sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 17k | content stringlengths 1 200k |
|---|---|---|---|---|
0e4c4119d2e4bf4d92803de9f07894c6bbb1ce673088a75c2bd0fbc3a53d3135 | Shell | 1,589 | 64 | #!/bin/bash
# Build and install GEOS on a POSIX system, save cache for later
#
# This script requires environment variables to be set
# - export GEOS_INSTALL=/path/to/cached/prefix -- to build or use as cache
# - export GEOS_VERSION=3.14.1 or main -- to download and compile
pushd .
set -e
if [ -z "$GEOS_INSTALL" ... |
e539b5125f7699d3edb37aa60d7e711ae8fe5a7a8fe8a96bd62a2ae6fe8bf9c7 | Shell | 1,602 | 39 | #!/bin/bash
SUBJECT_ID=$1
FSLDIR=/opt/fsl-6.0.7.1/
T1_in_fs=/subjects_dir/${SUBJECT_ID}/mri/rawavg.mgz
MICRO_TEMPLATE=/out_dir/$SUBJECT_ID/"$SUBJECT_ID"_space-native_desc-template.nii.gz
MICRO_IMAGE=/out_dir/$SUBJECT_ID/"$SUBJECT_ID"_space-native_desc-micro.nii.gz
MICRO_WARPED="/out_dir/${SUBJECT_ID}/${SUBJECT_ID}_sp... |
56657c7297213050dd68d34b5a616d91ef25726e0fc57592a62ab9674713d4d6 | Shell | 1,614 | 54 | #!/usr/bin/sh
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
set -o pipefail
source "$TOOL_WORKFLOW_LIB"
set -x
tmp_corrected_windowfile="${FILENAME_GC_CORRECTED_WINDOWS}.tmp"
tmp_correct... |
25908f1c0dd9843d33946479d814f2ccb5f60f909fa193f5bd594f7b56751af9 | Shell | 1,639 | 61 | #!/bin/bash
set -e
ROOT_DIR=`pwd`
export ROBOT_JAVA_ARGS=-Xmx7G
mkdir mirror
curl -L -o 'mirror/taxslim.owl' 'http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl'
curl -L -o 'mirror/taxslim-disjoint-over-in-taxon.owl' 'http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim-disjoint-over-in-taxon.owl'
curl... |
2de8aec4ee4dea23b914b607807223fa63e0ac9a009936fee69e0c3c92376320 | Shell | 1,649 | 67 | #!/bin/bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
set -o pipefail
source "$TOOL_WORKFLOW_LIB"
set -x
# Reformat original coverage file so it can be annotated with annotate_vcf.pl... |
d2e3e7b037b2af8d08b55709d0f9d2def1180f002dafa25497a4f843a6618a2b | Shell | 1,656 | 42 | #!/bin/bash
conda activate ops 2> /dev/null
#test -e logs || mkdir logs
#test -e logs/latest && rm -r logs/latest
#mkdir logs/latest
#mkdir -p plots
mem_arg='$(expr {resources.mem_mb} / {threads})'
#out_path=$(realpath ./logs/latest/)
#err_path=$(realpath ./logs/latest/)
#out_path='$(realpath {log})'
#err_path='$(re... |
8afb7ad78a8b3c43080622950c2f2236cbdbba11b2775bcf077afcd04128724a | Shell | 1,660 | 47 | #!/bin/bash
# Copyright (C) 2025 Sotiris Lamrpinidis
#
# This program is free software and all terms of the GNU General Public License
# version 3 as published by the Free Software Foundation apply. See the LICENSE
# file in the root directory of the project or <https://www.gnu.org/licenses/>
# for more details.
set ... |
1fd2d0740f09083227598731cdcc88f0339fb49326e12f820c20f62d90e29567 | Shell | 1,674 | 50 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
e28cdb353e286c3ae295d6718a18d4f32e32d126c554984252117cbff662927c | Shell | 1,675 | 50 | #!/bin/bash
# Publish documentation to the gh-pages site.
# The remote for pushing the docs (defaults to origin).
# This is where you will submit the PR to BVLC:gh-pages from.
REMOTE=${1:-origin}
echo "Generating docs and pushing to $REMOTE:gh-pages..."
echo "To build and view docs when not on master, simply do 'jeky... |
68eabb84334ea3f13b7810640f4f5f04e9451862557d660c8f62c55f4e23ddcc | Shell | 1,679 | 65 | #!/bin/bash
# Extract FT_job_id, accuracy, stderr, and log from MMLU evaluation results
# Usage: ./extract_mmlu_results.sh <results_file>
if [ $# -eq 0 ]; then
echo "Usage: $0 <results_file>"
exit 1
fi
results_file="$1"
if [ ! -f "$results_file" ]; then
echo "Error: File $results_file not found"
exi... |
b6a1ba185ff6c0a87c6692a9a67fc701e1f5b810aa947fbe5c9ba13c6df370ba | Shell | 1,688 | 48 | #main_folder=/Users/xm52195/data/Laura
#subject=STR_008
dcm_folder=DICOM
T1_ref=cT1_${1}.nii
#cd $main_folder/${subject}
mrresize -force $T1_ref T1_4mm.nii.gz -voxel 4
bet $T1_ref T1_mask -f 0.1 -R -m
# convert to nii
#mrconvert -strides $T1_ref $dcm_folder anat.nii.gz -force
echo "SELECT THE (unregistered) PWI"... |
15ba7b612140f4196bd62265402655c8ee380cfbdbaef60ea263b4cb37115554 | Shell | 1,716 | 30 | #!/bin/env bash
s=$1
echo "Processing sub-${s}"
module purge
module load R
module load matlab/r2019b
module load fsl
export R_LIBS="/home/tconstab1/R/x86_64-pc-linux-gnu-library/FIX"
cd /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/SingleEcho/MELODIC
fix_train_weights=/home/tconstab1/kg98... |
dcc7a6b0d136154488cad005771bac77e79e971227ef2f57ea0fbd799204932b | Shell | 1,719 | 51 | echo "Begin"
date
RootPath="/public/home/lishr2022/Project/Cross-modal/Preprocess"
ResultsPath=$1
T2_1=$2
T2_2=$3
T1_root=$4
echo "Reoriented2std"
date
echo "######################################"
fslreorient2std $T2_1 $T2_1
fslreorient2std $T2_2 $T2_2
echo "Brain Extraction"
date
echo "############################... |
f20fad2955e663cabecdbb6ae89bae20ed1e1a127c02a33c29eca6b6d7d4a6c0 | Shell | 1,721 | 74 | #!/bin/bash
# This wrapper script is for running GROMACS jobs on clusters.
# Command line switch indicates whether to do backups
do_bak=0
while [ $# -gt 0 ]
do
case $1 in
-b) do_bak=1 ;;
*) break ;;
esac
shift
done
# This is the command that we want to run.
COMMAND=$@
# Load my environme... |
d818c606ce9a5a2ee83ee0fbd9ca930a90d5f676f393a32c0cb4bc02685955dc | Shell | 1,733 | 59 | #!/bin/bash
# set paths and variables
T1_FILE=$1
T2_FILE=$2
SUBJECT_ID=$3
OUT_DIR=$4
SKIP_BC=$5
micapipe_simg=${SING_DIR}/micapipe-v0.2.3.simg
if [[ "$SKIP_BC" -eq 0 ]]; then
echo "Apply bias correction"
mri_nu_correct.mni --i $T1_FILE --o $OUT_DIR/$SUBJECT_ID/T1w_BC.nii.gz
mri_nu_correct.mni --i $T2_F... |
aa9be32d8aa1a9af949ec9d963bc7d2866febd7beafa9770568aed32b2c121d1 | Shell | 1,764 | 88 | module add apps/fsl/6.0
source ~/anaconda3/etc/profile.d/conda.sh
conda activate tats
export FREESURFER_HOME=/public/home/lishr2022/freesurfer
export SUBJECTS_DIR=/public_bme/data/lishr/Cross_modal/subjects
export FSFAST_HOME=/public/home/lishr2022/freesurfer/fsfast
export MNI_DIR=/public/home/lishr2022/freesurfer/mni... |
83a246641be9301a86d9330a3eb3c7c00758810904d713339c49be5820e5c89b | Shell | 1,778 | 93 |
#
# distribute.sh
#
# prepares rat-apps for distribution such that they can be copied
# to a new computer without an existing Python installation.
#
# To overide defalt parameters, set the folling variables:
# PY: Command to run python3 with
PY=""
# PYINSTALL_OPTS: Arguments to pass th pyinstaller.
PYINSTALL_OPTS="-... |
9e8932ff866ea6ff4f251df6a318dfbc7891523db6e1a8a5dabe72ecb9a6574b | Shell | 1,778 | 49 | #!/bin/bash
# Sarah Cappelle & Stefan Sunaert
# 15/12/2020
# This script is the first part of Sarah's Study1
# We have data from IDE, but this is cluttered
# We sort the data into named DICOM folders
# We delete unwanted derived data (MPRs mostly)
# We convert these dicoms to BIDS format
# STEP 1 - sort the dicoms
# w... |
a3acafe6afde8fe1abd3a5a132b592cbb2550e1622a4268175e69a8d5149f45f | Shell | 1,778 | 54 | #!/bin/bash
#The purpose of this script is to generate activations and run
#the regression for the contextual embeddings of untrained models.
#LLM.py: generates static and contextual embeddings.
#lua.py: performs linear (w/ a layer norm) uniform attention over the static embeddings
#call_banded_reg.py: runs the regre... |
35c4ceee3eade8c256a9e2b9b74ee856c7045af0ead2515bc476d87cbdb76ed6 | Shell | 1,782 | 79 | #!/bin/bash
#
# Jeff Eilbott, 2018, jeilbott@surveybott.com
#SBATCH --job-name=vsr_bott
#SBATCH --ntasks=1 --nodes=1
#SBATCH --mem-per-cpu=6000
#SBATCH --time=6:00:00
# process inputs
while getopts "u:d:b:e:g:l:" OPTION
do
case $OPTION in
u)
UPLOAD="$OPTARG"
;;
d)
DATA="$OPTARG"
;;
... |
814f955f0851f41138636edf19f1498973ca934c72096144c524afbc0942feca | Shell | 1,788 | 55 | #!/bin/bash
#The purpose of this script is to generate activations and run
#the regression for the contextual embeddings of untrained models.
#LLM.py: generates static and contextual embeddings.
#lua.py: performs linear (w/ a layer norm) uniform attention over the static embeddings
#call_banded_reg.py: runs the regre... |
20d88bcc374b8c32332dabc23da8d3a16e0947d57f36b1d4b6d883cf71667ff2 | Shell | 1,794 | 71 | #!/bin/bash
set -e
echo "=== Setting up RunPod Environment for Truesight Finetuning ==="
# Function to check if a command exists
command_exists() {
command -v "$1" >/dev/null 2>&1
}
# Install uv if not present
if ! command_exists uv; then
echo "Installing uv..."
curl -LsSf https://astral.sh/uv/install.sh... |
2517117b4deda855ec577fffa41db7c26969d01f3b61c1b807bdef9ac13988f1 | Shell | 1,808 | 55 | #!/bin/bash
# Collect coverage statistics for all BAM files in a sample using samtools
SAMPLE_DIR="$1"
OUTPUT_FILE="$2"
SAMTOOLS="/g/korbel2/weber/miniconda3/bin/samtools"
if [ -z "$SAMPLE_DIR" ] || [ -z "$OUTPUT_FILE" ]; then
echo "Usage: $0 <sample_dir> <output_file>"
exit 1
fi
if [ ! -x "$SAMTOOLS" ]; the... |
f2b2deb083fde0b56f4cc2bd7970223082c830df12a255a91037a7758bb10db7 | Shell | 1,827 | 58 | #!/bin/bash
# set paths and variables
ANAT_DIR=$1
SUBJECT_ID=$2
OUT_DIR=$3
RATIO_TYPE=$4
SKIP_BC=$5
micapipe_simg=${SING_DIR}/micapipe-v0.2.3.simg
for m in T1w $RATIO_TYPE ; do
echo "Create T1 and T2 average across all available runs"
singularity exec -B $ANAT_DIR:/anat_dir \
-B $OUT_DIR/$S... |
6206c75d5a8c6a42a747aa9fbc00dc86a0390f9ae672c889c9b8a0be2db6026f | Shell | 1,831 | 63 | #!/bin/bash
if [ $# -lt 2 ]
then
echo "Runs STAR alignment and outputs to current directory. "
echo "Usage: runSTAR genomeDir dirWith_R1.fastq.gz [star commands]"
echo "Genomes available:"
genomes=$(ls -d /gpfs/genomes/*.star)
for i in $genomes
do
echo ${i##*/}
done
else
GENOME=$1
DIR=$2
shift 2
STAR --ge... |
00003e543e49f82b78ca142faa06539c22bbf0546f8e3f94c0ca570fefed99b6 | Shell | 1,859 | 35 | echo "Begin"
date
RootPath="/public/home/lishr2022/Project/Cross-modal/Preprocess"
DataPath="/public_bme2/bme-liyuanning/lishr/Cross_modal/Data"
subject=$1
T1="${DataPath}/${subject}/anat/T1/T1_avg.nii.gz"
echo "register Str to MNI"
date
echo "########################################"
OutputSEG="${DataPath}/${subjec... |
d9edfd5476b59bbf618a542c7e2621a3ef5a0f659bfc42fe4f7f336b6ca4819c | Shell | 1,859 | 51 | #!/bin/bash
# Usage parse_log.sh caffe.log
# It creates the following two text files, each containing a table:
# caffe.log.test (columns: '#Iters Seconds TestAccuracy TestLoss')
# caffe.log.train (columns: '#Iters Seconds TrainingLoss LearningRate')
# get the dirname of the script
DIR="$( cd "$(dirname "$0")"... |
30a3bd5dcc93e6482a7281f156690b4da6710f084b54815a183ebbe4cd0ac219 | Shell | 1,879 | 48 | #!/bin/bash
INSTALL_PREFIX="$HOME/opt/mirtk-appimage"
SUDO='' # set to empty string if prefix is writable by $USER
APPIMAGE="$1"
if [ -z "$APPIMAGE" ]; then
GLIBC_VERSION="$(ldd --version | head -n1 | rev | cut -d' ' -f1 | rev)"
GLIBC_VERSION_MAJOR="${GLIBC_VERSION/.*}"
GLIBC_VERSION_MINOR="${GLIBC_VERSION/*.}... |
47b8222ec5ada2b9816e29acc9e1dfc6b2fc27aa3c056c21904d0eaed5a96b44 | Shell | 1,898 | 46 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License... |
356472cdd30ff24f1652174cf8189be926627ce1b2af245d0d26b391b9021675 | Shell | 1,938 | 62 | #!/bin/bash
# Control analysis 2
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
# First step: MVNN
echo "MVNN Encoding Analysis for Miniclips"
python ../../EEG/Encoding/mvnn_encoding.py \
--config_dir ../config.ini \
--config control_2 \
--inpu... |
f47b9ad672b53ebbe289a8a158331b0b89ecac797c80e5971933d9b2bc9a37ed | Shell | 1,950 | 63 | #!/bin/bash
#
# Submit SLURM jobs to pull MosaiCatcher pipeline containers in parallel
# Each container gets its own sbatch job
#
# Usage: ./pull-apptainer-containers.sh [cache_dir] [temp_dir]
#
# Example:
# ./pull-apptainer-containers.sh /scratch_cached/korbel/shared/apptainer_cache /tmp
#
set -euo pipefail
SCRIPT... |
10441b81e248008f29ca74a871a583fa168e215a98207c371253b906b8faca57 | Shell | 1,974 | 63 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
5c8023c04da7dd2c7ffc7cc60c475b79013b5169e0d189e04c2b7e95a897b33b | Shell | 1,976 | 63 | #!/bin/bash
# Control analysis 1
source /home/alexandel91/.bashrc
conda activate encoding
export LD_PRELOAD=$CONDA_PREFIX/lib/libstdc++.so.6
echo "MVNN Encoding Analysis for Miniclips"
# First step: MVNN
python ../../EEG/Encoding/mvnn_encoding.py \
--config_dir ../config.ini \
--config control_1 \
--inpu... |
9a91ee14bac0f36b192c4541ab6e19c253dc26ce92c5acffeb4684b633dbe8a1 | Shell | 1,984 | 51 | #!/bin/bash
#The purpose of this script is to generate activations and run
#the regression for the contextual embeddings of untrained models.
#LLM.py: generates static and contextual embeddings.
#lua.py: performs linear (w/ a layer norm) uniform attention over the static embeddings
#call_banded_reg.py: runs the regre... |
adbf1ddfa8096e7efc9b71f3c71a3fb597de787ce70535b29eaa97ec20c53bff | Shell | 1,990 | 68 | #!/bin/bash
# Should be run on bego.ipmc.cnrs.fr
# sh Run_Demuxafy_HuDeCa.sh ../data_analysis/hudeca/data/FN_S1256/FN_S1256.txt
# Job variables
WD="/data/analysis/data_mbouamboua"
DEMUXAFY="/data/analysis/data_mbouamboua/Demuxafy"
INDIR=${WD}/data_analysis/hudeca/data
OUTDIR=${WD}/data_analysis/hudeca
OUT=${OUTDIR}/W... |
eafde83f962ac954b3a0b5324053d9addb697b5249cf75b6c0c6b279595d8ee4 | Shell | 2,025 | 54 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
58f32b769ae735ce9e6cece92cf099a1e6c1a64031a4d081741c0cc31958a53e | Shell | 2,083 | 66 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
e80e50b545183123d257ae69881bc62ade3aee63668d6fd8c921962a8048e557 | Shell | 2,105 | 56 | module add apps/fsl/6.0
source ~/anaconda3/etc/profile.d/conda.sh
conda activate tats
export FREESURFER_HOME=/public/home/lishr2022/freesurfer
export SUBJECTS_DIR=/public_bme/data/lishr/Cross_modal/subjects
export FSFAST_HOME=/public/home/lishr2022/freesurfer/fsfast
export MNI_DIR=/public/home/lishr2022/freesurfer/mni... |
354e951abfbca0fc84647dc3451bdd80a065c43b771ab06e0d9d286b55f5c345 | Shell | 2,117 | 68 | #!/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... |
abb3c68ddead1a06dd00b853b2994ae960c16eff931c141265f84a940f251086 | Shell | 2,119 | 63 | #!/bin/bash
USE_AMBER=$1
USE_MSA=$2
USE_TEMPLATES=$3
ENV_NAME="alphafold37"
# Create and activate a new conda environment
if ! conda info --envs | grep -q ${ENV_NAME}; then
echo "Creating new conda environment: ${ENV_NAME}"
conda create -y -n ${ENV_NAME} python=3.7
fi
echo "Activating conda environment: ${ENV_NA... |
bf866f95f3941cc026b6d19f31c9dad8f4ba7ad22c9f7bcf518be5309ed1d7bc | Shell | 2,165 | 74 | #!/bin/bash
# set paths and variables
ANAT_DIR=$1
SUBJECT_ID=$2
SUBJECTS_DIR=$3
OUTPUT_DIR=$4
fastsurfer_sif=${SING_DIR}/fastsurfer-gpu.sif
micapipe_simg=${SING_DIR}/micapipe-v0.2.3.simg
# -----------------------------
# Check for singularity
# -----------------------------
if [[ ! -f $fastsurfer_sif ]] ; then
... |
766abb62d302edf495bca4caae9b58ee8c580d3b0bf9edc4e0ccee3d24d0089a | Shell | 2,177 | 69 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
67198de7884c08b1cfa67e4f7ce49feedab6b1b7f71b4b057b8280f177370043 | Shell | 2,215 | 67 | #!/bin/bash
# Exit immediately if a command exits with a non-zero status,
# treat unset variables as an error, and ensure pipelines fail on the first error.
set -euo pipefail
module load SAMtools/1.14-GCC-11.2.0
SAMPLE_FOLDER=$1
# Define directories
OLD_BAM_DIR="$SAMPLE_FOLDER/old_bam"
NEW_BAM_DIR="$SAMPLE_FOLDER/b... |
ca27487c7bea5af973dcd262778ecfe0d7df1760eae315984d2480536348d39a | Shell | 2,239 | 16 | cmd_time=`TZ=UTC-8 date "+%Y%m%d-%H%M%S"`
# # NGNNDGCNNGraphormer
# nohup python3 train.py --ngnn_code --grpe_cross --device 0 --cmd_time ${cmd_time} --num_heads 8 --dataset ogbl-citation2 --use_feature --use_feature_GT --use_edge_weight --epochs 15 --train_percent 8 --val_percent 4 --test_percent 0.2 --model NGNNDGC... |
ed2abd7d652b8eccc88a89ab12561becb5e05d1fc62a60e71c76e4f0e37065b3 | Shell | 2,251 | 77 | #!/bin/bash
#SBATCH --job-name=03_featureCounts
#SBATCH --mem=32GB
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=16
#SBATCH --error="./logs/03_featurecounts.err"
#SBATCH --output="./logs/03_featurecounts.out"
# RNA-seq Pipeline Step 3: Gene Quantification with featureCounts
# This script counts reads mapp... |
bd4b1b0d2ce969704aa6a54b047cd98d358c33c4e4e9366db9b544ed56ffaa02 | Shell | 2,253 | 71 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
a0f0c6f9962626d4aa264c090640c101d8fb9f86d9694bcf75f67e88b44eee80 | Shell | 2,262 | 63 | #!/bin/bash
################################################################################
# Example Usage Script
# Demonstrates various ways to use window_those_genomes.sh
################################################################################
echo "==================================="
echo "Genome Window... |
d82ca1c4c9d71dda834790f4a161181a8cb688cbf9d2c07952c177d1f41ec663 | Shell | 2,282 | 51 | #!/usr/bin/env bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# The sambamba version used for sorting, viewing. Note that v0.5.9 is segfaulting on convey during view or sort.
export S... |
89104bc93bad130258730fc3e5ae2e16d4a4eed49d5fbabe0c66854990f20bd3 | Shell | 2,319 | 48 | #!/bin/bash
# @ Stefan Sunaert & Ahmed Radwan- UZ/KUL - stefan.sunaert@uzleuven.be
#
v="v0.1 - dd 07/10/2020"
# This is the main script of the KUL_NeuroImaging_Toools
#
pbs_cpu=$(grep pbs_cpu $conf | grep -v \# | sed 's/[^0-9]//g')
pbs_mem=$(grep pbs_mem $conf | grep -v \# | sed 's/[^0-9]//g')
pb... |
cd6c68f740320ebe7b27474da857719771c6083578576b6c285f3ea1ed27f520 | Shell | 2,345 | 51 | #
# 1 Bond 2 Morse 3 Angle 4 Proper-Dih.
# 5 Per.-Imp.-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR)
# 9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Potential
# 13 Kinetic-En. 14 Total-Energy 15 Conserved-En. 16 Temperatu... |
740d09a81b433dd56ce38b37b28f14d74b08049dd447ed00c88f1b97f2130a14 | Shell | 2,353 | 83 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
ebd5220eb39f6ee359d94c7fafffedb5c7448db5f33d92f77264a86b417a087c | Shell | 2,374 | 83 | #!/usr/bin/env bash
# Exit if any command fails
set -e
# Navigate to the "src" directory
cd src
echo "Generating main figures..."
entire_runtime=0
# Iterate notebooks from 1 to 6
for i in {1..7}; do
echo "Running Figure${i}.ipynb..."
# Record the start time (in seconds)
start_time=$(date +%s)
# Run... |
2bb19adf1bc8391dec3335f3467840e23c2c09e376eaa31c72642db033351c2f | Shell | 2,393 | 75 | #!/usr/bin/env bash
# PLEASE NOTE: This script has been automatically generated by conda-smithy. Any changes here
# will be lost next time ``conda smithy rerender`` is run. If you would like to make permanent
# changes to this script, consider a proposal to conda-smithy so that other feedstocks can also
# benefit from... |
d77a2350678db4e904107ec97579a5e599f741f3e7206420d0719897c3deac7b | Shell | 2,456 | 56 | #!/bin/env bash
s=$1
echo "Running AROMA for sub-${s}!"
module load fsl/6.0.4
aroma_path="/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/SingleEcho/AROMA/RUN-AROMA"
brain_mask="/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest/sub-${s}/func/sub-${s}_t... |
b35855e7bc048a48d2c1590b236dc11f149a84f38a6a12dd231058822447a7eb | Shell | 2,465 | 82 | #!/usr/bin/env bash
# -*- mode: jinja-shell -*-
source .scripts/logging_utils.sh
set -xe
MINIFORGE_HOME=${MINIFORGE_HOME:-${HOME}/miniforge3}
( startgroup "Installing a fresh version of Miniforge" ) 2> /dev/null
MINIFORGE_URL="https://github.com/conda-forge/miniforge/releases/latest/download"
MINIFORGE_FILE="Mamb... |
589602d3de1db7fffc5fe58544e35fd5b351dba4b7dd4d0caa9086336886b85b | Shell | 2,502 | 16 | cmd_time=`TZ=UTC-8 date "+%Y%m%d-%H%M%S"`
# # DGCNN_noNeigFeat
# nohup python3 train.py --device 0 --cmd_time ${cmd_time} --dataset ogbl-vessel --use_feature --use_edge_weight --epochs 20 --train_percent 100 --val_percent 100 --test_percent 100 --model DGCNN_noNeigFeat --runs 10 --batch_size 256 --lr 0.0002 --num_wor... |
c325033f369a1eb2f7079ceec03b51ef3b13b531b28368d117ee6ed72e912991 | Shell | 2,601 | 100 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
b2a9f1652757c97ac57961120e3f768f7c6d0d3b22697a028f27b0aee7c30de8 | Shell | 2,649 | 101 | #!/bin/bash
extension=".nii" # Replace with your desired extension
directory="." # Replace with your desired directory
# Function to display the menu
display_menu() {
local count=0
for file in "${files[@]}"; do
echo "$count. $file"
((count++))
done
}
# Read files in the directory with t... |
85ffe67b9a85740f164bb5187d1e27c81d655103d684e7a6b5aa585fa140527a | Shell | 2,668 | 137 | #!/bin/bash -e
# Bash shell script to crop T1w
#
# Requires MRtrix3
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 19/03/2021
version="0.1"
kul_main_dir=`dirname "$0"`
source $kul_main_dir/KUL_main_functions.sh
cwd=$(pwd)
# FUNCTIONS --------------
# function Usage
function Usage {
cat <<USAGE
`basen... |
6f215c75c0400abe00b2f7631eea598484553f900c87c60a7accce4f847621b8 | Shell | 2,676 | 99 | #!/bin/bash
#SBATCH --job-name=02_STAR_align
#SBATCH --mem=64GB
#SBATCH --time=12:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=16
#SBATCH --error="./logs/02_star_alignment_%a.err"
#SBATCH --output="./logs/02_star_alignment_%a.out"
#SBATCH --array=1-6
# RNA-seq Pipeline Step 2: STAR Alignment
# This script aligns reads to ... |
685d946bc840dde8344be249506e9168599cfa3abcad286875c9904395f3eba9 | Shell | 2,678 | 79 | #!/bin/bash
# Copyright (C) 2025, 2026 Sotiris Lamprinidis
#
# This program is free software and all terms of the GNU General Public License
# version 3 as published by the Free Software Foundation apply. See the LICENSE
# file in the root directory of the project or <https://www.gnu.org/licenses/>
# for more details... |
2168392b7b73d727d7a7842e093f22c8af4b09fb4ca64e56e2c34fde0fd3e2f1 | Shell | 2,680 | 86 | #!/bin/bash
# Download latest version from website.
echo "Downloading source."
cctools="cctools-4.1.3"
cctools_src="$cctools-source"
rm -rf $cctools_src $cctools_src.tar*
wget http://www3.nd.edu/~ccl/software/files/$cctools_src.tar.gz
echo "Extracting archive."
tar xzf $cctools_src.tar.gz
cd $cctools_src
# Increase a... |
e66af6c3349b20357336a425cf7226f3b7ebaf6d47b409f8195ba7ea08eb5f46 | Shell | 2,734 | 110 | #!/bin/bash
# install dependencies
# (this script must be run as root)
BASEDIR=$(dirname $0)
source $BASEDIR/defaults.sh
apt-get -y update
apt-get install -y --no-install-recommends \
build-essential \
libboost-filesystem-dev \
libboost-python-dev \
libboost-system-dev \
libboost-thread-dev \
libgflags-de... |
adf884acae3867dbf91e92fbbd7f44742874e0a1c9f455c6b342917785fd30f4 | Shell | 2,797 | 63 | #!/usr/bin/env bash
track_dir="$1"
output_file="$2"
reference="$3"
# Debug print statements
printf "Debug: Track directory set to '%s'\n" "$track_dir"
printf "Debug: Output file set to '%s'\n" "$output_file"
printf "Debug: Reference genome set to '%s'\n" "$reference"
# Check if the directory exists
if [[ ! -d "$trac... |
4ec4dbad8ab88be8651d30d409ae474aaa87ea0e7536d052e7b85d3ad8cc2a4b | Shell | 2,815 | 76 | module add apps/fsl/6.0
source ~/anaconda3/etc/profile.d/conda.sh
conda activate tats
export FREESURFER_HOME=/public/home/lishr2022/freesurfer
export SUBJECTS_DIR=/public/home/lishr2022/Project/Cross-modal/test_data/subjects
export FSFAST_HOME=/public/home/lishr2022/freesurfer/fsfast
export MNI_DIR=/public/home/lishr2... |
69880f3a7528a9a9b547429cf49665d6563b6d8fa4e634bbe2288cf750624d0b | Shell | 2,819 | 36 |
# Auto-generated by MIRTK root CMakeLists.txt during CMake configure.
#
# To enable Bash completion of "mirtk" subcommands, add the following to your
# ~/.bashrc (Linux) or ~/.bash_profile (OS X) file:
#
# [ ! -f "$MIRTK_ROOT/share/completion/bash/mirtk" ] ||
# source "$MIRTK_ROOT/share/completion/bash/mirtk"
# ... |
e09370b054e2c22992c12561efb04b9f19636e2f65181de28af403ac7ef61c6c | Shell | 2,864 | 107 | ## Travis CI script
set -e
norm_option_value()
{
if [ "$1" = on ] || [ "$1" = ON ] || [ "$1" = yes ] || [ "$1" = YES ] || [ "$1" = y ] || [ "$1" = Y ] || [ "$1" = 1 ] || [ "$1" = true ] || [ "$1" = TRUE ]; then
echo ON
elif [ "$1" = off ] || [ "$1" = OFF ] || [ "$1" = no ] || [ "$1" = NO ] || [ "$1" = n ] || [... |
c44e109c8f0f03f49c3405bcc5b8004912dcc87c200c2294d7a374f84e7553f0 | Shell | 2,876 | 90 | #!/bin/bash
# Download latest version from website.
echo "Downloading source."
cctools="cctools-4.3.2"
cctools_src="$cctools-source"
rm -rf $cctools_src $cctools_src.tar*
wget http://www3.nd.edu/~ccl/software/files/$cctools_src.tar.gz
echo "Extracting archive."
tar xzf $cctools_src.tar.gz
cd $cctools_src
# Increase a... |
82ffd29ce8867f78023bb833b638c2b5e1dbe1e5a056506e8b2e93dfc476fa9c | Shell | 2,886 | 66 | #!/bin/bash
# ------------------------------------------------------------------------------
# Script name: internal_validity_masks.sh
#
# Description:
# Script to make figure showing dilated masks for internal validity analysis
#
# ------------------------------------------------------------------------... |
d0513710ff964aa4704c05c90b0c5126584dfb9455eaf5dbe4f378cc3711f427 | Shell | 2,957 | 89 | #!/usr/bin/env bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# This is a short script to compile the coverageQcD tool.
# ldc2-0.12.1-linux-x86_64/bin/rdmd --compiler=ldc2-0.12.1-li... |
de6262e144022c9cae2132cc9d8e4187fb9592490df145d7fa7d112514d8696a | Shell | 2,987 | 89 | #!/usr/bin/env bash
#
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# This is a short script to compile the coverageQcD tool.
#
# ldc2-0.12.1-linux-x86_64/bin/rdmd --compiler=ldc2-0.12.1... |
94c963504f9c8d31c410d3eb2a171393faebf9127600ed7d4404b1112f42f566 | Shell | 3,046 | 36 | #!/bin/env bash
#SBATCH --job-name=train10fix
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=18
#SBATCH --mem-per-cpu=12G
#SBATCH --time=12:00:00
#SBATCH --mail-user=toby.constable@monash.edu
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH --export=ALL
#SBATCH -A kg98
#Copy over mflirt
for sub in $(cat /fs03/kg... |
215c3f30c2f02f9c7be978916fb8feae5d67460db02605656a045d2ea2b6961b | Shell | 3,148 | 68 | #!/bin/env bash
#Here, I resample the T1 probability maps to NATIVE space, and use associated masks to extract timeseries
subject_list=$(cat /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/subjlist.txt)
for s in $subject_list; do
echo 'sub-${s}'
module load fsl
module load ants
#https://neurostars.org/t/moving-... |
4fab69ab9056be413e44d91fbd51be054019c9117bc95826db7531c8ce044065 | Shell | 3,180 | 70 | #!/usr/bin/env bash
# Build a distributable macOS .app + DMG of the Miniscope DAQ (Apple Silicon).
#
# Mirrors the Linux AppImage recipe (packaging/linux/build-appimage.sh): a conda
# env from environment.yml, built USE_PYTHON=OFF (no embedded Python /
# DeepLabCut tracker) so the bundle stays lean, then packaged with ... |
ff1388ed2441248500fc61e95acc3c4476194da6a9fe3ba6d1c0425c6c0813cc | Shell | 3,216 | 99 | #!/bin/bash
# Download latest version from website.
echo "Downloading source."
cctools="cctools-6.2.10"
cctools_src="$cctools-source"
rm -rf $cctools_src $cctools_src.tar*
wget http://www3.nd.edu/~ccl/software/files/$cctools_src.tar.gz
echo "Extracting archive."
tar xzf $cctools_src.tar.gz
cd $cctools_src
# Increase ... |
123051c7ed4f0c33acd783df039a3d8429af357effb4d87251d3a04948ab7f71 | Shell | 3,220 | 110 | #!/bin/bash
# ./run_alphafold.sh
# Export the GPU to use
export CUDA_VISIBLE_DEVICES=7
## === ##
# Enable unified memory and dynamic allocation for JAX
# export CUDA_VISIBLE_DEVICES=0,1,2,3,4,5,6,7 # Use 4 GPUs
# export XLA_PYTHON_CLIENT_ALLOCATOR=platform
# export XLA_PYTHON_CLIENT_PREALLOCATE=false
# export TF_FO... |
45e6825866898c845df66849b764c0d2dda3f46ff856dcb41b746cef13d15d77 | Shell | 3,251 | 59 | #!/bin/bash
#The purpose of this script is to generate activations and run
#the regression for the contextual embeddings of untrained models.
#LLM.py: generates static and contextual embeddings.
#lua.py: performs linear (w/ a layer norm) uniform attention over the static embeddings
#call_banded_reg.py: runs the regre... |
c83b81a89b74e0301ffebc71203db390bc7ac97cb9c7a0a706786e75e0191898 | Shell | 3,280 | 36 | #!/bin/env bash
#SBATCH --job-name=train10fix_MULTIECHO
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=18
#SBATCH --mem-per-cpu=12G
#SBATCH --time=12:00:00
#SBATCH --mail-user=toby.constable@monash.edu
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH --export=ALL
#SBATCH -A kg98
#Copy over mflirt
for sub in $(ca... |
f649422dc63dd42f44ae84ec83f52b82773b64865a22eca94849206faa0417c5 | Shell | 3,292 | 46 | #!/bin/env bash
s=$1
if [ ! -f /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/Multiecho/ME-ICA/FIX/Confounds/sub-${s}/merged_csf_wm_gm_confounds.csv ]; then
module purge
module load fsl
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
#... |
d9060a685df670052f9b1d273e7d897c1fc9dcd3fae3e376455963fdc52bc97d | Shell | 3,313 | 97 | #!/bin/bash
# Download latest version from website.
echo "Downloading source."
#cctools="cctools-6.2.10"
version="6.2.10"
cctools_src="cctools-$version-source"
rm -rf $cctools_src $cctools_src.tar*
wget http://www3.nd.edu/~ccl/software/files/$cctools_src.tar.gz
echo "Extracting archive."
tar xzf $cctools_src.tar.gz
cd... |
6781900916a22321479e7a422fe76c40d585bb8469610ce8b4604dd71a2c1be5 | Shell | 3,336 | 68 | #!/bin/bash
#This is ran from the command line in my work directory
#IMPORTANT NOTE - inclusion/exclusion criteria changes from MBBP634. Manually remove MBBP634+ for medication naive cohort.
source /home/tconstab1/kg98_scratch/Toby/python_venv/bin/activate
module load xnat-utils
#Delete old sublists, generate new sub... |
1d9a8e9247937a28572ad0771f825de1b8048717622bf81f6957c620e4c2617f | Shell | 3,343 | 59 | #!/bin/env bash
s=$1
module load fsl/6.0.1
#Spatial smoothing PRIOR TO MELODIC
#Create a dummy melodic file
#NOW run MELODIC
#run fsl FEAT thru GUI for one sject - incl brain extraction - set everything else to 0 - run melodic thru FEAT for a single sject. You are then given a .fsf file - replace the sject name for th... |
ccb2b383ec11117a304102c7cb0eed7eda84da9fde58f2261d77ca1641532c5f | Shell | 3,392 | 59 | #!/usr/bin/env bash
set -euo pipefail
# Make Source Data File.
RESULTS=/oak/stanford/groups/menon/projects/branigan/2023_abcd_glm/results
# Figure 3
mkdir -p $RESULTS/taskfmri/Source_data/Fig3
cp $RESULTS/taskfmri/more_second_level/permutations/2025_07_26/between_subjects.csv $RESULTS/taskfmri/Source_data/Fig3
cp ... |
f3f680cf21ef06e4da035738aadb388459661fc31610e2a617bdd18078ee7478 | Shell | 3,403 | 61 | #!/bin/env bash
#SBATCH --job-name=SE_Step2
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=25
#SBATCH --mem-per-cpu=16G
#SBATCH --time=15:30:00
#SBATCH --mail-user=toby.constable@monash.edu
#SBATCH --mail-type=FAIL
#SBATCH --mail-type=END
#SBATCH --export=ALL
#SBATCH -A kg98
fmriprep=/home/tconstab1/kg98_scratch/Toby/WHOL... |
937a145f22c05504b6e6a4bf510e1bcddda86a6bc69c0a748c736961a7f30cb8 | Shell | 3,441 | 202 | #!/bin/bash -e
# Bash shell script to run mrtrix_connectome
#
# Requires docker
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
# 07/09/2021
version="0.1"
kul_main_dir=`dirname "$0"`
source $kul_main_dir/KUL_main_functions.sh
cwd=$(pwd)
# FUNCTIONS --------------
# function Usage
function Usage {
cat <<U... |
f1e858a83c6e192fc14badff65e5e6de9bff60f50b6c92584e6f2597543efdd8 | Shell | 3,453 | 95 | #!/bin/bash
#==========================================================
# voxelwise_snr.sh
#
# Compute voxel-wise SNR map for a T1-weighted image using:
# Smoothed Image Substraction technique (McCann et al., 2013)
# "This method has been formulated as an alternative to existing
# single-image approaches. It eliminate... |
79f37fae7c3a9e5d5091427c3a0924f2affe028772519bef4173fa247de3a594 | Shell | 3,536 | 139 | #
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# Library of BASH function. Please import using
#
# source "$TOOL_BASH_LIB"
BASHLIB___SHELL_OPTIONS=$(set +o)
set +o verbose
set +o x... |
34eaca497b766ecefe780f51c1353f12119a82857728d9d21408e0f7693a208e | Shell | 3,560 | 98 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
32fa83ea6d899b3cf8ba68c50b71f7370f5f69c09168e128c3bb06117aa7ef1e | Shell | 3,572 | 49 | #!/bin/env bash
s=$1
if [ ! -f /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/Multiecho/ME-ICA/FIX/Confounds/sub-${s}/merged_csf_wm_gm_confounds.csv ]; then
module purge
module load fsl
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
#N... |
5e5e6c8a59fe58aefca85fbae0c52de94d5c108e9ead3f6bf694014e1a7d4d24 | Shell | 3,592 | 112 | #!/bin/bash
#
# Creates a summary of information of the BIDS directory
# Information gathered is:
# - subjects
# - sessions
# - available data (T1w, T2w, FLAIR, func, dwi)
#
# Requires Mrtrix3
#
# @ Stefan Sunaert - UZ/KUL - stefan.sunaert@uzleuven.be
#
# v0.1 - dd 16/02/2019 - alpha version
v="v0.1 - dd 16/02/2019"... |
c2a4a1bed3ef3629010ecfbba446335508caea0208a3402cc9c0130a940addfa | Shell | 3,605 | 74 | #!/bin/bash
m=$1
echo "Defining FSLDIR"
FSLDIR=/opt/fsl-6.0.2/
cd /anat_dir
# Extra parameters
StandardImage="$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz"
StandardMask="$FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz"
# Image List
imageList=$(ls -1 *"${m}"*.nii.gz)
num_scans=$(ls *"${m}"*.nii.gz | wc -l)
e... |
18cff74ab638ab60e9c58d37854d2f05e736391d7913189b2699b0b1ee81634b | Shell | 3,627 | 52 | #!/bin/env bash
s=$1
if [ ! -f /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/Multiecho/NO_ME-ICA/AROMA/Confounds/sub-${s}/merged_csf_wm_gm_confounds.csv ]; then
module purge
module load fsl
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/... |
3555e7d9790549b1430b4491db7c3fa58fb73fd814814a7381921dc862c48ff1 | Shell | 3,638 | 51 | #!/bin/env bash
s=$1
if [ ! -f /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/Multiecho/NO_ME-ICA/FIX/Confounds/sub-${s}/merged_csf_wm_gm_confounds.csv ]; then
module purge
module load fsl
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest... |
46e678ecb4a22d1183473cc99a41b641b6bb77f2b49f9c1c988c542e9bf8c32e | Shell | 3,646 | 127 | #!/bin/bash
echo
echo '****************************************'
echo '*** NeuroMiner ***'
echo '*** SGE joblist manager: ***'
echo '*** Preprocess features ***'
echo '*** (c) 2022 N. Koutsouleris ***'
echo '****************************************'
echo ' ... |
8ccfe8b79f7ea3831e365297d915942edc169f90e77d591e8bf6ac5f41030603 | Shell | 3,653 | 103 | #!/usr/bin/env bash
# PLEASE NOTE: This script has been automatically generated by conda-smithy. Any changes here
# will be lost next time ``conda smithy rerender`` is run. If you would like to make permanent
# changes to this script, consider a proposal to conda-smithy so that other feedstocks can also
# benefit from... |
69f9d34eb9e48d4fd735af62057077a3bc75f84fdd938123af1eb0b0fd2c7147 | Shell | 3,654 | 126 | #!/bin/bash
echo
echo '****************************************'
echo '*** NeuroMiner Elessar DEV ***'
echo '*** SGE joblist manager: ***'
echo '*** Preprocess features ***'
echo '*** (c) 2017 N. Koutsouleris ***'
echo '*** Updated Jun2021: Dom and Riya ***'
echo '********... |
9e256ddb3a9c1f5c8c5c10bd293a9c83581a373c3516a24ba74945b51320d92b | Shell | 3,727 | 124 | #!/bin/bash
#SBATCH --job-name=metaprofiles
#SBATCH --mem=64GB
#SBATCH --time=8:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=16
#SBATCH --mail-type=ALL
# Activate conda environment with deepTools
conda activate snakemake # Adjust to your environment name
# Set WORKDIR to your CUT&TAG analysis directory
WORKDIR="" # e.g... |
b839cd9afbf5b0bc37ebc541355a2e09cb1a37d388813ca1d4219cf32f4713bb | Shell | 3,745 | 127 | #!/bin/bash
# Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
8fd969b276e8d5e3ae84e12db23372c32ead0ed7141ab0a532598a4136fe4de2 | Shell | 3,758 | 53 | #!/bin/env bash
s=$1
if [ ! -f /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/Multiecho/ME-ICA/AROMA/Confounds/sub-${s}/merged_csf_wm_gm_confounds.csv ]; then
module purge
module load fsl
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest... |
bdc1b7de06c5618d70b680690b4ac0286ca4b3a7662c9dfb1ad47dbe92235a45 | Shell | 3,798 | 54 | #!/bin/env bash
s=$1
if [ ! -f /home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/PipelineComparisons/Multiecho/NO_ME-ICA/NO_AROMA_or_FIX/Confounds/sub-${s}/merged_csf_wm_gm_confounds.csv ]; then
module purge
fmriprepDir=/home/tconstab1/kg98_scratch/Toby/WHOLEMBBP/workspace/derivatives/fmriPREP_pepolar/rest
... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.