_MAIN_FILE=(
models/sample # 1
models/models # 2
gt/gt # 3
generalization/generalization # 4
navi/navi-self-gated # 5
navi/highres # 6
motion/motion2 ... |
787e6546e03eb046872772cae6bdf9a499af81cb8461386719edf27c0d3c5d00 | Shell | 1,590 | 63 | #!/bin/bash
# Function to check if a file exists
file_exists() {
if [ -f "$1" ]; then
return 0
else
return 1
fi
}
# Check if the correct number of arguments is provided
if [ "$#" -ne 6 ]; then
echo "Usage: $0 <niftyreg_executable> <fixed_image> <moving_image> <transformed_image> <trans... |
b4ad131de82950469cb6de581fa43b20edab5791cafabf4e9a2ef53d6a9e99d6 | Shell | 1,596 | 69 | #!/usr/bin/env bash
set -euo pipefail
if [ "$#" -ne 4 ]; then
echo "Usage: $0 <hippocampus_file> <hemi> <lut> <output_dir>"
exit 1
fi
hippocampus_file="$1"
hemi="$2"
lut="$3"
output_dir="$4"
DOCKER_IMAGE="hipsta:lxgcustom"
# Check FS_LICENSE
if [ -z "${FS_LICENSE:-}" ]; then
echo "Error: FS_LICENSE is n... |
2dfac0b3ff50d8a973ee550194f8f9a23c71020149410234e59c2e9b1df0a4af | Shell | 1,602 | 37 |
MODEL="wavlm_base"
SEED="1 2 3 4 5"
for s in $SEED
do
for m in $MODEL
do
TAG="bs8_lr5e-5_ep50_seed${s}"
CUDA_VISIBLE_DEVICES=0 python main.py --tag $TAG \
--dataset psychiatry \
--seed $s \
... |
d160752daf4b05ef3ae896902a16fe96781c230a51e40dcdfa5704de1e8f2892 | Shell | 1,603 | 37 |
MODEL="hubert_base"
SEED="1 2 3 4 5"
for s in $SEED
do
for m in $MODEL
do
TAG="bs8_lr5e-5_ep50_seed${s}"
CUDA_VISIBLE_DEVICES=0 python main.py --tag $TAG \
--dataset psychiatry \
--seed $s \
... |
06abe03e7fef70cfbf8d0347e861fb2c0fb5dd4edff12e40a77c9dbf94c65e6d | Shell | 1,607 | 68 | #! /bin/bash
set -e
all_agg() {
local m=$1
shift 1
sleep 10
python -m rscvp.behavioral.$m \
-D 210315,210401,210402,210409,210402,210407,210409,210416,210604,210610,210514,210519,211202,211209,211203,211208,211202,211208,221018,221019 \
-A YW006,YW006,YW006,YW006,YW008,YW008,YW008,YW008,YW010,YW010,YW017... |
1919a071b41822fcdf18d5a46ffad0e527e6bab119fdb054c66600be3a181754 | Shell | 1,607 | 37 |
MODEL="wavlm_base"
SEED="1 2 3 4 5"
for s in $SEED
do
for m in $MODEL
do
TAG="bs32_lr5e-5_ep50_seed${s}_5s"
CUDA_VISIBLE_DEVICES=0 python main.py --tag $TAG \
--dataset psychiatry \
--seed $s \
... |
156003964abf931f5d650e2b8d48024e6419a0c185d15cd59c145acd4e166a56 | Shell | 1,608 | 37 |
MODEL="hubert_base"
SEED="1 2 3 4 5"
for s in $SEED
do
for m in $MODEL
do
TAG="bs32_lr5e-5_ep50_seed${s}_5s"
CUDA_VISIBLE_DEVICES=0 python main.py --tag $TAG \
--dataset psychiatry \
--seed $s \
... |
6b843775091f40de33b5fad2a59302235ef6dbcce0a0e1ba2c03fda87bcf3a94 | Shell | 1,609 | 37 |
MODEL="wav2vec2_base_960"
SEED="1 2 3 4 5"
for s in $SEED
do
for m in $MODEL
do
TAG="bs8_lr5e-5_ep50_seed${s}"
CUDA_VISIBLE_DEVICES=0 python main.py --tag $TAG \
--dataset psychiatry \
--seed $s \
... |
20fc9bee5e8619dd9da09cd8c433dc0f4e6e142db35fcbea77274751e266d4ed | Shell | 1,614 | 37 |
MODEL="wav2vec2_base_960"
SEED="1 2 3 4 5"
for s in $SEED
do
for m in $MODEL
do
TAG="bs32_lr5e-5_ep50_seed${s}_5s"
CUDA_VISIBLE_DEVICES=0 python main.py --tag $TAG \
--dataset psychiatry \
--seed $s \
... |
76f007bdfc137250b0ef3e03939fd2feb9a3585678349881b5cfd52bd7f59fef | Shell | 1,615 | 43 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=00:30:00
#SBATCH --output=/dev/null # suppress default output file
#SBATCH --error=/dev/null # suppress default error file
######################
# setup f... |
07d2e8ae20bd71f58c9e4530896bd2ebaf8d1d639baa42b61550cbf87689a61e | Shell | 1,617 | 72 | #!/bin/bash
#-------------------------------------------
# Parameters
# Required parameters:
# Transcript annotation (BED file)
BED=input/sample.bed
# output FASTA prefix
FASTAFILE=output/single.fa
# reference chromosome
REFERENCE=input/reference.fa
# Optional parameters
# Read length
READLEN=75
# Number of reads ... |
c7561a772493177f814bb5f1c13d002ff076548e191f70d9742dda8ed872745d | Shell | 1,634 | 72 | #!/bin/sh
#
# Downloads assembled sequence for M. musculus (mouse) from NCBI.
#
# From README_CURRENT_BUILD:
# Organism: Mus musculus (mouse)
# NCBI Build Number: 37
# Version: 1
# Release date: 05 July 2007
#
M_MUS_FTP=ftp://ftp.ncbi.nih.gov/genomes/M_musculus/Assembled_chromosomes
M_MUS_MT_FTP=ftp://ftp.ncbi.ni... |
a519415509dd5ad1d6e897d58a7f09c75f717309b85ef10765d38acbd55d445d | Shell | 1,635 | 39 | #!/bin/bash
# submit this with ./b00_wrapper_transforms.sh
datasets=("PNC" "HCPD" "HBN")
for dataset in "${datasets[@]}"; do
config_file="/cbica/projects/luo_wm_dev/two_axes/code/config/config_${dataset}.json"
# where to save output and error logs
logs_dir="/cbica/projects/luo_wm_dev/two_axes/cod... |
116d1a415fd822ca5dd298e8a1a330b7d9a9aa1dcb4f100e62e3edbfbbffec90 | Shell | 1,636 | 72 | ############################################################
#Script to create pseudobulk peaks: #
# input: a file with column1 cellid and column2 clusterid #
#output: a peak file for every cluster #
# #
#Autor: Tommaso... |
353f0d112e17c95010554660fa43a6c81850f5e72c874ee68df4d707e70857a8 | Shell | 1,637 | 72 | #!/bin/bash
#-------------------------------------------
# Parameters
# Required parameters:
# Transcript annotation (BED file)
BED=input/sample.bed
# output FASTA prefix
FASTAFILE=output/single-stranded.fa
# reference chromosome
REFERENCE=input/reference.fa
# Optional parameters
# Read length
READLEN=75
# Number ... |
6778bbbf67b23755e86e1a4ae81867f8c509bb9c6d2fec199e372971422b2c0f | Shell | 1,643 | 71 | #!/usr/bin/env bash
set -euo pipefail
# === Argument parsing ===
SUBJECTS_DIR=$1
SUBJECT_ID=$2
FSQC_OUTPUT_DIR=$3
if [[ $# -ne 3 ]]; then
echo "Usage: $0 <subjects_dir> <subject_id> <fsqc_output_dir>"
exit 1
fi
mkdir -p "$FSQC_OUTPUT_DIR"
# === Check fsqc ===
if ! command -v run_fsqc &> /dev/null; then
echo "... |
09ae099ddcb3a2ad94e04c8e1e3362b31f0f21fc974ea760a46cf1d4e06a0ba1 | Shell | 1,649 | 54 | #!/bin/bash -l
#SBATCH -J eiann_gpu_mnist_parallel
#SBATCH -o /ocean/projects/bio240068p/chennawa/logs/EIANN/eiann_gpu_mnist_parallel.%j.o
#SBATCH -e /ocean/projects/bio240068p/chennawa/logs/EIANN/eiann_gpu_mnist_parallel.%j.e
#SBATCH --requeue
#SBATCH --nodes=1
#SBATCH --ntasks=1 # Single task, ... |
d1657d9fe67781101ebec8d20d8bbfda3f63f246e22cb07f414e629144754250 | Shell | 1,656 | 52 | #!/bin/bash
#
# register_fs-to-vasoT1_no-manual.sh <vaso_T1_file> <fs_dir>
#
# - converts FS T1 to nifti
# - uses init.txt
# - runs non-linear registration using ants
bold_file=$1
fs_dir=$2
cwd=$3
mri_convert ${fs_dir}/mri/brain.mgz fs_brain.nii
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=4
export ITK_GLOBAL_DEFAULT_NUMBER... |
159790dd6999c9a2654579a3d1ecc5b86be992d8cdf559bff9e9d8fe3d011d67 | Shell | 1,658 | 46 | #!/bin/bash
#SBATCH --account=proj72 # PUT YOUR PROJ HERE
#SBATCH --job-name=convert_t_type_nrrds_to_me_type_nrrds # Job name
#SBATCH --array=0-628 # Job array range
#SBATCH --output=./logs/batch_%A_%a.out # Output file
#SBATCH --error=./logs/batch_%A_%a.err # Error file
#SBATCH --time=24... |
a8624836611dd02ec41d89e894460e7035a52a3ee880a052813d971b802db762 | Shell | 1,673 | 53 | #!/bin/bash -l
#SBATCH -J eiann_gpu_mnist_mpi
#SBATCH -o /ocean/projects/bio250022p/chennawa/logs/EIANN/eiann_gpu_mnist_mpi.%j.o
#SBATCH -e /ocean/projects/bio250022p/chennawa/logs/EIANN/eiann_gpu_mnist_mpi.%j.e
#SBATCH --requeue
#SBATCH --nodes=1
#SBATCH --partition=GPU
#SBATCH --gres=gpu:v100-32:8
#SBATCH --ntasks=5 ... |
defa4f6c054d14bb93a2b69a1414a3ab306171f6d01048622f9d0a1d6d5b1470 | Shell | 1,674 | 61 | #! /bin/bash
# brief: Import various CNN models from the web
# author: Karel Lenc and Andrea Vedaldi
# Models are written to <MATCONVNET>/data/models
# You can delete <MATCONVNET>/data/tmp after conversion
# TODO apply patch to prototxt which will resize the outputs of cls layers from 205 -> 1000 (maybe sed?)
overwr... |
52ab069cb6aef60cd5a7a891a21fbbc67d009ab42f91b85c7ae2b4f58e833fdd | Shell | 1,678 | 64 | #! /bin/csh -f
echo "This directory contains binary executables" >& RTMP
switch ($OSTYPE)
case linux:
echo "making statically linked ELF excutables for linux"
echo "meant for the LINUX operating system\n" >& RTMP
setenv CC "gcc -static -O"
setenv FC "g77 -static -O"
setenv OS "linux"
echo "C compi... |
68309a5b2956a528d356ed132b77806cd3af0406ca7c9d7ac280f86984ffe5df | Shell | 1,678 | 50 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=00:30:00
#SBATCH --output=/dev/null # suppress default output file
#SBATCH --error=/dev/null # suppress default error file
######################
# setup for... |
7e96e7678c856b0f0a35780aa3c8c4f98340205cb4faaa20876cd4a1d45ec592 | Shell | 1,681 | 40 | #!/bin/bash
# bold correction taking asymmetric readout timing into account by doing linear interpolations
# based on Renzo's bold correction method (taken from afni_VASO_eval_SPM.sh)
# extends it by using readout timing dependent weights
# (adapted from a script written by Renzo Huber)
# boldcorrect_lin.sh <basename>... |
b5fe82f28a1048a2bc977c0624fba305a1b0f7f24b8d608ebcbfee85d7271272 | Shell | 1,682 | 53 | #!/bin/bash
#
# register_fs-to-bold_no-manual.sh <vaso_T1_file> <fs_dir>
#
# - converts FS T1 to nifti
# - uses init.txt
# - runs non-linear registration using ants
bold_file=$1
fs_dir=$2
cwd=$3
mri_convert ${fs_dir}/mri/brain.mgz fs_brain.nii
n4bold_file=$(remove_ext ${bold_file})_n4.nii
N4BiasFieldCorrection -i ${... |
0bdf3821d797296d02494040359589559b587764c7c88c6775c2a14305f07c08 | Shell | 1,687 | 36 | #!/bin/bash
# 100 dimension
python run.py --do_train --cuda --do_valid --do_test --evaluate_train \
--model TransE -n 128 -b 512 -d 100 -g 30 -a 1.0 -adv \
-lr 0.0001 --max_steps 200000 --cpu_num 2 --test_batch_size 32
python run.py --do_train --cuda --do_valid --do_test --evaluate_train \
--model DistMult -n ... |
6f99ea80fefc4469cb59a938446f9b0aa87a91b9682490c38da7ac928e1e4ab6 | Shell | 1,687 | 69 | #!/bin/bash
# Export the current date and time for job labeling
export DATE=$(date +%Y%m%d_%H%M%S)
export LABEL="$1"
export JOB_NAME=eiann_gpu_mnist_ray_"$LABEL"_"$DATE"
# Environment variables to optimize performance
export OMP_NUM_THREADS=4
export MKL_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OPENBLAS_NUM_T... |
42a207a3684de8be97142da40ad26ba2404f40ee48688941c95bf2e4fe0eb3e2 | Shell | 1,689 | 72 | ############################################################
#Script to create pseudobulk peaks: #
# input: a file with column1 cellid and column2 clusterid #
#output: a peak file for every cluster #
# #
#Autor: Tommaso... |
5417b7ba098de82b726c5aaf3d0ff3dc23ff9c4142f766ebee1c313025ff4d09 | Shell | 1,690 | 35 | #!/bin/bash
iskids="$1"
task="$2"
contrast="$3"
START=$(pwd)
OUT="$(mktemp -d /tmp/stich.XXXXX)"
cp "../bids_dataset/derivatives/bootstrap_clusters/figures/${iskids}_plot-surfInf_second-level_task-${task}_contrast-${contrast}"*.png "$OUT"
cd "$OUT" || exit 1
for f in *.png; do convert "$f" -transparent white tmp.p... |
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