sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2b1349e07f883dc40fefcad8762b2c449a3d9ef86b51127683da0cb35d884017 | Shell | 3,933 | 114 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
8b8919014640d4e86d522f0dc602ad6f0ebe69e7e086e026b9f38d4ae552c9f1 | Shell | 3,933 | 90 | #!/bin/bash
###########################################################
### Proofread-restricted NBLAST redo across all datasets
###
### Goal: lift FAFB / MaleCNS / MANC / FANC / hemibrain / LR
### / native NBLAST coverage of BANC v888 by re-running every
### `proofread == TRUE` neuron with redo=TRUE, then compile
### ... |
5e4aca316af36ab6892c1959354a3ec15c189a5b44e4b35ea7eadf60490a22f5 | Shell | 3,947 | 68 | #!/bin/bash -e
echo "Do not use this script. Use the python colabfold_search instead"
exit 0
set -x
export OMP_NUM_THREADS=100
MMSEQS="$1"
QUERY="$2"
DBBASE="$3"
BASE="$4"
DB1="$5"
DB2="$6"
DB3="$7"
USE_ENV="$8"
USE_TEMPLATES="$9"
FILTER="${10}"
THREADS="${11}"
SENSITIVITY=8
EXPAND_EVAL=inf
ALIGN_EVAL=10
DIFF=3000
QSC... |
e86652464027bc2ec697f901a5435c5d0ed84adcc509926e847406c07d8ea22f | Shell | 3,950 | 125 | #!/bin/bash
echo ""
echo "This script is the main tool for computing brainAge. We are expecting as input a 3D FLAIR in NIFTI format (nii or nii.gz) and the biological age."
echo ""
echo "Execution: $0 main_filename.nii.gz 35"
echo " "
source /opt/conda-p3.9/etc/profile.d/conda.sh
source ${FSLDIR}/etc/fslconf/fsl.sh
e... |
8eba5384c2d7d21d7093f88873c0fcacbb96719add2ab4b0365bfe02ee189458 | Shell | 3,958 | 118 | #!/usr/bin/env bash
set -euo pipefail
# ------------------------------------------------------------
# Striatum atlas (MNI152NLin6Asym) -> subject native T1w space
# Reference grid = T1w-space BOLDREF (matches FEAT/EPI resolution)
# One transformed mask per subject to ./masks
# ----------------------------------------... |
e97e2ec1bd8a39d566ffbd4e153398c4732d9e3971d4caaf739e5dee2c68e491 | Shell | 3,958 | 123 | #!/bin/bash
SERIES=$1
if [[ -f $SERIES.urls.list ]]
then
>&2 echo "WARNING: File '$SERIES.urls.list' exists! This should not happen; overwriting the file.."
rm $SERIES.urls.list
fi
for i in `cat $SERIES.run.list`
do
TYPE="SRA" ## we always default to SRA. This could cause problems for very fresh datasets.
... |
5fe49a6fe1d6dc2ede6357b6d06418e704de0823d8c23edec458876e4651d041 | Shell | 3,967 | 121 | #!/bin/bash
####################################################################################################################################
# run_4_nonlinearRegistration.sh
#
# Performs nonlinear registration of preprocessed brain images to a resolution-matched MNI152 template
# using ANTs. Registration proceeds i... |
48325b16290ff4540a4f2497480ad2098e1f691ea74526c22f40bb05a4d323d5 | Shell | 3,968 | 132 | #!/usr/bin/env bash
set -euo pipefail
# ============================================================
# Make non-promoter windows (CLI version)
# Usage:
# bash make_nonpromoters_cli.sh \
# --workdir /path/to/raw1 \
# --species human,mouse_mm39 \
# --windows w2k1k,w1k1k,w3k1k
# ================... |
83dad44fc37241a70542effd44c3d16284ee0891f13a91755e98b5706a245c10 | Shell | 3,968 | 102 | #!/bin/sh
# /media/StorageOne/HTS/VirusMeta/SAM_BAM/HBB_test/circos_pipeline_v2.sh /media/StorageOne/HTS/Projects/2013_H5_RNA-NMSC_v3 /media/StorageOne/HTS/Projects/2013_H5_RNA-NMSC_v3/CaskiRNA.read1.fastq.gz /media/StorageOne/HTS/Projects/2013_H5_RNA-NMSC_v3/CaskiRNA.read2.fastq.gz
##########################
export pr... |
b4d712fe02717d0119fcf64fd2189c9f4c6e1c84bc1bb5f73919cac12642289c | Shell | 3,974 | 113 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script creates a new VCF file by extracting a set of N variants from a
# given Funcotator-annotated VCF file of each type of VA... |
fef211e1be0d4b81d0106e1661cdc2e3fabc6b42b48dff61772690ccd64ba29c | Shell | 3,977 | 128 | #!/usr/bin/env bash
set -euo pipefail
usage() {
echo "Usage: $0 [--dry-run] OWNER/REPO SHA"
echo "Rerun failed jobs for a commit; skip if checks are pending or a failed run"
echo "has exhausted MAX_RETRIES (default: 3, excluding the initial attempt)."
}
if [[ $# == 1 && ( "$1" == --help || "$1" == -h ) ]]; then... |
a15053f67166667e1d6079237f1692bbbcd556a5c8a970c4471975232e12d64c | Shell | 3,978 | 107 | #!/bin/bash
#SBATCH --job-name=soMAPHIFI
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=250G
#SBATCH --error=joblog_error_mapHiFi_%A_%a.txt
#SBATCH --output=joblog_output_mapHiFi_%A_%a.txt
#SBATCH --array=0-1
#### source library
path_script="/gpfs/scic/da... |
92713a000dac4dca69ccf11e1c4b857f03ba353bc65f632b8468d49689d78adf | Shell | 3,979 | 78 | #!/bin/bash
tools_dir=$(realpath $(dirname $(command -v $0)))
[[ -d $tools_dir/pkg/mcr ]] && rm -rf $tools_dir/pkg/mcr
mkdir -p $tools_dir/pkg/mcr
pushd $tools_dir/pkg/mcr > /dev/null
# check the USER's MATLAB_VERSION from env file
[[ -f $tools_dir/../.env ]] && export $(grep -v '^#' $tools_dir/../.env | xargs)
if [[... |
d20ea2a29e23373614e90f010d15b1f31f1026c03d175868d5e26ea470a89457 | Shell | 3,989 | 103 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO IMAGE REGISTRATION (FLIRT/FNIRT)
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATIONS*****!!!!!
##
## R-fMRI master: Xi-Nian Zuo. Dec. 07, 2010, Institute of Psy... |
8f819c129f11b7c16b97e73a424e5b73c5807022f2c5dca652c91b2e4cb44eb8 | Shell | 4,014 | 100 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=GATK
#SBATCH --ntasks=50
#SBATCH --cpus-per-task=4
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=30G
#SBATCH --chdir /data7/WGS_processing/src # TODO: set dir to project dir
#SBAT... |
bc6e71f9b331969debed1fe204b623fbb734495b563178cbc3463086535d6551 | Shell | 4,016 | 35 | # ------------ 1. 没有inverse-------------
#CUDA_VISIBLE_DEVICES=4 python train_snn.py --model AVresnet18 --node-type ReLUNode --dataset KineticSound --epoch 100 --batch-size 32 --num-classes 31 --step 1 --modality audio-visual --alpha 0.8 --modulation OGM_GE --fusion_method concat --seed 2025 --inverse --output ./exp_jo... |
42504c9ad743adfbabb04229dccbb58e6d1fa65ecd5242ee136b9da627314957 | Shell | 4,024 | 112 | #!/bin/bash
nline_per_set=2000
if test $# -ge 1; then
nline_per_set=$1
fi
rm -fr set.*
echo nframe is `cat box.raw | wc -l`
echo nline per set is $nline_per_set
split box.raw -l $nline_per_set -d -a 3 box.raw
split coord.raw -l $nline_per_set -d -a 3 coord.raw
test -f energy.raw && split energy.raw -l $nline_... |
9e524f3b25feb717488287fa08016df22a587459420fb1b1d9a6ce45848d0cae | Shell | 4,033 | 117 | #!/bin/bash
# precon_all logging utilities — sourced from surfing_safari.sh
# Provides: full log + timestamped event log, run_step wrapper, summary.
# Does NOT modify behaviour of underlying scripts.
# ---------------------------------------------------------------------------
# Setup. Call once at the start of surfin... |
18683dadcf1b7d2a5ed21d105816599b56e5952b2d96f7912315b0c53bdefbdb | Shell | 4,041 | 122 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# retrieve input argument to find correct instructions
instructDir="$1"
# ------------------- #
# GENERAL DEFINITIONS
# ------------------- #
source $MRCATDIR/setupMrCat.sh
structRootDir="/Vo... |
7cf1c31af309fd31ca85ca8f08eb8a22316bd72bc6befe485dc88d6ae4b61256 | Shell | 4,045 | 95 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script runs Oncotator and will process the output files so that they can
# be ingested by `makeComparisonForOncotator.sh` to com... |
0dabe75be97107577f62394b5a310f3c1dd985f42916c6bd66f62a82eed23620 | Shell | 4,060 | 144 | #!/usr/bin/env bash
### REGENIE TEST SCRIPT
## For version<1.0.5.6, will get error if WITH_GZ is set since option '--gz' did not exist
info_msg="Usage: ./test_bash.sh OPTIONS\n"
info_msg+=" --path path to Regenie repository\n"
info_msg+=" --gz Flag to specify compilation was done with Boost Iostream library\n"... |
17877b0d150b9a640b9cb70e9b34056cf91a3266e2fb063759526e2c94ba5df8 | Shell | 4,060 | 100 | #!/bin/bash
set -u
usage() {
echo "Usage: $0 --version <finngen_tag> [--image <name>] [--push] [--registry refinery|sandbox] [--base-regenie-docker <image>]"
echo " --version required. Suffix appended to regenie's own VERSION file to build the pushed tag (e.g. cond_firth)"
echo " --image ... |
86eacded90d6fee5b7634bae63797ae843353973ed319645c6f0e1bb04f1e3a5 | Shell | 4,063 | 112 | #!/bin/sh
# This function replicate the kernel ridge regression results in the GSP dataset shown in Li et al., 2019
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################
# setup for CIRC cluster
########################
curr_dir=$(pwd... |
7cb6a87be8c607690c9a99af09913ff5176e77f22a4b02a485fea07cc50611fa | Shell | 4,069 | 94 | #!/bin/bash -e
## v3.1 of STARsolo wrappers is set up to guess the chemistry automatically
## newest version of the script uses STAR v2.7.10a with EM multimapper processing
## in STARsolo which on by default; the extra matrix can be found in /raw subdir
SIF="/nfs/cellgeni/singularity/images/starsolo_2-7-10a-alpha-... |
94f2db7ce8ddd45a8e5614b76dc015b616da23cb7bc3f3bc47c3583fdb056a4f | Shell | 4,069 | 128 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# cut out the first n seconds (default: 10) until a steady state of radio-frequency excitation
# ------------------------------ #
# Help
# ------------------------------ #
usage() {
cat <<E... |
411c00975a9778918ddffe9f292650d71f3c580c6330e2222a003e97b154b4a1 | Shell | 4,071 | 83 | set -e
# To run these tests do
# ./tests/tests.sh <license_key>
# Test device type selection function
pytest -v tests/test_device_type.py
# Test config helpers
pytest -v tests/test_config.py
# Test task registry + totalseg_info command (no GPU/model needed)
pytest -v tests/test_registry.py
# Smoke test the introsp... |
85cf5fb97491b97c45c07fd0a93c6317229e636e7aed3e3d90a6e35387e27f69 | Shell | 4,071 | 102 | #!/bin/bash
#SBATCH -c 12
#SBATCH -t 0-11:59
#SBATCH -p short
#SBATCH --mem-per-cpu=10G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_cosine_v888v2_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_cosine_v888v2_%j.err
###############################################################################
# Whole-brai... |
4c0d189a664207b32b7c1ff9ad1c1130f73683175cf175b879ae56b7ddc9a882 | Shell | 4,084 | 113 | #!/bin/sh
# Note the current bldnrnmac.sh build script I use to prepare a pkg
# distribution is included at the end of this file
# assume InterViews sources in $HOME/neuron/iv
# assume NEURON sources in $HOME/neuron/nrn
# assume that you are using a Terminal window
SOFT=$HOME/neuron
# if configure does not exist in... |
4f8e042040a6ad1bfcffbf3699e7fafb72441b32dd933298e7c49b00f711c4f9 | Shell | 4,086 | 91 | #!/bin/bash
#numbers=(1 2 4 12 14 17)
numbers=(4)
for num in "${numbers[@]}"; do
echo "Sample 4: AHA $num"
python /mnt/d/Code/HeartModelling/generateSimFiles/genS2AHA.py \
--filePath /mnt/e/Paper4/Simulations/invivo/mi_EHT2_highcond/sample4/settings_mi_CL600_1800ms_stimAHA${num}_first3beats.json \
--outPath ... |
1109e9d53dc721bbc8ce5aa1fc7feaed0e0ce93e837fe67bb3012292f6436963 | Shell | 4,089 | 114 | #!/usr/bin/env bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
# study-specific inputs
sm=0 # check templates to ensure no additional smoothing is being applied
sub=$1
ses=`ze... |
416dc36a78022be55a2b1a3ef1b8763bcee517dce9e3f190e2a8e35590872e7d | Shell | 4,096 | 111 | #!/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 "Licen... |
2c931f7122c925791444bfbde0d5acf136f8e58a61de9151d4ddd55a137088d3 | Shell | 4,113 | 91 | #!/bin/bash -e
## v3.1 of STARsolo wrappers is set up to guess the chemistry automatically
## newest version of the script uses STAR v2.7.10a with EM multimapper processing
## in STARsolo which on by default; the extra matrix can be found in /raw subdir
SIF="/nfs/cellgeni/singularity/images/starsolo_2-7-10a-alpha-... |
5e21a367797263df353830188d03a49f05766f1596424efb8e91edcb729c37b9 | Shell | 4,116 | 183 | #!/usr/bin/env bash
# This script runs through the code in each of the cpp examples.
# The purpose is just as an integration test, not to actually train models in any meaningful way.
# Optionally specify a comma separated list of examples to run.
# can be run as:
# ./run_cpp_examples.sh "get_libtorch,run_all,clean"
# ... |
0362c7cee917d853742861a73c159e2dd97b52d39ddba93598e510a9ce47428c | Shell | 4,123 | 123 | #!/bin/bash
# Copyright (c) Meta Platforms, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# Conda build script for habitat-sim (scikit-build-core).
#
# Build options are passed via environment variables that map to ... |
730689ad161912dd905605fd63b319e87c4ee28c2390dc810da56341775d4d91 | Shell | 4,127 | 83 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
63e36f177e5b19f57f138fcc7ade976a357a5054c6e3503c01d9a5cba14146b8 | Shell | 4,129 | 112 | #!/usr/bin/env bash
# Smoke test: venv, (optional) pip install -e ., path checks (+ optional LEGUS download), run_pipeline --check-only.
#
# Usage (Gadi login — has outbound internet for pip):
# bash scripts/hpc_login_smoke_test.sh
#
# Gadi compute nodes usually have NO internet → pip cannot reach PyPI (errno 101).
#... |
d297dd8fc8c73691a7ac38005474ae98758f6dd82003376b910bc89a8d29e068 | Shell | 4,163 | 82 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
a34d0e2d294b8a582f670ea21624d4888f5beb47d6cdb2370d296eba269aa0db | Shell | 4,168 | 140 | #!/usr/bin/env bash
set -euo pipefail
IFS=$'\n\t'
###############################################################################
# CONSTANTS
###############################################################################
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
readonly MOTIF_FILE=... |
c0840998f09935ce846bbf06c1a7485dddf76bedd4827187fb2a254befb536ef | Shell | 4,170 | 167 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script will create a table comparing two internally configured reference
# dictionary files.
# It must be internally configured ... |
1fcb3530cbc7642f946b95b24d442219b28e1e1d4aecec7f0fb5a5b74e6f69ba | Shell | 4,192 | 156 | #!/bin/bash
top_level=$(git rev-parse --show-toplevel)
branch=$(git rev-parse --abbrev-ref HEAD)
version=$(git describe --always --tags --match "Release_*")
case $(uname) in
Linux)
;;
*)
# install the required packages into a venv
uv venv --allow-existing --python 3.11 --managed-python "$top... |
48bd09b4b30b217a3a58c4618f26854de4c91a7ce5ebb1baee17748c75b8b3d9 | Shell | 4,193 | 121 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2015 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
e224718b7bff308f155fa00f5bdb833ebe4dcf09182ffcede1e56c8f6c9741ec | Shell | 4,193 | 130 | #!/bin/sh
#####
# This wrapper script submits job to the schduler to run the specified type of regression, using
# the specified input FCs. These scripts are for the HCP dataset.
#
# Input:
# -regression:
# The type of regression to use. Can be "KRR" or "LRR".
# Append "_sh" for the split-half analysis us... |
880d3862bb3f87d59c984ad7055e3366380fede4eb15dfb6e7a45823a203ec91 | Shell | 4,195 | 79 | #!/bin/bash
#####
# This script projects parcellations to the native volume space and converts them to a mif format.
#
# Written by Leon Ooi and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#####
###############
# set up environment
###############
parcellation=$1
parcels=$2
expo... |
bfd5305966d4f5b3f2f5df5574fcef9292b78325e3003c03afa00dcab9930501 | Shell | 4,196 | 126 | #!/usr/bin/env bash
set -e # stop immediately on error
# ------------------------------ #
# usage
# ------------------------------ #
usage() {
cat <<EOF
rotbvecs.sh: apply a rigid-body rotation to a list of b-vectors. This allows you
to rotate your bvecs along with the same transformation of the "raw" diffusion... |
d74a2c5415fb123908db73f33a2446051720c51f2a78ad92b3a0d814b60eee17 | Shell | 4,197 | 88 | #!/bin/bash
set -e # Stop on error
install_ucsc_tools_369() {
# takes in conda env name and find conda bin
CONDA_BIN=$(conda run -n $1 bash -c "echo \$(dirname \$(which python))")
curl -o "$CONDA_BIN/fetchChromSizes" "https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/fetchChromSizes"
curl -o "$CONDA... |
73284298952c978e6222cefc1336570365852be6e031d4f16f24127cf223e187 | Shell | 4,204 | 80 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
16921a3134b210c3b447fb68d162f86489813bb53569acc04e962838f366a9a5 | Shell | 4,239 | 160 | #!/bin/bash -e
#/*
#* SVRTK : SVR reconstruction based on MIRTK
#*
#* Copyright 2018-2020 King's College London
#*
#* 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.apac... |
a071f8f1d92ccba024c2450945ffa9ed94688c8272a22b9c5da6e0f68ee2c7ea | Shell | 4,258 | 84 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
a8abc4db5057cfd1025b35f92b2d128013c8a7f1e7710a0db902897ce5a9ed98 | Shell | 4,265 | 174 | #!/bin/bash
set -e
# Install MIES with potentially skipping the hardware XOPs. The installation is
# either done from the git repo, from the release package or the installer itself.
usage()
{
echo "Usage: $0 [-x skipHardwareXOPs] [-s [git|release|installer]]" 1>&2
exit 1
}
skipHardwareXOPs=0
sourceLoc=git
whil... |
9eca86018ef6928a78f6af199c4fb644487b013cd373576764a95d1bd2dd590a | Shell | 4,269 | 91 | #!/bin/bash -e
## v3.1 of STARsolo wrappers is set up to guess the chemistry automatically
## newest version of the script uses STAR v2.7.10a with EM multimapper processing
## in STARsolo which on by default; the extra matrix can be found in /raw subdir
SIF="/nfs/cellgeni/singularity/images/starsolo_2-7-10a-alpha-... |
79e7efb4dbf25f0c7a71962cf89a09cc2f329a089c743de17fe421926570d829 | Shell | 4,278 | 157 | #!/bin/bash
echo "" > /tmp/temp.tmp
idir=/Applications/NEURON-7.7/nrn
#for testing on linux
#idir=$HOME/neuron/nrnmpi
#function osascript() {
# echo "osascript $1 $2 button returned:Yes" >> /tmp/temp.tmp
# echo "button returned:Yes"
#}
#Use .bashrc if it exists, otherwise .bash_profile
#also add to .cshrc, .tcshr... |
163ff920db719853470762329a1ac02590fe6ded9df0c187159aed060fe31b69 | Shell | 4,280 | 110 | #!/bin/bash
#
#This is a shell program to batch reconstruct images using 9 different methods from LCMboost.
#
function write_neuron_tracing_command {
outputScript=$1;
METHOD=$2;
vaa3dProgramPath=$3;
inimgfileTracing=$4;
finalfileFolder=$5;
smooth_inimgfileTracing=${inimgfileTracing}.g.v3draw;
#LCM_boost... |
4db21b926abcf0f47ce8a9a90740e1e9644128d094b0e789ba8eb9d0f318e349 | Shell | 4,291 | 93 | #!/bin/bash
## this is a master script for one-pot download and processing of a 10x dataset
## in case of a particular sample not being recognized as 10x, fastq files would be gzipped (if necessary) and left alone;
## for now, tested use cases would be limited to a GSE (GEO series), E-MTAB (AE series), and a PRJ (Bi... |
4642c1a5a098330ae9436360ca5dd76464e82dc1d65fc724174d40cc65d761e4 | Shell | 4,299 | 96 | #!/bin/bash
# Written by Yapei Xie and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# Wrapper for MATLAB functions: extract combat cog, stability, Cohen's d, sex-stratified stability, sex effect
# source config
source ${CBIG_CODE_DIR}/stable_projects/predict_phenotypes/Xie2025_LBC... |
aace7b6dd51d6fa8129aa998bfdb5aaaea258eb30669d96552a157e114477346 | Shell | 4,300 | 78 | #!/bin/bash
# Copyright (c) Meta Platforms, Inc. and affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# NOTE: run this script from habitat-lab/ directory
# TO PLOT RESULTS SEE RUN `python scripts/hab2_bench/plot_bench.py`
mkdir -p ... |
5196c6072f2bf86874d0c7dac50c4f0be982358e09bdde5f8c5d2f1522bb4972 | Shell | 4,309 | 143 | #!/usr/bin/env bash
set -euo pipefail
usage() {
cat <<'EOF'
Usage:
run_cross_dataset_evaluation.sh [--skip-predict] <source_dataset_name> <target_dataset_name> <trainer> <nnunet_root> [config] [fold]
Arguments:
source_dataset_name Training dataset name, for example Dataset2154_mind_remap.
target_dataset_name... |
8474ca1396f6ec8dd9be2cca0152f2aee152f22f3070b9582e40e28d2b59affa | Shell | 4,311 | 105 | #!/usr/bin/env bash
##########################################################################################################################
## SCRIPT TO RUN GENERAL CCS ANATOMICAL PREPROCESSING
##
## This script can be run on its own, by filling in the appropriate parameters
##
## Written by the R-fMRI master: Xi-N... |
44a11234b8ed5153b5bb3ac04130823bc8866149082af778443ff73c7aad8e1e | Shell | 4,312 | 81 | #!/usr/bin/env bash
# Author: Bram Van de Sande
# Latest update: 18 DEC 2018
# Outline: This script tests the command line interface of pyscenic.
# Prerequiste: The python package needs to be installed in the currently active python environment.
DATA_FOLDER="./cli_test_data/"
CORES=6
DB_FOLDER="/Users/bramvandesande/... |
b6bb081bd0be0bc0577b87164bfae1aa2a88cf5e57426eff80faf9cf38468392 | Shell | 4,341 | 119 | #!/usr/bin/env bash
# This script takes a bam (plus context), rolls back the effects of MarkDuplicates and BQSR, and runs the BAM
# through Picard/GATK 3 and GATK 4 and compares the legacy results with GATK 4.
#
# This requires that PICARD_JAR and GATK3_JAR be set.
#
# Example usage
# ./validate-reads-spark-pipeline.s... |
03be67a6e2c1b99b934af25e501c83cdf6f626f736cf06a5382fd360c8aad61c | Shell | 4,344 | 93 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO GENERATE THE GROUP AVERAGE T1
##
## Modified by R-fMRI master: Xi-Nian Zuo. Dec. 07, 2010, Institute of Psychology, CAS.
## Email: zuoxn@psych.ac.cn.
##
######... |
068150679eefe7f675eb1540fe8cfdc0401584238c54950fe029270a8263684b | Shell | 4,349 | 76 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO FINAL PREPROCESSING STEPS OF RESTING_STATE SCAN
##
## R-fMRI master: Xi-Nian Zuo.
## Email: zuoxn@psych.ac.cn or zuoxinian@gmail.com.
######################... |
81e1372ec4565ad5a6d405ae7d81d238fcbf671168d41b3e257a7614b181d4f9 | Shell | 4,356 | 114 |
#!/bin/bash
#PBS -l walltime=12:00:00
#PBS -N L2stats-t1w
#PBS -q normal
#PBS -m ae
#PBS -M matt.mattoni@temple.edu
#PBS -l nodes=1:ppn=14
# load modules and go to workdir
module load fsl/6.0.2
source $FSLDIR/etc/fslconf/fsl.sh
cd $PBS_O_WORKDIR
umask 0000
# ensure paths are correct
shareddir=/gpfs/scratch/tug87422/... |
136fa6fa3b9e70be62768c373675c545643dc4d1bfcac0ee19fa40dc6fa2fc7d | Shell | 4,364 | 103 | #!/bin/bash
export project_work_dir=$1
export PB_dir=$2
cd $PB_dir
echo 'nt_final<-read.csv("nt_final.csv")
write.table(nt_final[,c("Queryid","Division")],"tmp_nt_final.txt",row.names=F,col.names=F,quote=FALSE, sep="\t")
' > tmp_nt_final.R
R CMD BATCH --no-save tmp_nt_final.R
awk -F"\t" '{if($2 == "Human") {print $... |
9ac2c273f25282e39b8fe7f3f585f5ed592ce9bf4ca94b1cb6a01b06164c5d97 | Shell | 4,366 | 103 | #!/usr/bin/env bash
# fetch_sociopatterns.sh
# =====================================================================
# Récupère le jeu de données SocioPatterns "Primary School" depuis la
# source officielle, conformément à la licence CC BY-NC-SA 4.0.
#
# LICENCE : CC BY-NC-SA — usage non commercial uniquement.
# Ne PAS... |
6d991b24e5a55de518dfc76d09d48600e360c1d8341e0e7c00ed5d1ff220991b | Shell | 4,375 | 101 | #!/bin/bash
#SBATCH --job-name=soYAHS
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=250G
#SBATCH --error=joblog_error_yahs_%A_%a.txt
#SBATCH --output=joblog_output_yahs_%A_%a.txt
#SBATCH --array=0-2
#### source library
path_script="/gpfs/scic/data/projec... |
b3a212e99603466c7c414fc8193ec90910269a0f1096d12f6a0a1ed26d7b228e | Shell | 4,375 | 128 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script processes files created by Funcotator and Oncotator to create
# output files that can be diffed by Beyond Compare (or yo... |
2757cf549fba7859cdb10a9ef79edfab5f027fcde98b19ca0c4b7db3cceebaae | Shell | 4,382 | 130 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# retrieve input argument to find correct instructions
instructDir="$1"
# ------------------- #
# GENERAL DEFINITIONS
# ------------------- #
source $MRCATDIR/setupMrCat.sh
origDir="/Volumes/... |
bf27ced94bcb873b7ce7f858c7a7421b1da24bf6596046b193fdf15a2775a5f5 | Shell | 4,385 | 139 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
# parse the input arguments
flgPurge="FALSE"
for a in "$@" ; do
case $a in
-f|--force|--purge) flgPurge="TRUE"; shift ;;
-e=*|--example=*) example="${a#*=}"; shift ;;
*) unknown="$unknown $a"... |
dbd589f35f5b6f703b69d7acd60b64387a0639139349151c6fa0760f420858eb | Shell | 4,387 | 113 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO SEGMENTATION OF FUNCTIONAL SCAN
##
## R-fMRI master: Xi-Nian Zuo at the Institute of Psychology, CAS.
## Email: zuoxn@psych.ac.cn
## References:
## [1]. Bis... |
d7f25236335824a50ebf8ed9465297d083f1696642639c785d50a073bc95f2c4 | Shell | 4,398 | 101 | #!/usr/bin/env bash
set -euo pipefail
# ---- paths relative to this script ----
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
fmriprepdir="${maindir}/derivatives/fmriprep"
# ---- edit as needed ----
#subs=(101 103 104 105)
subs=(103)
sessions=(01 02 03... |
3c5c294b08f305a0ed645c94a97c040a1861e2242c9c253fc5ee85e92008e485 | Shell | 4,420 | 89 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
11f549a0475cab601a9e68e720ac75bf27091402f6211c3e8406654bb38638b2 | Shell | 4,421 | 102 | #!/bin/bash
# Create reference assembly FASTA file (4 chromosomes, 100 bp each)
cat > reference.fasta << 'EOF'
>chr1
ATGCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGAT
>chr2
GCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGCTA... |
21f4b168a0fa576ec05b0e44c28058ccca9391aad68316c0bd1e3b9a11896478 | Shell | 4,421 | 131 | #!/bin/bash
#
#This is a shell program to batch reconstruct images using 10 different methods for the comparison.
#
function write_neuron_tracing_command {
outputScript=$1;
METHOD=$2;
vaa3dProgramPath=$3;
inimgfileTracing=$4;
finalfileFolder=$5;
smooth_inimgfileTracing=${inimgfileTracing}.g.v3draw;
#APP... |
41787972e51c056256f779b321d200fba509d8350b33e5cd3a1e4b74e15617da | Shell | 4,425 | 123 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO CALCULATE SEED-BASED RESTING-STATE FUNCTIONAL CONNECTIVITY
##
## This script can be run on its own, by filling in the appropriate parameters
##
## Written by C... |
81cf4257bf8ab6875af7323f1cc255e648ab0aa02ff4353387a3926568d53f3f | Shell | 4,432 | 126 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# correct the intensity bias caused by RF field inhomogenieties
# ------------------------------ #
# Help
# ------------------------------ #
usage() {
cat <<EOF
rsn_biascorr.sh: Correct th... |
5546e26a9bcbaba1641c3bab104e839eb0439a0cf22968a24b659d5cc3feec8f | Shell | 4,445 | 92 | #Fetch plDDT from predicted structures and analyze results
#########New dimers###########
MODELDIR=/proj/berzelius-2021-29/users/x_patbr/results/af2/new_dimers/af_std_and_hhblits_msas/model_1/recycle_10/
METRICDIR=/proj/berzelius-2021-29/users/x_patbr/results/af2/new_dimers/af_std_and_hhblits_msas/model_1/recycle_10/
... |
21742770f7c5e9baf99a3b79ea7e346e5930feab110a313971e9e0d3410e33ea | Shell | 4,447 | 90 | #! /bin/sh
# This config is used in the process to shrink packages
# by removing redundant files not used in the fMRI preprocessing pipeline.
# In summary, the process involves:
# 1. running fMRI preprocessing unit tests with this config
# and using strace to identify files accessed during execution.
# 2. The ident... |
3b50ab23268cb201f4f160cfcf7538b81ae07b9820bc48a149092da8c7181765 | Shell | 4,455 | 134 | #!/bin/bash
# Script to automatically detect and resubmit failed tasks from a run directory
# Usage: ./resubmit_failed_tasks.sh <run_directory_name>
if [ $# -ne 1 ]; then
echo "Usage: $0 <run_directory_name>"
echo "Example: $0 Run3"
exit 1
fi
RUN_DIR="$1"
CURRENT_USER=$(whoami)
# User specific variables... |
841e6eeb841b7dc593cd51cd56c5984fab178f2762e10f1100a36bf2b9d1654e | Shell | 4,456 | 92 | #!/usr/bin/env bash
# Bash port of filter_hits_regions.py -- same operations, for local testing without python, shaped
# to paste directly into extract_cond_regions's WDL command block (hardcoded inputs instead of a
# CLI, matching how regenie_conditional_bash was inlined). See filter_hits_regions.py for the
# authorit... |
52593c76c9ce4283f88d08b27d3f8d8206bb9adbf610924ae374425f6c646bd5 | Shell | 4,458 | 88 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
3423059461ed84e1aabb45400ae4dab764391c1bbccd246eb81f893c4cecb492 | Shell | 4,459 | 150 | #!/bin/bash
# Launcher for perceive.app on macOS (MATLAB Runtime only; no MATLAB license).
set -euo pipefail
MIN_RUNTIME_YEAR=2023
RUNTIME_LABEL="R2023a or newer"
RUNTIME_URL="https://www.mathworks.com/products/compiler/matlab-runtime.html"
SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
LOG_FILE="${SCRIPT_DIR}/runtime_ch... |
344c8efd9dd300b363ea54d7baf7c178c69d8bb6cd2d2d924daec23e26247d20 | Shell | 4,460 | 100 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=cafe5
#SBATCH --error=error_%x_%j.txt
#SBATCH --output=output_%x_%j.txt
# =============================================================================
# CAFE5 gene family e... |
327ed9279976485795b48a7c4e675a9d06f4d053b8badf133049034ce57ac412 | Shell | 4,461 | 112 | #https://github.com/apetkau/microbial-informatics-2014/tree/master/labs/ffp-phylogeny
#**** How do I implement the block-FFP method mentioned in
#Sims GE, Jun SR, Wu GA, Kim SH. (2009) Alignment-free genome comparison
#with feature frequency profiles (FFP) and optimal resolutions.
#PNAS, 106,2677-82.
#
#There is cur... |
28df4c8c6f9d847f585298e8f7d923766c72faca27dbd1bc1f310750d754c1ed | Shell | 4,464 | 127 | #!/usr/bin/env bash
umask u+rw,g+rw # give group read/write permissions to all new files
set -e # stop immediately on error
# ------------------- #
# GENERAL DEFINITIONS
# ------------------- #
source $MRCATDIR/setupMrCat.sh
studyDir="/Volumes/rsfMRI/anaesthesia"
anaDir="$studyDir/analysis"
mkdir -p $anaDir/map
#... |
e84284f2f76148c42243ab690c27ee193b3f513d662a4d78596463c2bdb7dc26 | Shell | 4,468 | 104 | #!/bin/bash
# combined_cromwell_gcp_sync.sh
# This script extracts outputs from a Cromwell JSON, creating local files.
# It then copies files from specified lists to GCS.
# It supports an optional --test mode, which limits all list file processing
# to the first 10 items. Cromwell outputs are always fully extracted lo... |
bb97427ae75e18185fb230b4d97d6931945e84220f52cbe3d7a0ddefcdd979e2 | Shell | 4,470 | 132 | #!/usr/bin/env bash
#
# Generate base and main Dockerfiles for Nipype.
set -e
USAGE="usage: $(basename $0) [-h] [-b] [-m]"
function Help {
cat <<USAGE
Generate base and/or main Dockerfiles for Nipype.
Usage:
$(basename $0) [-h] [-b] [-m]
Options:
-h : display this help message and exit
-b : generate ba... |
969211ccfe44324dff6eeed9f847bbda9bc116d1fcfcee4bc04322f5ba285aa0 | Shell | 4,477 | 108 | #!/bin/bash
set -eu
if [[ "$#" -lt 6 ]]; then
echo -e "Please provide:"
echo -e " [1] local directory of GATK build (required)"
echo -e " [2] project name (required)"
echo -e " [3] cluster name (required)"
echo -e " [4] absolute path to the output directory on the cluster (HDFS,required)"
... |
9adcb4737f655efc3ba143cd6eeb6cdb87626c7856138f9eff634a485a78f85f | Shell | 4,480 | 131 | #!/usr/bin/env bash
# Reproducible A/B harness for the RAD-input inference phase.
#
# The input RAD is created once and reused, so every arm sees identical packed
# equivalence classes and the measurement excludes mapping. Results are appended
# to results.tsv; quant.sf is retained for bitwise and numerical comparisons... |
cd6c4a22efb1f44ec3857da975fadf005da7117dff98774e0859019548f105ff | Shell | 4,481 | 126 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO CALCULATE SEED-BASED RESTING-STATE FUNCTIONAL CONNECTIVITY
##
## This script can be run on its own, by filling in the appropriate parameters
##
## Written by C... |
46c74d060143b728528d50c3121f0a42aadd240c3a321862ff50b1d89e63d46c | Shell | 4,505 | 92 | #!/bin/sh
# Written by Pansheng Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
## general setup
node_name=$(hostname)
if [ $node_name != 'headnode' ]; then
echo "All replication jobs shoulde be submitted via headnode!"
exit 1
fi
base_dir=$CBIG_CODE_DIR"/stable_projects/p... |
1caf61867c4bd8bb6899c8c08c075d4d01f6ece9e4d605709f0e6e30517edcaa | Shell | 4,524 | 111 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO SURFACE-BASED FUNCTIONAL IMAGE PREPROCESSING (FREESURFER)
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATIONS*****!!!!!
##
## Written by R-fMRI master: Xi-Nian ... |
cda3be5132fd390ba19a3a36182ae6b34cba8acaf4843fdcf7ff0ec4eb0d53c0 | Shell | 4,568 | 155 | #!/bin/bash
# Launcher for perceive on Linux (MATLAB Runtime only; no MATLAB license).
set -euo pipefail
MIN_RUNTIME_YEAR=2023
RUNTIME_LABEL="R2023a or newer"
RUNTIME_URL="https://www.mathworks.com/products/compiler/matlab-runtime.html"
SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
LOG_FILE="${SCRIPT_DIR}/runtime_check.... |
aa867da8fa7a476573ccf85b52ffdf2fd8ff2964e50b0bfb03860f1ff66b7358 | Shell | 4,569 | 132 |
#!/bin/bash
#PBS -l walltime=2:00:00
#PBS -N L2stats
#PBS -q normal
#PBS -m ae
#PBS -M matt.mattoni@temple.edu
#PBS -l nodes=1:ppn=28
# load modules and go to workdir
# module load fsl/6.0.2
# source $FSLDIR/etc/fslconf/fsl.sh
cd $PBS_O_WORKDIR
umask 0000
# ensure paths are correct
shareddir=/gpfs/scratch/tug87422/s... |
6a1a7aa4695d5364d4ae160ba63ad016f56a08f07e0f4c85f55f6f1d11fc4ceb | Shell | 4,575 | 78 | #!/bin/bash
export path_htsa_dir=$1
export path_pipeline=$2
export diginorm_work_dir=$3
export PAIR1=$4
export PAIR2=$5
########################################
#DIGINORM
########################################
if [ -d $diginorm_work_dir ];
then
rm -r $diginorm_work_dir
fi
mkdir $diginorm_work_dir
cd $diginorm_w... |
cb91284ad0575a66a27f1fe5ae7677c5fb1df6712e5a807726f074dfceb95cd7 | Shell | 4,585 | 118 | #!/bin/bash
#SBATCH --job-name=soMAPHIC
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=250G
#SBATCH --error=joblog_error_mapHiC_%A_%a.txt
#SBATCH --output=joblog_output_mapHiC_%A_%a.txt
#SBATCH --array=0-5
#### source library
path_script="/gpfs/scic/data/... |
90cc759a81992209a71dd29cc197c82bea6e15bb8593c5e409e6fffe6f257e4a | Shell | 4,587 | 134 | #!/usr/bin/env bash
#
# Generate base and main Dockerfiles for Nipype.
set -e
USAGE="usage: $(basename $0) [-h] [-b] [-m]"
function Help {
cat <<USAGE
Generate base and/or main Dockerfiles for Nipype.
Usage:
$(basename $0) [-h] [-b] [-m]
Options:
-h : display this help message and exit
-b : generate ba... |
40f92ded7bdf6575d599a4e8f83da07774c1891537642aa38643a61675bd932a | Shell | 4,594 | 116 | #!/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 "Licen... |
32a0678e23d21d6c8f30d0b3fd6c8c6f919556f89f4104c9a67fb78a680095af | Shell | 4,607 | 122 | #!/usr/bin/env bash
MIN_SYNL="$1"
MAX_SYNL="$2"
TRIES="$3"
ALWAYS_SYNTHON_WRITEIN="${4:-0}"
SKIP_SYNTHON_WRITEIN="${5:-0}"
POWER_RUN="${6:-0}"
IP="${7:-192.168.3.4}"
SER="${8:-/dev/ttyACM0}"
WEIGHT_WRITEIN=1
TS=$(date +%Y-%m-%d_%H-%M-%S)
TS_DAY=$(date +%Y_%m_%d)
for ((synl_idx=MIN_SYNL; synl_idx<MAX_SYNL; synl_idx++)... |
7dd21931010b8e001bcdca9dbe29772ad8f108f7e6f296cdfb08d2869c4526be | Shell | 4,607 | 130 |
# --model_name_or_path zhihan1996/DNABERT-2-117M \
# --model_name_or_path jaandoui/DNABERT2-AttentionExtracted \
# transformers==4.29.2
##-------------------------------------------------------------------------------------------------------------------
# try diff lengths for specific folders on both models
##---... |
215bf109b1e353a7639df65995821dcce47b0b4ff93eb4398923dda60b9edef4 | Shell | 4,633 | 95 | #!/bin/bash
###################################################################
#created by Davit Bzhalava on 2014-07-08 #
#compares sequence database with itself using ncbi blast #
###################################################################
#nohup /media/StorageOne/HTS/viralm... |
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