sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
9f277b4f1bbb05bbeb7fbacd1a8e8068f1ea5b35777535b26734896fc689dcd5 | Shell | 1,686 | 43 | # Moderate effect size genes project
# Author: Madison Caballero
# Desription: A set of steps to annotate and extract variants in the non-neuro cohorts.
# These steps were used for 1kGP, BioMe, and All of Us.
# Similar to that for deleterious variants
# Single sample extraction, keeps all loci
bcftools view --threads ... |
2be8c70a299aaacdbc32bc7b792cd95724692a3ef562ebba93d23754cbe4791c | Shell | 1,688 | 50 | #! /bin/bash
step=2
## Copy QC figures
if [[ $step -eq 1 ]]
then
sour_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/NIIDATA/T1
targ_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/QCDATA/T1
sublist=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/LIST/sublist.txt
## Loop subjects
f... |
eca89ad2546e216dd33782fd7856d8146bc39dcfccf6520717ddcac4fbb06d7f | Shell | 1,688 | 44 | #!/bin/bash
V3D="../../../../v3d_external/bin/vaa3d"
if [ ! $# = 4 ]
then
echo -e "\nscript for neuron comparison, Usage:"
echo -e "sh blastneuron_plugin.sh <featurebase.nfb> <query_neuron.swc> <candidate_number> <output_folder>\n"
else
neuron_featurebase=$1
query_neuron=$2
cand_num=$3
output_folder=$4
if [ -d $... |
1f3be6fe6053580065604c72c2014f732c03076b869e9da26eb14610bf1c74c6 | Shell | 1,690 | 42 | #!/usr/bin/env bash
# This script trains the PRISM dataset in the drug_blind split setting.
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$ROOT"
for SPLIT_IDX in 1 2 3 4 5; do
python train.py \
--gpu 0 \
--dataset_dir "data/PRISM" \
--num_workers 4 \
--dataset_name PRIS... |
5e05f9a0702eb32917205dc9ba5e85809f06b7fd0394027c2a73d52864ed8e98 | Shell | 1,692 | 81 | #!/usr/bin/env bash
# Script to upload the release package and the installer to gitub
#
# Expectations:
# - Github OAuth token is provided as the first argument. (automatically set when running on CI)
# - The release and installer packages are in the working tree root
# - Either the main or a release branch are checke... |
dfc61ca9d779adf76f02bd41fd0feb93f6cf5a76d3d89468ee209f74f06af56d | Shell | 1,695 | 42 | #!/usr/bin/env bash
# This script trains the PRISM dataset in the cell_blind split setting.
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$ROOT"
for SPLIT_IDX in 1 2 3 4 5; do
python train.py \
--gpu 0 \
--dataset_dir "data/PRISM" \
--num_workers 4 \
--dataset_name PRIS... |
1d8d8e889c876375608ad131e8ee94e3c7eeb32a3ecd2b74046e36acfa890fe3 | Shell | 1,696 | 64 | #!/usr/bin/env bash
set -o pipefail
LOGFILE="clangd-tidy-report.log"
# check if log file exists and make a backup if it does
if [[ -f "$LOGFILE" ]]; then
mv "$LOGFILE" "${LOGFILE}.bak"
fi
# Only stdout goes to the log file; stderr (where --tqdm draws its
# progress bar via carriage returns) stays on the terminal... |
cb071c1c30d522ac1098136d1f171e661e5157ae885f3f7e119ee4eb32f92e7e | Shell | 1,698 | 58 | #!/bin/bash
# Configuration
EMB_FOLDER="../notebooks/download/embeddings_augmented"
MODEL_PATH="../notebooks/download/learned_models_nn/hyena_model_36302.keras"
#MODEL_PATH="models_output/hyena_mean_model_36302.keras"
OUTPUT_RESULTS="test_results"
TARGET_PATH="${EMB_FOLDER}/fusionai_test_target.csv"
# Create output d... |
e862076c6bebc0731814cff259202b56422c7a785c1b82a1fa11f86661139343 | Shell | 1,699 | 43 | #!/usr/bin/env bash
# Usage: claude --output-format stream-json ... | .claude/scripts/stream.sh [output-file]
tee "${1:-/dev/null}" \
| jq --unbuffered -r '
{
Bash: "💻", Read: "📖", Write: "📝", Edit: "✏️",
NotebookEdit: "✏️", Glob: "📁", Grep: "🔬",
WebSearch: "🔍", WebFetch: "🌐", Task: "🤝"... |
4c6d68b13076f176b051510ec55c122036e91a5a558e8a5c5794961dde85fa31 | Shell | 1,700 | 57 | #!/bin/bash
SEARCH_FOR="$1"
USER_NAME="$2"
PORT="${3:-"3311"}"
HOST="${4:-"127.0.0.1"}"
CHEMBL="chembl_24"
DTADB="dtadb_1_37"
mysql -u"$USER_NAME" --port="$PORT" --host="$HOST" -D"$CHEMBL" -p <<EOF
SELECT # di.mesh_id,
# di.mesh_heading,
# md.pref_name,
# md.chembl_id AS molecule_chembl_id,
# di.max_phase_for_in... |
6b23f222432a1509e3e06a0ca2f0038dc215eae07e150c1ce47e88773cfa44c0 | Shell | 1,704 | 50 | #!/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
# "Lice... |
0da9288134da514a3a29e23f25c3e575dcb27fae610fad178cb87db79bb5c476 | Shell | 1,709 | 39 | #!/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
#... |
dcc2e02f70d8cc971ab82d59b87dfc9c0a6d8bdfb4cfea091b76dadbf7ea4719 | Shell | 1,711 | 44 | #!/bin/bash
#####################################################################
# Copyright 2023-2024 Blue Brain Project / EPFL
# 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:/... |
74d367dc39ed6a097c68e8088d1e1012a0ac07cb83789f23c61b85017f2cba0a | Shell | 1,713 | 61 | #!/bin/bash
#SBATCH --time=00-03:00:00
#SBATCH --mem=60G
#SBATCH --cpus-per-task=24
# Purpose: call gvcf files for a bam file using HaplotypeCaller
# Prepare the bed files for each chromosome like this:
# - cd /path/to/ref/folder
# - mkdir chromosome_beds
# - make a list of chromosome names in a file (e.g. chr.list... |
bd1ecd92ef032a01dbc070946a1e8873e631c7a1961ba67665f9f689320058c1 | Shell | 1,713 | 49 | #!/bin/bash
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -b <behav_ind> -s <fold_start> -... |
cb1341e1a2ec4c303069e394b4152a55132a364b15531be93c6235efd4b1cab5 | Shell | 1,713 | 54 | #!/bin/bash
#SBATCH --job-name=hi
#SBATCH --mail-type=END,FAIL
#SBATCH --mail-user=16amz1@queensu.ca
#SBATCH --qos=privileged # or SBATCH --partition=standard
#SBATCH --cpus-per-task=5
#SBATCH --mem=30GB # Job memory request #SBATCH --tmp=20GB # Temporary memory
#SBATCH --time=1-10:00:00 # Day-Hours-Minutes-Seconds
... |
f393353f620750a8cb805118298bf6ced60a2d5c8f47dac5035221d45fc236df | Shell | 1,713 | 60 | #!/bin/bash
# This script calculates the dS ratio of the two exons of VTR1Ab gene separately, using the VTR1Ab gene of the reference genome.
# mafft v7.526
# biopython 1.80
source Scripts/functions_bash.sh # To access functions defined in functions_bash.sh
# Paths
path_aln="Data/11.dS_ratios/in/VTR1Ab_exons/"
path_dS... |
74f86ffbc3107f908d7cb568926cdb32f3b6072e25518a2fa3d42c6ac581f004 | Shell | 1,716 | 52 | #!/bin/bash
# Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
# Download ILSVRC2012 ImageNet dataset https://image-net.org
# Example usage: bash data/scripts/get_imagenet.sh
# parent
# ├── yolov5
# └── datasets
# └── imagenet ← downloads here
# Arguments (optional) Usage: bash data/scripts/get_... |
ac0e05fb2311e8ab6cadad873ae5c01f1728c3009d1373a750400e5219259439 | Shell | 1,721 | 45 | #!/bin/bash
# This script extracts the consensus sequences for each gene and individual from the BAM files and merges them to create a consensus for each species obtained from transcriptomes.
# seqtk version 1.4-r122
# bcftools Version: 1.9
# samtools Version: 1.21
source Scripts/functions_bash.sh # To access custom ... |
e659d034c76d47af6349de91aa21f6deba3598e18d6ff2f87d2cf8933c03f144 | Shell | 1,725 | 56 | #!/usr/bin/env bash
set -eu
# See ../docs/releasing.md for instructions.
branch="$1" # branch name, e.g. release-3.3
commitPrefix="$2" # prefix to use to filter commits, e.g. fix, chore(deps), build, ci
# If dryRun is unset or `true`, only print the list of commits to be cherry-picked.
# Otherwise, cherry-pick the com... |
e8896822171ccb55039b823b4b7a394e7adb8cfcea99188b3b96d0f2be46d50d | Shell | 1,730 | 91 | #!/bin/bash
# Various utility functions used through CI.
# Finds Cargo's `OUT_DIR` directory from the most recent build.
#
# This requires one parameter corresponding to the target directory
# to search for the build output.
cargo_out_dir() {
# This works by finding the most recent stamp file, which is produced b... |
673ff944d3bf3a888b071730af958424986a9017148e9b9b5634c82332824edc | Shell | 1,731 | 41 | # !/bin/bash
# command line tests of the tabix mapper
MAPPING_FILE="/data/mapping_files/b37/gwas_norm.biallelic.vep.b37.vcf.gz"
REF_ASSEMBLY="/data/reference_genomes/Homo_sapiens.GRCh37.dna.toplevel.fa.gz"
INPUT_FILE="/home/rmjdcfi/analysis/CardiacMRI/gwas_hits/results/SummarLeadSNPMay2021_mapped_nearest_genes.txt"
OUT... |
c159b662067ae71a760afe981ab5ba45148c6cfcda056607821d0c86d2abbb11 | Shell | 1,732 | 42 | # !/bin/bash
# command line tests of the tabix mapper
MAPPING_FILE="/data/mapping_files/b37/gwas_norm.biallelic.vep.b37.vcf.gz"
REF_ASSEMBLY="/data/reference_genomes/Homo_sapiens.GRCh37.dna.toplevel.fa.gz"
INPUT_FILE="/home/rmjdcfi/analysis/CardiacMRI/gwas_hits/results/SummarLeadSNPMay2021_mapped_nearest_genes.txt"
OUT... |
9d3f4343415924df0ccf9812ea9a896e8885570cc4b9d67531ff62dcb886a9bd | Shell | 1,735 | 34 | set -e
# To run these tests do
# ./tests/tests_subtasks.sh <license_key>
# Test vessel predictions
TotalSegmentator -i tests/reference_files/example_ct_sm.nii.gz -o tests/unittest_prediction -ta lung_vessels -d cpu # ~1min
pytest -v tests/test_end_to_end.py::test_end_to_end::test_lung_vessels
# Test total_mr
Total... |
d032e067b3208189442b27499234a5db324bd221a6827e394f8ddbc019dc0ca0 | Shell | 1,736 | 58 | #!/usr/bin/env bash
# Usage:
# Creates a sqlite3 database file based on a COSMIC download file.
# This resulting database file will only contain records that have either
# genome positions or protein positions so they can be matched to variants
# by Funcotator.
# To change the input file, change the `COSMIC_FILE` vari... |
f451c0f338ff5b0ab0b0085fb0cc739db698de6733cb135184e88ed584a27904 | Shell | 1,739 | 54 | #!/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.
function install_92 {
# Install MAGMA for CUDA 9.2
pushd /tmp || exit
wget -q https://anaconda.org/pytorch/magma-... |
963690a9b4c6bae689e0a503970c1f59751f4aa4c2721e688882c14fb293c87c | Shell | 1,740 | 78 | #!/bin/bash
CHROMFA=$1
OUTFILE=$2
TRF=$3
NUMPROC=$4
BASE=$(basename -- "$0")
usage()
{
BASE=$(basename -- "$0")
echo "Generate a GangSTR reference file
Usage:
$BASE ${CHROMFA} ${OUTFILE} ${TRF} ${NUMPROC}
${CHROMFA} is a directory of fasta files (chr1.fa, chr2.fa, ...chr22.fa)
${OUTFILE} path to o... |
56417dcf13abca52de6afbc64f821276ea3fada6017c075c8c886a47d78f7c36 | Shell | 1,742 | 74 | #!/bin/bash
#SBATCH --cpus-per-task=16
#SBATCH --mem=60G
sample=$1
genome=$(echo $sample | cut -d "_" -f 1)
ncores=16
# create output folders
cd /tmp
mkdir $sample
wd=/tmp/$sample
name1=cellSNP
name2=vireo
mkdir $wd/$name1
mkdir $wd/$name2
# specify paths to input data (= the output of cellranger)
bam=/data/share/... |
64605a675cd1359f5fae5541b994ce36103f019cc72a8a68eea759bb24cba890 | Shell | 1,743 | 42 | #!/usr/bin/env bash
# This script trains the PRISM dataset in the drug_sim_blind split setting.
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$ROOT"
for SPLIT_IDX in 1 2 3 4 5 6 7 8 9 10; do
python train.py \
--gpu 0 \
--dataset_dir "data/PRISM" \
--num_workers 4 \
--da... |
ffcad061ad90d2d72ce301783e3ab6360dce71c012c65e2d4dac2a4596477ae5 | Shell | 1,743 | 49 | #!/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 "Licens... |
7a34bbc6e0282de9e4dd10935da910a95d3af5439586179cc0ef5af93711f38b | Shell | 1,748 | 42 | #!/usr/bin/env bash
# This script trains the PRISM dataset in the cell_sim_blind split setting.
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
cd "$ROOT"
for SPLIT_IDX in 1 2 3 4 5 6 7 8 9 10; do
python train.py \
--gpu 0 \
--dataset_dir "data/PRISM" \
--num_workers 4 \
--da... |
2e8a7ac4ad1baef0ddfe03524ec1dd67b969dcf52d074537b11b04659e1a3575 | Shell | 1,749 | 51 | #! /bin/bash
step=2
## Extract default ROI-based measures
if [[ $step -eq 1 ]]
then
sour_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/NIIDATA/T1
targ_dir=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/STATS/T1/ROIDATA
sublist=/Data/sharehome/huyang/HuYang/HY_20250709/PROCDATA/LIST/sublist_init... |
f428239aaacda9badbebf36b90d2dd8b294cde474045b0d6ff8699c2f8e58021 | Shell | 1,750 | 44 | #!/bin/bash
#SBATCH -J banc_ngl_upload
#SBATCH -c 4
#SBATCH -t 0-12:00 # short partition cap
#SBATCH -p short
#SBATCH --mem=16G
#SBATCH --array=0-19 # 20 disjoint shards
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_ngl_upload_%A_%a.out
#SBATCH -e /home/ab714/banc... |
3e0f0958965977156d74a74239bde92c03426cf3f82beccde6eafc271821b3c7 | Shell | 1,751 | 54 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=sescDNA
#SBATCH --error=joblog_error_%j.txt
#SBATCH --output=joblog_output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
# data source
path_biotools="/gpfs/sci... |
a36b3f4f29d2b64765d719d8a160be34cb195aca5062a82e65d2276eabed4be3 | Shell | 1,751 | 74 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cuttlefish
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=soMAPHIC
#SBATCH --error=error_%j.txt
#SBATCH --output=output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
reportElapsedTime() {
eval "echo elapsed ... |
882ee9e58c61fdc03a9efb1ea5a9931dde2cb125c59c358cb66ee564a6e79409 | Shell | 1,754 | 40 | # !/bin/bash
# command line tests of the tabix mapper
MAPPING_FILE="/data/mapping_files/b37/gwas_norm.common.biallelic.vep.b37.vcf.gz"
REF_ASSEMBLY="/data/reference_genomes/Homo_sapiens.GRCh37.dna.toplevel.fa.gz"
INPUT_FILE="/home/rmjdcfi/analysis/CardiacMRI/gwas_hits/results/SummarLeadSNPMay2021_mapped_nearest_genes.t... |
c826b787d92da13e91ed5085c646f030be2c55d1eef7b75de01f04cee4352051 | Shell | 1,758 | 45 | #!/bin/sh
#/media/StorageOne/HTS/VirusMeta/ffp/ffp_step2.sh /media/StorageOne/HTS/PublicData/nt_pb/virus_species_ffp_7 /media/StorageOne/HTS/PublicData/nt_pb/virus_block_ffp_7 species
#/media/StorageOne/HTS/VirusMeta/ffp/ffp_step3.sh /media/StorageOne/HTS/PublicData/nt_pb/virus_genomes_ffp_7 /media/StorageOne/HTS/Pub... |
b2c2a50e4bc22ca6e9f6cbd40fb2ccb108000f52c3f5294c7fdce5a420559682 | Shell | 1,761 | 31 | #!/bin/sh
export path_htsa_dir=/media/StorageOne/HTS #path to HTSA analysis dir
export path_pipeline=VirusMeta
export Project_dir=$1
export virus_index_file=$2
export case_control_id=$3 #tab delimited file: column1 - index names; column2 - 1 if case and 0 if ctrl
export NR_cases=$4
export NR_ctrl=$5
export CLUSTER_cu... |
b92bc90479981cabbdc39c977fd33b8a884f5c5c15f34268bc333b7b59edc829 | Shell | 1,761 | 36 | #!/bin/sh
#####
# This is a wrapper script to run prediction algorithms in the HCP dataset.
#
# EXAMPLE:
# CBIG_ME_HCP_runRegressions_wrapper.sh
#
# Written by Leon Ooi and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#####
### set up data directories
ME_CODE_DIR=$CBIG_CODE_... |
110456859bf3bf6758da42e862e675165c9dc45467c029dee491462613853c34 | Shell | 1,763 | 53 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=128G
#SBATCH --job-name=trinity
#SBATCH --error=joblog_error_%A.txt
#SBATCH --output=joblog_output_%A.txt
path_biotools="/gpfs/scic/software/biotools"
path_micromamba="${path_bio... |
f057c3e26f7a9e76ed68e1f14a77c75ede14fbd2c0728c839d043263c0a02900 | Shell | 1,763 | 56 | #!/bin/bash
# Test the CI pipeline locally using Docker.
#
# This simulates the GitHub Actions Ubuntu environment to catch issues
# (missing dependencies, import errors, build failures) before pushing.
#
# Usage:
# bash scripts/test_ci_local.sh # test with Python 3.12 (default)
# bash scripts/test_ci_local... |
d562734a6d899e27c4524a5170c10cad50d90ffe1b620cb39418668ed31f63c3 | Shell | 1,764 | 75 | #!/bin/bash
id=$1
plink_resources="--memory 32000 --threads 1 --seed 42"
chr=$(echo $id | cut -f1 -d_ | sed 's/chr//')
echo "running for locus $id on chr $chr"
#preparation
base=data/finemapping/susie/ld_matrices/
out=$base/out/$id
mkdir -p $out
#take variant data that was used to generate association results
snp_... |
586cd6a31ddfbac07a294006527f66fb0f7f99365df6725e040a7df65760670d | Shell | 1,767 | 28 | #!/bin/bash
set -eu -o pipefail
# Retrieve data for doing cancer calling evaluation using synthetic dataset 3
# from the ICGC-TCGA DREAM challenge:
# https://www.synapse.org/#!Synapse:syn312572/wiki/62018
# Full input data
#wget --no-check-certificate https://cghub.ucsc.edu/software/downloads/GeneTorrent/3.8.5a/GeneTo... |
f81ac699796120aec8184045a8e1c739b7da58b0124a54324c55f88596d1f33d | Shell | 1,768 | 46 |
#Evaluate the Docking
##########new_dimers#######
##AF2
DOCKQFILES=./dockqstats_newdimers_af2 #Path to file location
OUTFILE=./dockqstats_newdimers_af.csv
#python3 ./eval_docking.py --dockqfiles $DOCKQFILES --outfile $OUTFILE
##########Marks###########
##RF
DOCKQFILES=./dockqstats_marks_RF #Path to file locati... |
7d80a8f1b22a7ccc140c4a67dc776b31fa227e18005145a8ff3bcf616b6e05bf | Shell | 1,777 | 79 | #!/bin/bash
#
# Currently the script only support single channel stitching
# parse options
AxisOrder=''
ImagePath=''
channel=''
Flatfield=''
ImageListFileName=''
Resolution=''
print_usage() {
printf "Usage: Stitching for a single frame and a single channel"
}
while getopts 'a:b:c:fi:r:' flag; do
case "${flag}" ... |
d862005947f9d09115ed2e835dbaa144434e6199c650513a8981c413c1b36a26 | Shell | 1,778 | 67 | #!/usr/bin/env bash
set -ex
# Function to build TypeDoc for a package
build_tsdoc() {
local package_path=$1
local package_name=$2
local output_path=$3
echo "Building TypeDoc for $package_name..."
# Store the absolute path to the analytics file before changing directories
local analytics_js_p... |
763697df55591e57151c4210367fce38128b80fce884dff0313afe7f82805946 | Shell | 1,780 | 45 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
03b44622f21b5dc02817a2741ec8ed9eb3be92d897961574c9f507471b714fb1 | Shell | 1,781 | 54 | #trime adaptor
#use slurm job
#!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=do_trim_ipsc_npc
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=20
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=20G
#SBATCH --chdir # TODO: set dir t... |
7bc4c2ddffef511b549e9a696cb914ccd5279384041fc89e410f20958e04baeb | Shell | 1,788 | 38 | #!/usr/bin/env bash
# Download all required data for exomes and store in HDFS. Use this for non-GCS clusters.
TARGET_DIR=${1:-exome_spark_eval}
hadoop fs -stat $TARGET_DIR > /dev/null 2>&1
if [ $? -eq 0 ]; then
echo "$TARGET_DIR already exists. Delete it and try again."
exit 1
fi
set -e
set -x
# Create data di... |
5cdb7cb8c4c1a875c59b3f6d130dede90e9b288d8676b9c357c4bb6be4d8998b | Shell | 1,791 | 51 | #!/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
# "Lic... |
9eef987c0dfce171eec23331a0a89a24814da038a95011c3af8199074484ee6b | Shell | 1,801 | 37 | #!/bin/bash
## Select variants from af-only-gnomad.raw.sites.b37.vcf.gz
module load bcftools
## Need to split multi-allelic sites across multiple lines, see
## https://gatkforums.broadinstitute.org/gatk/discussion/10975/use-select-variants-on-a-gnomad-vcf-for-mutect2-contamination-filtering
bcftools norm \
-f "/proj... |
eb605ab4a63c738f8ee7b0dc221f4a8d3057f2c81317ac718abbbcb8881cd1e5 | Shell | 1,801 | 51 | #!/bin/bash
# This script calculates the coverage depth for each position of CDS regions for genomes and transcriptomes using the BAM files obtained with script 01
# Samtools depth version 1.21
source Scripts/functions_bash.sh # To access custom functions defined in functions_bash.sh
# Files
bam_list_file_gn="Local/p... |
8156cd8b431197eaf8f838d1d2a7ed1022dfa1716a8607e8de21e736f08a2a21 | Shell | 1,803 | 65 | #!/usr/bin/env bash
# FFmpeg with h264
mkdir -p ~/ffmpeg_sources ~/bin
# Dependencies
sudo apt-get update -qq && sudo apt-get -y install \
autoconf \
automake \
build-essential \
cmake \
git-core \
libass-dev \
libfreetype6-dev \
libsdl2-dev \
libtool \
libva-dev \
libvdpau-dev \
libvorbis-dev ... |
18783a5a6fbf91df2ebe3d5d7e68c86ac37493523be15a10ee98fc8bc1d942bd | Shell | 1,804 | 33 | #!/bin/bash
cd /global/project/projectdirs/m2043/BigNeuron/Data/bigneuron_annotation_consolidated_20150715/gold166/
j=1;
for i in {1..27}
do
# if [[ ( $i != 1 && $i != 5 ) && ( $i != 6 && $i != 8 ) && ( $i != 21 && $i != 18 )]];
# then
var=1;
echo $i
# mkdir /global/project/projectdirs/m2043/BigNeuron/zhi/bigneuron_... |
e3c44b99adae2251d5b9d2150259b9d9c93ccff3dc5de2c8aed5d163cacd67d4 | Shell | 1,804 | 33 | #!/bin/bash
cd /lustre/atlas2/nro101/proj-shared/BigNeuron/data/bigneuron_annotation_consolidated_20150715/gold166/
j=1;
for i in {1..27}
do
# if [[ ( $i != 1 && $i != 5 ) && ( $i != 6 && $i != 8 ) && ( $i != 21 && $i != 18 )]];
# then
var=1;
echo $i
# mkdir /lustre/atlas2/nro101/proj-shared/BigNeuron/zhi/bigneuron_... |
19048cb680367e0aef6eef56e1509402a29516fb8b504d3bd5934d61bf342915 | Shell | 1,808 | 51 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
37ee05d62576ffdbd87d97375f16fd04a312d88ce7410cb87718e25e81f7e643 | Shell | 1,808 | 81 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ConfigFile="/home/joonho345/1_Epilepsy_RNA/script/Scratch_settings.sh"
source ${ConfigFile}
#ConfigFile=$1
#source ${ConfigFile}
#####
OutPath_35=${Mouse_IndexPath_35_A}
OutPath_50=${Mouse_IndexPath_50_A}
OutPath_75=${Mouse_IndexPath_75_A}
OutPath_100=${Mouse_IndexPath_100_A}
OutP... |
b6be96ffa9d9aecc39f8efa55fb6d77ab98abd096b6c4a9b5c8b212bb38b4849 | Shell | 1,808 | 53 | #!/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
#... |
10f318b4e16eb68576a7df9dd96c28a547635c510a53f0e520f8ed1ec2b9258b | Shell | 1,809 | 51 | #!/bin/bash
set -xe
# spack repository
cd $TRAVIS_BUILD_DIR
git clone --depth 1 https://github.com/pramodskumbhar/spack.git -b stable
# enables spack command line support
set +x
source $SPACK_ROOT/share/spack/setup-env.sh
set -x
# add spack packages repository
cd $TRAVIS_BUILD_DIR
git clone --depth 1 https://gith... |
50ea88bc4faac7f64f40ea83c2d245ad396b50352533ea2aef3168a390c54323 | Shell | 1,809 | 45 | #!/bin/bash
#SBATCH -c 11 # Request cores
#SBATCH -t 0-12:00 # Runtime in D-HH:MM format
#SBATCH --partition gpu_quad # Use a quad GPU
#SBATCH --gres=gpu:rtx8000:1,vram:26G # Number to use
#SBATCH --mem-per-cpu=10G # Memory per co... |
046adac948013d91a8d1147c0dac935fb9dc72896cedab14922d6a4d76009976 | Shell | 1,810 | 44 | #! /bin/sh
# Last successfully run on Mar 20, 2022
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
$FREESURFER_HOME/bin/clear_fs_env.csh
fi
# PLEASE ... |
80b1a6e88878a3b9b90f889341d80ea758c0a27d320d2ae7b688835844e58ba7 | Shell | 1,812 | 44 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
6acb92424d8b5e666536ea28ff4ff25695f6f2d806076984f2888d6ce232ff92 | Shell | 1,813 | 61 | #!/bin/bash
# This script calculates the dS ratios of each gene and species separately, using the genes of the reference genome.
# It uses Yang and Nielsen method (Yang & Nielsen, 2000).
# mafft v7.526
# biopython 1.80
source Scripts/functions_bash.sh # To access custom functions defined in functions_bash.sh
# Paths... |
046d00dc2dc23a250af9262a7682edbb2f88eeee0144aef94192d412c0d748ed | Shell | 1,815 | 66 | #!/bin/bash
# LaTeX PDF生成スクリプト
# Usage: ./build_pdf.sh [tex_file]
set -e # エラーで停止
# デフォルトのTeXファイル
TEX_FILE="${1:-paper/main.tex}"
# ファイルが存在するかチェック
if [ ! -f "$TEX_FILE" ]; then
echo "エラー: $TEX_FILE が見つかりません"
exit 1
fi
# ファイル名とディレクトリを取得
TEX_DIR=$(dirname "$TEX_FILE")
TEX_BASENAME=$(basename "$TEX_FILE" .te... |
1ae89c8ae87e14778882abc190bf8604557181f84c1b344ce1660998690c2bd3 | Shell | 1,819 | 48 | #!/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... |
3f789a9d950ab4fdeadc04b113edbd7198afa5b2dfe58640c99239160339855b | Shell | 1,821 | 46 | #!/bin/bash
# Path to the folder containing subject folders
subjects_folder="/beegfs_data/scratch/iandrulyte-diffusion"
FA_folder="/beegfs_data/scratch/iandrulyte-diffusion/FA_maps/for_Ieva_FA_maps"
CC_divided_files="/beegfs_data/scratch/iandrulyte-diffusion/Divided_CC_three_parts"
# Create a CSV file for full AF F... |
686f3ab61086fbe4be6baf616b453c09ba3e8cda90179052b3af02ad8f2d4a61 | Shell | 1,822 | 49 | #!/usr/bin/env bash
set -euo pipefail
# Create service account and token
kubectl create serviceaccount argo-sdk-test -n argo 2>/dev/null || true
kubectl create rolebinding argo-sdk-test --clusterrole=argo-server-cluster-role --serviceaccount=argo:argo-sdk-test -n argo 2>/dev/null || true
export ARGO_TOKEN="Bearer $(ku... |
621de2b066e6df68a4f774c2f28a099b1043b1f7f8fb249e1a0ef7e2281d45ec | Shell | 1,824 | 77 | #!/bin/sh
########################################
#SOAP
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export SOAP_work_dir=$3
export diginorm_work_dir=$4
echo "starting soap denovo assembly"
if [ -d $SOAP_work_dir ];
then
rm -r $SOAP_work_dir
fi
mkdir $SOAP_work_dir
cd... |
5d3ad7860c5655829f555afce90e5d897ce7f981f165989efcaf532dd45e4e4f | Shell | 1,825 | 49 | #!/usr/bin/env bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
# study-specific inputs
sub=$1
ses=$2
TASK=$3
run=$4
me=$5 # 1 on, 0 off
space=$6
sm=5 # 5mm smoothing
# zerop... |
13d3992e991fe6643898470339df01db63a7c18f3d073ae9ae108a48c60114c4 | Shell | 1,826 | 81 | #!/bin/sh
########################################
#SOAP
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export SOAP_work_dir=$3
export PAIR1=$4
export PAIR2=$5
echo "starting soap denovo assembly"
if [ -d $SOAP_work_dir ];
then
rm -r $SOAP_work_dir
fi
mkdir $SOAP_work_di... |
d4fdee9e1e29ffdd81e4d0efd92da328bd5cadf9ace4fcf58714936868953b6c | Shell | 1,826 | 54 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO SEGMENTATION DIFFUSSION SCAN
##
## R-fMRI master: Xi-Nian Zuo at the Institute of Psychology, CAS.
## Email: zuoxn@psych.ac.cn
##
## Last Modified: 12/20/20... |
100b600c01c1955e47f9234d78595def82fac584c69c171d12c8bd396f2f75a1 | Shell | 1,827 | 67 | #!/bin/bash
# This is a script shell for deploying a pymeshlab-portable folder.
# Requires a properly built PyMeshLab (see 1_build.sh).
#
# Without given arguments, the folder that will be deployed is pymeshlab, which
# should be the path where PyMeshLab has been installed (default output of 1_build.sh).
#
# You can gi... |
64ed85f06ce9a2df821029623c3f62aae30b630f51dc327e6bf34503b16a4ef9 | Shell | 1,830 | 57 | #!/bin/bash
# Run a test build using docker on local PC, this can be used to debug CI/CD
# gitlab builds without repeated commits. The documentation is uploaded to
# pCloud static web pages for viewing.
# This will create a container called gwas_norm and do the build before closing
# and removing the container. The con... |
2557a1cd8e268709498bc305d78302d5b33aa7796e656792469ad7aaafe2fbc5 | Shell | 1,832 | 81 | #!/bin/bash
#$ -cwd
#$ -S /bin/bash
ConfigFile="/home/joonho345/1_Epilepsy_RNA/script/Scratch_settings.sh"
source ${ConfigFile}
#ConfigFile=$1
#source ${ConfigFile}
#####
OutPath_35=${Rat_IndexPath_35_A}
OutPath_50=${Rat_IndexPath_50_A}
OutPath_75=${Rat_IndexPath_75_A}
OutPath_100=${Rat_IndexPath_100_A}
OutPath_125=... |
ce417b0f1af1433432a2d742bdd098137d8a879adda5b432d7c8b5d5ff1fa672 | Shell | 1,832 | 57 | #!/bin/bash
# Run a test build using docker on local PC, this can be used to debug CI/CD
# gitlab builds without repeated commits. The documentation is uploaded to
# pCloud static web pages for viewing.
# This will create a container called gwas_norm and do the build before closing
# and removing the container. The con... |
13f7823ced1024cd6279d2ddc03822e7d5b59b1a388d4be89e4f63c3feaf81b6 | Shell | 1,834 | 65 | #!/usr/bin/env bash
### in this directory should be only dose and info files
GENOTYPE_DIR=$1
SAVE_DIR=$2
HASEDIR=$3
STUDYNAME=$4
SUBJECT_ID_FILE='SUB_ID.txt'
SUBJECT_FAM_FILE='SUB_FAM.txt'
SNPs_INFO='SNPs_info.txt'
CWD=`pwd`
cd $GENOTYPE_DIR
id_file=`ls | grep dose | head -n1`
rm -f ${SAVE_DIR}/${SUBJECT_ID_... |
8cb80b8f23ea80d2d5de2fae69261f0c549c8fadda712cd592173983fa2a4199 | Shell | 1,837 | 41 | # !/bin/bash
# command line tests of the tabix mapper
MAPPING_FILE="/data/mapping_files/v20220402/gwas_norm.v20220402.common.biallelic.vep.b37.vcf.gz"
TABIX_MAPPING_FILE="/data/mapping_files/v20220402/gwas_norm.v20220402.biallelic.vep.b37.vcf.gz"
# MAPPING_FILE="/data/mapping_files/b37/gwas_norm.common.biallelic.vep.b3... |
5c10fdc158dcb5c139e2281cd461c9031d0464c997981f43d24609f258761cb6 | Shell | 1,839 | 51 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
67c06bda2115b8d4dc03bf2bc19078abbf4bacdd00559ad46925bf52b6720838 | Shell | 1,848 | 64 | #!/usr/bin/env bash
# Reproduce all paper experiments end-to-end. CPU runtime ~6-8 h, GPU ~1.5 h.
#
# Phases:
# 1. Table 3 benchmark (Phase 2)
# 2. KD-DM Task A drift compensation (Phase 3 — 21 chunks via analysis_main.py)
# 3. Random vs chronological protocol sensitivity (RM-1)
# 4. Wörner cross-platform valid... |
d2b17ff054bd5dee61efb7ea72baa3b0d96c3ef502de69ce1a0c48293bb4b9cc | Shell | 1,849 | 67 | #!/bin/bash
# LaTeX PDF生成スクリプト (Supplementary用)
# Usage: ./build_supplementary.sh
set -e # エラーで停止
# Supplementary TeXファイル
TEX_FILE="paper/supplementary.tex"
# ファイルが存在するかチェック
if [ ! -f "$TEX_FILE" ]; then
echo "エラー: $TEX_FILE が見つかりません"
exit 1
fi
# ファイル名とディレクトリを取得
TEX_DIR=$(dirname "$TEX_FILE")
TEX_BASENAME... |
2644e582ecce660f00fc9cd35db32cd4a5d881e50cf90b89fd6c1a40cd5e3596 | Shell | 1,850 | 54 | #!/bin/sh
# Written by Yapei Xie and CBIG under MIT license:
# https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#####
# This script calls the matlab function to run generate the null models. User needs to provide the following variables.
# 1. feature_path: path to feature mat file
# 2. outdir: output directo... |
c1226cdb176e39cbe400ec76adb8508772bd51fcd20e488225540f6d72a9d931 | Shell | 1,854 | 64 | #!/bin/bash
#
#
#
function write_c_exe_script {
outputScript=$1;
inputfolder=$2;
Vaa3Dfolder=$3;
shiftnumber=$4;
echo "#include <stdio.h>" >> $outputScript;
echo "#include <unistd.h>" >> $outputScript;
echo "#include \"mpi.h\"" >> $outputScript;
echo "" >> $outputScript;
echo "int main(int argc, cha... |
451fbb2f88a79bd4eb0fcec69a940e3f9691b21663b34f549c3c260d95fdf320 | Shell | 1,859 | 44 | #!/bin/bash
#SBATCH -c 1 # Request cores
#SBATCH -t 0-12:00 # Runtime in D-HH:MM format
#SBATCH -p short # Partition to run in
#SBATCH --mem-per-cpu=100G # Memory per core
#SBATCH -o jobs/deform_cpu%j.outb # File to whic... |
a5f6c3e3d5dd381b1fe12e6c66e946f2e7b0aa251e9a8f649d7458b20aeaa302 | Shell | 1,859 | 58 | #!/bin/sh
#
# Long running tests go here
echo "WARNING: THIS TEST SUITE IS NO LONGER USED"
gemma=../bin/gemma
export GSL_RNG_SEED=100
testPlinkStandardRelatednessMatrixK() {
testname=testPlinkStandardRelatednessMatrixK
datadir=../example
outfn=output/$testname.sXX.txt
rm -f $outfn
$gemma -bfile $... |
769da0db818bd27716eab8acb48afcf33d99757a5a9569e982cc1b80b3b31204 | Shell | 1,862 | 64 | #!/bin/bash
#
#
#
function write_c_exe_script {
outputScript=$1;
inputfolder=$2;
Vaa3Dfolder=$3;
shiftnumber=$4;
echo "#include <stdio.h>" >> $outputScript;
echo "#include <unistd.h>" >> $outputScript;
echo "#include \"mpi.h\"" >> $outputScript;
echo "" >> $outputScript;
echo "int main(int ar... |
0fe134b06f879e32c6c4b2ffd39a20345dd8fe820dd7d9ac5686cd4b72b914ba | Shell | 1,865 | 64 | #!/bin/bash
#
#
#
function write_c_exe_script {
outputScript=$1;
inputfolder=$2;
Vaa3Dfolder=$3;
shiftnumber=$4;
echo "#include <stdio.h>" >> $outputScript;
echo "#include <unistd.h>" >> $outputScript;
echo "#include \"mpi.h\"" >> $outputScript;
echo "" >> $outputScript;
echo "int main(int ar... |
213068c43dfe9e256acd5a9de8d4da098ac850d98caf58fceba2621f5a0c51bf | Shell | 1,870 | 78 | #!/bin/sh
########################################
#SOAP
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export SOAP_work_dir=$3
export diginorm_work_dir=$4
echo "starting soap denovo assembly"
if [ -d $SOAP_work_dir ];
then
rm -r $SOAP_work_dir
fi
mkdir $SOAP_work_dir
cd... |
67114c6d0f433e9fe3866adbd8e0b8bafe2b89b10dd601c25207da3ad39d5ef0 | Shell | 1,871 | 79 | #!/bin/sh
########################################
#SOAP
########################################
export path_htsa_dir=$1
export path_pipeline=$2
export SOAP_work_dir=$3
export diginorm_work_dir=$4
echo "starting soap denovo assembly"
if [ -d $SOAP_work_dir ];
then
rm -r $SOAP_work_dir
fi
mkdir $SOAP_work_dir
cd... |
9e5dcb2f256e27395766fff52f43d4ac70781aacd56ca2e7a06079686a6d6116 | Shell | 1,871 | 47 | #!/usr/bin/env bash
#
# Reproduce every ProVerif verdict reported in the paper
# "Closing the HNDL Window in Consumer eSIM Provisioning".
#
# Requirements: ProVerif 2.05 on PATH (https://bblanche.gitlabpages.inria.fr/proverif/).
# Usage: ./run_all.sh
#
# For each model the script runs ProVerif, saves the full lo... |
f8dd410f469fa90a562803d343b651966e28f4f4a0c7f1d8464809af751ced83 | Shell | 1,873 | 55 | #!/bin/sh
#####
# This script calls the matlab function to run generate FC matrices in the HCP dataset.
#
# Input:
# -output_dir:
# Path to store FC matrices
#
# -mins:
# The scan duration (in minutes) that is used to calculate the FC
#
# -vers:
# The manner in which to calculate the the first t... |
96017d4fe49915523c75a0d0e360639051ae2a060bda2d6e72806704c265b42c | Shell | 1,877 | 46 | #!/usr/bin/env bash
umask 0000
SUBLIST="sublist.txt"
while read -r SUBJ; do
[ -z "$SUBJ" ] && continue
for ses in $(seq -w 1 12); do
SRC="/gpfs/scratch/tug87422/smithlab-shared/night-owls/derivatives/anat-only/"
DST="/gpfs/scratch/tug87422/smithlab-shared/night-owls/derivatives/fmriprep/sub-${SUBJ}/ses-... |
ab16abbd2e8366bf2c80b926993db1fdbd13abb4fa1797cf7d292735f031b603 | Shell | 1,879 | 81 | #!/bin/bash -v
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2048
#SBATCH --partition=main
#SBATCH --time=12:00:00
################################################################################
#
# subject_tractography
# --------------------
#
# A batch to construct a tractogram for a HCP subject
#
#... |
d2b62388944635266419004cafc583ee57e05889850cdd686e655e16f44819a2 | Shell | 1,879 | 28 | # linux
python train.py --model utnetv2 --dimension 3d --dataset acdc --batch_size 1 --unique_name acdc_3d_utnetv2 --gpu 0 >> utnetv2.txt
python train.py --model unet --dimension 3d --dataset acdc --batch_size 1 --unique_name acdc_3d_unet --gpu 1 >> unet.txt
python train.py --model unet++ --dimension 3d --dataset acdc... |
a3e2038736d230daaf72d4b15e32cd6dec8648b584d5d28edf8a75ff714f9cdd | Shell | 1,880 | 64 | #!/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... |
d8e5c08c8cfbd9e462f0bb61235da68b0443060c8906a9b1e716b1eb0c3d3e6b | Shell | 1,882 | 80 | #!/usr/bin/env bash
#####
## For use with Docker
help_menu="
Usage regenie_docker.sh OPTIONS
Options:
--build create docker image
--test test a generated docker image
--with-bio compile with Boost Iostreams library
--with-mkl compile with MKL library
--file custom docker file to use
--rg-dir p... |
1f579de8bde524d7fee24e6dd66cd5aff1e7ce8c51a2334a97108891b1193d51 | Shell | 1,884 | 56 | #!/bin/bash
# Run elastix to register the BANC's VNC to the JRC2018 female VNC template
#
# This isn't meant to be run by BANC users but instead to provide a record of
# how registration was done in case we want to reproduce it or improve it later
img_fn=banc-synapse-cloud-v1.1_sizethresh6_blursigma1_16bit0-3_VNC.nrrd... |
bdb1d1dade8e7241ffc1415928efabadbfde5c2484e265f2a175e1e264785413 | Shell | 1,884 | 44 | #!/bin/bash
# Written by Ruby Kong and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
orig_mesh=${1} # original data mesh
resample_mesh=${2} # target mesh of resampling
project_dir=${3} # output directory
data_type=${4} # data_type = metric/label.
version=${5} # version = 201... |
327a88de639c170a23def9f3db7a79c90a2b9021e97cdd2d8c58cdaa75c223af | Shell | 1,886 | 85 | #!/bin/bash
NSUBJECTS=20
NSESSIONS=4
# Get the directory of the script
CURR_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
# Parse command line arguments
SUBJECT=""
SESSION=""
VISIT_TYPE=""
FOLDERNAME=""
ROINAME=""
# Function to display usage information
usage() {
echo "Usage: $0 --subject SUBJECT --se... |
0cff25714535e8679f4f907601a2babf51d12f1e983b274410394814da4a83f2 | Shell | 1,890 | 44 | #! /bin/sh
# Last successfully run on May 27th, 2021 with git repository version v0.19.2-Yeo2011_Schaefer2018-develop-24-gd2f3c6b4
# Written by CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$F... |
c5f1cf0ea5830fb63b09f2a642f21fcbb7224360f61ebc62d611817881a31c22 | Shell | 1,890 | 61 | #!/bin/bash
#
#This is a shell program to batch reconstruct images using 21 different methods.
#
function write_vaa3d_job_config {
outputScript=$1;
jobpath=$2;
vaa3dProgramPath=$3;
echo "## Check which project you may use" >> $outputScript;
# echo "#PBS -q dque" >> $outputScript;
echo "#PBS -A NRO101" >> ... |
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