sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
52059dd8ae4c6d522a67737b7276e8770381963c7e33b6852c071fbe87007241 | Shell | 2,552 | 71 | #!/bin/bash
#SBATCH -c 4 # Cores
#SBATCH -t 0-18:00 # Runtime — bumped from 4h after job 38760183
# timed out reading split CSVs in v2 Section 5
# (v3 + v2 each need ~2-3h for Section ... |
38cf79bdcad2b9faed827b3cb4b40adb91351b4235db1213d45a65d3c4cb10e5 | Shell | 2,553 | 54 | #!/bin/bash
WELQRATE_DIR="welqrate"
DATASET_DIR="${WELQRATE_DIR}/datasets"
ZIP_DIR="${WELQRATE_DIR}/zip"
mkdir -p ${ZIP_DIR} ${DATASET_DIR}
# Array of AIDs
aids=("AID1798" "AID1843" "AID2258" "AID2689" "AID435008" "AID435034" "AID463087" "AID485290" "AID488997")
# Arrays of URLs
raw_urls=(
"https://vanderbilt.b... |
160dab64bf7d0a3525456d3f34c0cbd8e5b3c76180e235b05713bb852c097d0f | Shell | 2,555 | 74 | #!/bin/bash
## GATK pre-proccess intervals for CNV calling
## See https://software.broadinstitute.org/gatk/documentation/article?id=11682
gatk PreprocessIntervals \
-R /projects/verhaak-lab/verhaak_ref/gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta \
--bin-length 1000 \
--padding 0 \
--interval-merg... |
cb8bc4a45823fbce85e30179a2b20fa5b1625cb657b2f47df7faec31ec9c25da | Shell | 2,555 | 50 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=gnomad_CNV
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=20G
#SBATCH --chdir /data7/iPSC_corrine/CNV/src
#SBATCH -o logs/2_mappability... |
dab298cb17e7633be452710949c9badc0279ef8f226948ff421f4eb86f0b5e0e | Shell | 2,557 | 64 | #!/usr/bin/env bash
# DB host bootstrap. Runs once on first boot via cloud-init.
# Templated by Terraform — variables ${git_repo}, ${git_ref}, ${backup_bucket}.
set -euxo pipefail
exec > >(tee /var/log/user-data.log) 2>&1
# --- Docker + Compose -------------------------------------------------------
dnf install -y doc... |
b973d88ae8a283b03c309cc4aef39af1e1d62a5dccd9f6043272aa09b6ff9aaa | Shell | 2,564 | 56 | #!/bin/bash
#SBATCH -c 4 # 4 cores (mostly I/O + classify_status)
#SBATCH -t 0-04:00 # 4 hours (load 3 parquets + 12 CSVs)
#SBATCH -p short # short partition
#SBATCH --mem-per-cpu=48G # 4 * 48 = 192G total (was ... |
cdef3d0d3bb4d18de2f87b54e24fb10c954ed268fe93b3ba1cf2dbee75aafbc1 | Shell | 2,567 | 81 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
eeeff57b4ae7fb17432e3637f8981b167d9d12367237a45286d46ec74adeb627 | Shell | 2,568 | 68 | #!/bin/bash
# Copyright 2023 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
bb8bf618474de2a91d6e070091f5f0d58065e6c25236b69c07b045284cec6bcb | Shell | 2,570 | 73 | #!/bin/sh
# This function replicate the linear ridge regression results in the GSP dataset shown in Li et al., 2019
# Only two behavioral measures are included: Shipley_Vocab_Raw and Matrix_WAIS
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
##########... |
22eb824972570097dbecf8046d80ad557f0b4ccaddb20284fb5ae335d38c7e8f | Shell | 2,571 | 70 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
input_dir=$pd/data/validations/ATAC_seq_BAM_nameSorted
bl_dir=$pd/data/validations/ATAC_seq_blacklists
output_dir=$pd/data/validations/ATAC_seq_peaks
mkdir -p $output_dir
# human iPSCs
rep1=${input_dir}/human_H1c2_iPSC.bam
rep2=$... |
40f957d83978f991fe0dbd0b2646eeddda058ded706833e0eeb8a76747a3156f | Shell | 2,574 | 66 | #!/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 where possible
SIF="/nfs/cellgeni/singularity/images/starsolo_2-7-10a-alpha-220818_samtools_1-15-1_seqtk-1-13_bbmap_38-97_RSEM-1-3-3.sif"
CMD="... |
7d58cc18f8fc5260d7692f8136a4cac29023f1c9e79221e243d051b1d86144c2 | Shell | 2,575 | 70 | #!/bin/sh
set -e ${DEBUG:+-x}
NGINX_CONFIG=$OPT_DIR/nginx/nginx.conf
echo >&3 "=> Copy nginx config file..."
mkdir -p "$OPT_DIR/nginx"
\cp -f /etc/nginx/nginx.conf $NGINX_CONFIG
echo >&3 "=> Configure system resolver..."
# Process each nameserver individually, wrapping only valid IPv6 addresses in square brackets.
#... |
a644e75a7f3afee0664af7751c8e541e3c8c6a58b20f9b0c52f6079c2d92c989 | Shell | 2,577 | 77 | #!/bin/bash
#####
# This wrapper script submits job to the schduler to run curve fitting to each dataset.
# Dataset, and type of analysis needs to be specified. A .sav file will be the output with
# the theoretical and log curves fitted from the 3rd T point onwards (e.g. if ABCD is 2min
# to 20mins, the curves will ... |
a6ff2e2d15efba64ee932d9ebe6f36953e55ea70e906f8c34f718577e54a43cb | Shell | 2,586 | 102 | #!/usr/bin/env bash
set -euo pipefail
unset PGPASSWORD
DB_HOST="${DB_HOST:-localhost}"
DB_USER="${DB_USER:-postgres}"
DB_NAME="${DB_NAME:-mimiciv}"
TARGET_SCHEMA="${TARGET_SCHEMA:-}"
if [[ -z "${TARGET_SCHEMA}" ]]; then
echo "TARGET_SCHEMA is required, e.g. TARGET_SCHEMA=sofa_gov_20260619_rebuild_v1 bash run_steps... |
44fcb9cf1df2304ab69c9afbeb17c7ed6dc8bafbf07717f6c53d7f7fef898652 | Shell | 2,588 | 87 | #!/usr/bin/env bash
# Sample CPU and memory usage while running a command, then post mermaid
# xychart-beta line charts to GITHUB_STEP_SUMMARY (or stdout if running
# locally outside GitHub Actions).
#
# Usage: dev/profile.sh <command> [args...]
#
# Environment overrides:
# PROFILE_INTERVAL_SECONDS sampling interval... |
4d298169bc093327bc895ea09edb03d1e7ae6c68348e6ea49b75c105af792121 | Shell | 2,593 | 68 | #!/bin/bash
#SBATCH -c 8
#SBATCH -t 0-04:00
#SBATCH -p short
#SBATCH --mem-per-cpu=12G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_prep_v888v2_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_prep_v888v2_%j.err
###############################################################################
# Re-prep WB alig... |
82d3771e559e9c15b4bc64ef1444fdf10e3a91ef2321e8ccc6bbbff870de67f0 | Shell | 2,596 | 87 | #!/bin/bash
# Script para compilar el paper LaTeX
# Uso: ./compile_paper.sh
set -e
PAPER_DIR="/workspaces/Bucle2D/paper"
MAIN_TEX="main.tex"
echo "=========================================="
echo "Compilando Paper: Agentic-Racing-Vision"
echo "=========================================="
echo ""
cd "$PAPER_DIR"
# V... |
4e32d279a90b003d72596a637c3fcd04f4f91d67e1fde6fdf3aa80b6309d9745 | Shell | 2,597 | 59 | #!/bin/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"); yo... |
3e52f35ff12a418d7d2e1febd4e5ecfa9d3b1cbba1eff1a3e677cb42ec5c834d | Shell | 2,601 | 73 | #!/bin/bash
#SBATCH --job-name spacetop_dk_proj
#SBATCH --time 2:00:00
#SBATCH --nodes 1
#SBATCH --ntasks-per-node 1
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 1
#SBATCH --hint=nomultithread
#SBATCH --output dk_spacetop_logs/atlas_%a.out
#SBATCH --error dk_spacetop_logs/atlas_%a.err
#SBATCH --account dbic
#SBATCH --ar... |
1a0c4cc2da00a431d5ae2c140c1d7e2c7072913679a3c83098b34606ddb586a9 | Shell | 2,604 | 72 | #!/bin/bash
# $1: file containing arguments for batch-consistency-plot-merged3.r
# File has 4 tab-delimited fields
# [nPairs]\t[combOutFilePrefix]\t[pairOutFilePrefix,...]\t[combPeakFile]
# $2: idrThreshold (OPTIONAL: default is 0.1)
# $3: fdrThreshold (OPTIONAL: default is 0.7)
# Rscript batch-consistency-plot-merged2... |
7babb77b48daad64fa4d9fadbcb2c3b30f316f7c5686ecce69a4ddf821b3547d | Shell | 2,607 | 79 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO CALCULATE VARIOUS QCP METRICS
##
## This script can be run on its own, by filling in the appropriate parameters
##
## Written by Xi-Nian Zuo. For more informat... |
3ad009937651344bb7e86f919bdbdfb8673071109740cdc7ebed7ac507fba9ab | Shell | 2,609 | 49 | #!/usr/bin/env bash
set -euo pipefail
promotion_sql="sql/promote_sofa_gov_20260619_rebuild_v1.sql"
post_promotion_sql="tests/validate_post_promotion_sofa_gov_20260619.sql"
shadow_validation_sql="tests/validate_shadow_promotion.sql"
approval_token="I_HAVE_REVIEWED_AND_APPROVE_SOFA_GOV_20260619"
test -f "${promotion_sq... |
387dfadd10dc896788ee4978bebf17cbf9c5cd573ff68f46eea121c93f741d78 | Shell | 2,615 | 51 | #!/bin/bash
train_iteration=1 # could be 1, 2, ..., and indicates which pre-training iteration we are in
batch_size=100 # each file contains (93, kmeans_dim) tensors, meaning that partial_fit operates on 100 * 93 samples at a time
layer=8 # only for logging purposes, to better distinguish clustering on latent represen... |
8b3d1852abe7d5214290160ed222ff74599af8512ee92270fd3a5a4157c4392e | Shell | 2,618 | 76 | #!/bin/bash
# Per-dataset NBLAST + image generation
# Usage: sbatch [SBATCH_OPTIONS] o2/o2_banc_nblast_dataset.sh <dataset>
#
# Recommended SBATCH settings per dataset:
# fafb: -c 1 -t 0-96:00 -p medium --mem-per-cpu=25G
# fanc: -c 1 -t 0-12:00 -p short --mem-per-cpu=10G
# hemibrain: -c 1 -t 0-9... |
3993b801a3f621812ddbc7fe81ae04cd64dab52f45a8f2dbf83b0853539fab51 | Shell | 2,620 | 105 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_maa_benchmark_finetune_layer_${LAYER}
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/refer... |
cd974546f1db4e98e3f2947fedcfa40d5c6e92ee6ed1546d19116e0116db3e28 | Shell | 2,627 | 67 |
GENOTYPE_DIR=$1
SAVE_DIR=$2
HASEDIR=$3
STUDYNAME=$4
START=$5
FINISH=$6
CHUNK_NUMBER=$7
get_minimac_chunk(){
echo "***"
echo $@
echo "***"
iter=0
file_ind=0
for i in $( cat ${SAVE_DIR}/files_order.txt | awk '{print $1}' ); do
file=`ls ${GENOTYPE_DIR} | grep ${i}.dose`
file_ind=... |
dc75f864b5edf5c51e48f345cd119162f07aa3de79f188bf2c79952cb5f96fc8 | Shell | 2,627 | 72 | #!/bin/bash
####################################################################################################################################
# run_1_preprocessing.sh
#
# Applies background noise removal to MP2RAGE UNI images using MPRAGEise (github.com/srikash/MPRAGEise),
# converting them to MPRAGE-like images sui... |
f5cfd99743ad955d51f624f172e01e4c829863faf3d88b52730b313c749bb475 | Shell | 2,627 | 39 | # ===========================================================
# 2d loss contours for ResNet-56
# ===========================================================
mpirun -n 4 python plot_surface.py --x=-1:1:51 --y=-1:1:51 --model resnet56 \
--model_file cifar10/trained_nets/resnet56_sgd_lr=0.1_bs=128_wd=0.0005_save_epoch=1/... |
f7c76147d2133a29df636b0ae0ec386522fdd4e471b223a11a68f90bd3492090 | Shell | 2,628 | 102 | #those steps tested on Ubuntu 18. and all linux distribution should works.
cd ~
mkdir gcta_build
cd gcta_build
rootdir=`pwd`
cd $rootdir
wget https://yanglab.westlake.edu.cn/data/gcta_dep.tar
tar -xf gcta_dep.tar
cd $rootdir/gcta_dep
#if you have problems to do this please just copy the mkl file to here $rootdir/mkl... |
2516d48544e6df4e79e31364c883d27786dd2e58950193b51d380702431b9aae | Shell | 2,631 | 54 | #!/bin/bash
# Output file for HTCondor submit
submit_file="submit_run_SHAP-IQ_AutoGluon_Juelich.submit"
# Clear the existing submit file if it exists
> $submit_file
# Define the number of cores (CPUs)
num_cores=1
# Write the environment settings to the submit file
echo "# The environment" >> $submit_file
echo "univ... |
149dfabf6b43c9aef89f0a767c2e987d08aa51eb5b372af66381c4d65e80dd1a | Shell | 2,633 | 91 | #!/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... |
f78f27b1edbd953f0cac0ec9c8e2e9eb30c298ae0172de58b38a0b5322d410ee | Shell | 2,636 | 101 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# This is template script for a simple fixed processing pipeline
# ------------------------------ #
# usage
# ------------------------------ #
usage() {
cat <<EOF
This is template script f... |
f016993fb39f2486af6000165d62b6051173783c52732059a2da25eda710e1fd | Shell | 2,650 | 67 | #!/usr/bin/env bash
# Answer a question with a web search, through the gateway's OpenAI surface.
# The proxy attaches the credential, so no token is needed here.
#
# TODO: delete this script and drop `--disallowed-tools WebSearch` from
# `review.yml` once the gateway serves Anthropic's own web_search. Today it
# reache... |
56ad7f7db757aa946886fe86642a9a577c3d732ab9948bbaf3f420d660b9850a | Shell | 2,654 | 59 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
9493255c7d723c2d048fc83eaed3d7dcafa7fde4b91f6f16162fb94ea3f6fc95 | Shell | 2,654 | 80 | #!/bin/bash
#
# script to extract ImageNet dataset
# ILSVRC2012_img_train.tar (about 138 GB)
# ILSVRC2012_img_val.tar (about 6.3 GB)
# make sure ILSVRC2012_img_train.tar & ILSVRC2012_img_val.tar in your current directory
#
# Adapted from:
# https://github.com/facebook/fb.resnet.torch/blob/master/INSTALL.md
# https:/... |
537858f0bce0c6f89db54ec89ee6ded16f0c70c8488140e2e3439f14368ca698 | Shell | 2,660 | 83 | #!/bin/bash
set -e ${DEBUG:+-x}
function copy_and_export() {
dest_dir=$OPT_DIR/_pg_ssl_certs
mkdir -p $dest_dir
local src_path=$1
if [[ -f "$src_path" ]]; then
src_filename=$(basename -- $src_path)
cp $src_path $dest_dir/
chmod 600 $dest_dir/$src_filename
echo "$dest_dir/$src_filename"
fi
}
... |
8768551f4dbcd241098bc07f9da005413138cd5f6a0adb15794731c38758d6e5 | Shell | 2,666 | 67 | # Author: Javier Gonzalez-Castillo
# Date: January 20th, 2023
#
# Description:
# This script takes two input parameters: subject and run name
#
set -e
echo "++ Load FSL, AFNI and ANTs modules"
module load afni
module load ANTs/2.2.0
# Unset DISPLAY variable
# ----------------------
echo "++ Unset DISPLAY variable"
uns... |
8f876c0660fbc5b56e0bf7c088451e203d7f3cc24b221b4c9ab5e4f75e64c549 | Shell | 2,668 | 63 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
51ae8a0eed1545ac4fe552d2b76701e57c95436dbb9054026b996e99bd93e615 | Shell | 2,671 | 72 | # load packages
module load samtools/gcc/1.10
module load cellranger/8.0.1
module load picard/2.10.3
module load seqtk/1.2-r94
module load bbmap/38.46
# convert bam file to fastq using awk
#!/bin/bash
# packages
module load samtools/gcc/1.10
# go to the correct directory
#cd /home2/gkonop/project/00_BAM_DOWNLOADED/... |
b029b5ede7c3cdde057b01ff416f3f9a237cb9f856b6e6377f3544c9e75408f6 | Shell | 2,673 | 96 | #!/bin/bash
#SBATCH -c 10 # Request cores
#SBATCH -t 4-00:00 # Runtime in D-HH:MM format
#SBATCH -p medium # Partition to run in
#SBATCH --mem-per-cpu=12G # Memory per core (bumped from 8G after 38901939 OOM 2026-05-09)
#SBAT... |
6d0c23fd21a8c62edfb6aa12561732552ae99e2e18e11e154bd8a362ad9ed291 | Shell | 2,679 | 78 | #!/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:/... |
edaae08b24ebae637a2deb8a6b71df6dd026d178d8df51b7273d340cbe8bfae8 | Shell | 2,681 | 74 | #!/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: $0 -i <input_dir> -f <feature_file>... |
f3c5dc1186eb38241d5cc455173df145c8b88975e54631a76edfe70ccfed5e73 | Shell | 2,682 | 105 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
LAYER=0
RUN_NAME=mecap_mca_benchmark_finetune_layer_${LAYER}
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/refer... |
e39fcb5b895783bd55c1e0be132a6b9af4e0fdee7dde3410ef045fd32e2d8379 | Shell | 2,685 | 88 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
# a wrapper to register diffusion and structural images
#--------------------------------------------------------------------------
# version history
# 2016-03-01 Lennart created
#
# copyrigh... |
ecdb9540fe245a371929a97abba17645008a3b6612d932a81ffc67e45a76c6aa | Shell | 2,692 | 59 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO FINAL PREPROCESSING STEPS OF RESTING_STATE SCAN
##
## R-fMRI master: Xi-Nian Zuo.
## Email: zuoxn@psych.ac.cn or zuoxinian@gmail.com.
######################... |
f363d28b103d19f78945c59f23c98aa442f1d2dc5d0fb5b3fb9a168c99320955 | Shell | 2,693 | 69 | #!/bin/bash
# Generate a small VCF, LD, corrlation matricises and allele counts/MAFs
OUTDIR="/data/plink_tests"
mkdir -p "$OUTDIR"
# REF_POPS="/data/merit/refpops"
REF_POPS="/gwas_atlas/ref_genomes/1000genomes_v5a_grch37/POPS"
GENE="ENSG00000097007"
CHR_NAME="9"
START_POS=133589333
END_POS=133763062
FLANK=10000
start... |
31404457c41c2b22dce34c18910d2792751133f300f3bf83c03e21e702c076d6 | Shell | 2,697 | 111 | #!/bin/bash
set -euo pipefail
usage() {
cat <<'EOF'
Usage:
consensus_label.sh --subject SUBJECT --hemi lh|rh [--subjects-dir DIR] [--surf white]
Description:
Creates ?h.subcortex.label from vertices where ?h.curv == 0 and
?h.cortex.label from all other vertices, for one hemisphere.
Required arguments:
--s... |
0e77272912ff627797d928253220e1ffc269356c0f2416786eed5d32af89fd84 | Shell | 2,698 | 67 | #!/bin/bash
# register_brain_extracted_volume.sh — user brain extracted images to get non linear warps
# precon_1 or precon_all -n should be run before running.
set -euo pipefail
usage() {
cat <<EOF
Usage: $(basename "$0") <precon_dir> <animal>
precon_dir path to existing precon_all output directory ... |
f32fbbe676cfc71795a98b7617bd9609cf4f70d6a8882ed3ce912eeae28dd5f3 | Shell | 2,710 | 119 | #!/usr/bin/env bash
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!#
#*********************************#
#.......Make sure you have........#
#*********************************#
#<!-- TREEVIEW START -->
#<!-- TREEVIEW END -->
#*********************************#
#Tags inserted into your README.md#
#********************************... |
23e9fed1533b390f7b5a6283c601e2f86e285b17061f9e5338e58d065b948b28 | Shell | 2,711 | 108 | #!/bin/bash
set -euo pipefail
# Extract druggable targets from a somalogic platform dataset. All targets in a
# separate file
DATA_FILE="$1"
DATA_SET="$2"
TISSUE="$3"
TECHNIQUE="$4"
FLANK="${5:-1000000}"
TMP="/data/tmp"
DATA_TYPE="eqtl"
TARGET_FILE="/gwas_atlas/merit/target_list_grch37.txt"
OUTDIR="/gwas_atlas/merit/d... |
8a93ab2c44a3b9b8638bcd0fe93017102cff41f49e14905f96a8a63b8b8b11fc | Shell | 2,711 | 52 | #!/bin/bash
# Output file for HTCondor submit
submit_file="submit_run_XGBoost_SHIP_htcondor.submit"
# Clear the existing submit file if it exists
> $submit_file
# Define the number of cores (CPUs)
num_cores=1
# Write the environment settings to the submit file
echo "# The environment" >> $submit_file
echo "universe... |
c8b5405d070640c19c5e7200386ee8b1f93e21d5b4e890982c2dc0450fb0cf5f | Shell | 2,723 | 89 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=ilmnrna
#SBATCH --error=jobstar_error_%j.txt
#SBATCH --output=jobstar_output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
function getSampleName {
local f... |
45c29a87d7ad0931be4653e540fe3ab754a9111c9d65cda479337ce954c13cc1 | Shell | 2,725 | 68 | #!/bin/bash
#SBATCH -c 16
#SBATCH -t 2-12:00
#SBATCH -p priority
#SBATCH --mem-per-cpu=15G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_align_v888v2_only_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_align_v888v2_only_%j.err
###############################################################################
#... |
97ebaf5950fd4cedb6f36fb3885a34da4cc2bc8afe5d3d5901b8d6749b7b4793 | Shell | 2,734 | 78 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cuttlefish
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=soYAHS
#SBATCH --error=error_%j.txt
#SBATCH --output=output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
# inputs
file_assembly_contigs="$1"
file_assemb... |
88000159ec8719fe2a7f0ca3226be67d720366ce2fe4ca41e6f5f7006870f844 | Shell | 2,741 | 97 | #!/bin/bash
#SBATCH --job-name=loo-analysis
#SBATCH --output=logs/loo_data2_%A_%a.out
#SBATCH --error=logs/loo_data2_%A_%a.err
#SBATCH --array=1-44
#SBATCH --time=00:45:00
#SBATCH --cpus-per-task=4
#SBATCH --mem=8G
# Create logs directory if it doesn't exist
mkdir -p logs
# Get the subject number from the array task ... |
966d54ad6b93f27164d09d5aec0f477979fbd38e91b878657792148ee1452b03 | Shell | 2,744 | 60 | ## uninstall pre-installed mysql 8.0
sudo sudo apt-get remove --purge mysql*
sudo apt-get autoremove
sudo apt-get autoclean
sudo rm -rf /var/lib/mysql
sudo rm -rf /etc/mysql
## install mysql 5.7
# set deb-conf database answer so we are not prompted when configuring mysql-apt-conf
export DEBIAN_FRONTEND=noninteractiv... |
e5e076fa6458def9c30f46fc962634020de9735dc24a73ca57626261ae283325 | Shell | 2,749 | 69 | #!/bin/bash
#SBATCH -c 16
#SBATCH -t 2-06:00
#SBATCH -p priority
#SBATCH --mem-per-cpu=15G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_ensemble_ind_v888v2_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_ensemble_ind_v888v2_%j.err
#############################################################################... |
ade539e91bdbbc58b48942bd947a206f4ca1935d11d1fa32e25679cf899e9831 | Shell | 2,751 | 67 | #!/usr/bin/env bash
set -eu
# sanity 0: must have jar
echo
if [[ ! -f ${GATK_DIR}/build/libs/gatk-spark.jar ]]; then
echo "Cannot find GATK spark jar, maybe you forgot to build? Given GATK dir.: ${GATK_DIR}"
exit 1
fi
# when debugging minor script changes, it's nice to be able to continue running even if the... |
0c8090dfb9355b5f673d3932d2b9d2012b2aa9c3cd54609c288eb37502531439 | Shell | 2,755 | 78 | #!/bin/bash
# =============================================================================
# STARsolo CLI - Smart-seq / Smart-seq2 platform
# =============================================================================
# Plate-based, no UMIs. Requires a manifest TSV file.
# ===========================================... |
2bb57115918a895faa7dbef1333f2d53a52a578e7aae39a90540618229ec3e3e | Shell | 2,758 | 72 | #!/bin/bash
SCRIPT_DIR=$1
SUBJECT_ID=$2
DST=$3
MODEL_ARGS=$4
echo ${MODEL_ARGS}
if [ -z "$FREESURFER_HOME" ]
then
echo " ERROR: Did not find \$FREESURFER_HOME. A working version of FreeSurfer $FS_VERSION_SUPPORT"
echo " is needed to run the surface reconstruction."
else
if grep -q "${FS_VERSION_SUPPORT}" "$... |
aba8fd9cb1f491c92e28ada482471709a2df51696f71eec3dd3173578be25f77 | Shell | 2,761 | 80 | #!/bin/bash
# =============================================================================
# STARsolo CLI - BD Rhapsody platform
# =============================================================================
# CB_UMI_Complex with 3 barcode segments and 8 bp UMI.
# =====================================================... |
b709cc27c08c0f1412fddfb07f504eed95ebafcd33f228597600e40083111951 | Shell | 2,764 | 93 | #!/bin/bash
#SBATCH --partition=gpus
#SBATCH --ntasks-per-node=1
#SBATCH --time=100:00:00
#SBATCH --cpus-per-task=32
#SBATCH --job-name=ilmnscell
#SBATCH --error=jobstar_error_%j.txt
#SBATCH --output=jobstar_output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
getSampleName() {
local file_fastq="$1"... |
1b3ea56ee0c4dc78d2bf9b62d73679838018cc12b2863c27359af536887ff2b7 | Shell | 2,774 | 67 | #!/bin/bash
# Run elastix to register the BANC's brain to the JRC2018 female brain template
#
# This isn't meant to be run by BANC users but instead to provide a record of
# how registration was done in case we want to reproduce it or improve it later
img_fn=banc-synapse-cloud-v1.1_sizethresh6_blursigma1_16bit0-3_brai... |
b18d1c392840feed84d1b46580f1e6c4dadabb5c46bfc39ad64edaef21b39d16 | Shell | 2,775 | 60 | #!/bin/bash
set -e
WDL=atac.wdl
VER=$(cat ${WDL} | grep "String pipeline_ver = " | awk '{gsub("'"'"'",""); print $4}')
DXWDL=~/dxWDL-v1.50.jar
# general
java -jar ${DXWDL} compile ${WDL} -project "ENCODE Uniform Processing Pipelines" -f -folder \
/ATAC-seq/workflows/$VER/general -defaults example_input_json/dx/templa... |
63593a69ec3a3e083c95c710721c8a62690e4c3b011cffdbab62395672ffdd53 | Shell | 2,776 | 89 | #!/usr/bin/env bash
# change the value between quotes to change what folder in your computer tierpsy
# will have access to.
# If you don't need either the local folder or the network folder, you can leave
# them as empty strings.
#
# e.g :
# Give Tierpsy access to the Desktop
# local_folder_to_mount="$HOME/Desktop/"
... |
36409daca32bf6092affef0f7fbac8f59ef8e72b33c3f060d67bd77c9ea48084 | Shell | 2,780 | 69 | #!/bin/sh
# Last successfully run on March 25, 2026 with git repository version
# a93125d3
# Written by Yapei Xie and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREESURFER_HOME" ]; then
... |
e032205dca6b3c9a7c2700ddc61ed4750215396ccefbbd757e41b948eb6c27db | Shell | 2,783 | 69 | #!/bin/bash
#SBATCH --account=girirajan # TODO: set account name
#SBATCH --partition=girirajan # TODO: set slurm partition
#SBATCH --job-name=gnomad_CNV
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --time=400:0:0
#SBATCH --mem-per-cpu=20G
#SBATCH --chdir /data7/iPSC_corrine/CNV/src
#SBATCH -o logs/1_gnomad.log
... |
282af9381826317e0fddfe37effe654896be373f4723127dad9737532664776a | Shell | 2,792 | 163 | #!/bin/sh
# mos2nrn2 zipfile simdir running
ARCH=x86_64
MODSUBDIR=x86_64
if test "x${NRNHOME}" = x ; then
prefix="/home/hegan/DeepDendrite"
exec_prefix="/home/hegan/DeepDendrite/x86_64"
NRNBIN="${exec_prefix}/bin/"
else
prefix="$NRNHOME"
exec_prefix="${prefix}/${ARCH}"
NRNBIN="${exec_prefix}/bin/"
fi
if test "... |
602353cf98a0ad723e12bb90f2ef30c47f3aaf9b0f8fc6e48e165c650f327d54 | Shell | 2,797 | 43 | # VGGSound_100
CUDA_VISIBLE_DEVICES=0,1 python train_incremental_lwf.py --dataset VGGSound_100 --num_classes 100 --class_num_per_step 10 --modality audio --max_epoches 300 --num_workers 0 --lr 1e-3 --lr_decay False --milestones 100 --weight_decay 1e-4 --train_batch_size 256 --infer_batch_size 128&
PID1=$!;
CUDA_VISIB... |
46d63d9de5a07ab1a46fdd5f9f45043898d66597ae151403bc2062ab7d8d8dae | Shell | 2,800 | 93 | #check if one command line argument is provided else throw an error
if [ $# -ne 1 ]; then
echo "Usage: $0 <name of env>"
exit 1
fi
# print nice message to the user
echo "#################################################"
echo "# Building PQAnalysis conda package #"
echo "###############################... |
2ea777381271bd07a6c39f896d1ae335ffeb1d97e09ba761508f722a64bffca8 | Shell | 2,807 | 86 | if [[ "$DISTRIB" == "conda" ]]; then
# Deactivate the travis-provided virtual environment and setup a
# conda-based environment instead
if [ $TRAVIS_OS_NAME = 'linux' ]; then
# Only Linux has a virtual environment activated; Mac does not.
deactivate
fi
# Use the miniconda installer for faster down... |
af53f3269ac513e560a59206b32afb60d1ea8422ee0b0372c749a151f2b33b8b | Shell | 2,807 | 31 | #!/bin/bash
set -e
docker run \
--env-file ~/env.list \
--mount type=bind,source=$PWD,target=/local1/github_worker,bind-p... |
e50469a49a4809a8697b975031d5fe535dbd543a41b133b6d86f71246106eb21 | Shell | 2,817 | 74 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO REFINE IMAGE REGISTRATION USING GROUP SPECIFIC TEMPLATE
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATIONS*****!!!!!
##
## R-fMRI master: Xi-Nian Zuo. Dec. 07, 20... |
6b83c2a04e8a84b541cd66675cad7fe38a3bca9d33de6c0ef4547983dce1715c | Shell | 2,819 | 74 | #!/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... |
b94cc7238fa8a17a02ff19b7bea6890620e93b22170b735295609f1042185da3 | Shell | 2,822 | 119 | #! /bin/bash
CORE_NUM="8"
tgt="target.tif"
sbj="subject.tif"
output="out"
channel="1"
log="log"
if [ "$#" -eq "1" ]
then
output=$1
log="$1.log"
fi
if [ "$#" -eq "3" ]
then
tgt="$1"
sbj="$2"
output="$3"
log="$3.log"
fi
if [ "$#" -eq "4" ]
then
tgt="$1"
sbj="$2"
output="$3"
log="$3.log"
channel="$4"
fi
# ch... |
444641b9cf47228aa29ae997d5c9ea972d4259dcb351112ead3b10bdb4895be6 | Shell | 2,823 | 80 | #!/bin/bash
####################################################################################################################################
# run_2_brainMask.sh
#
# Performs brain masking/skull stripping and iterative bias field correction on MPRAGEised MP2RAGE images.
# Uses FreeSurfer's mri_synthstrip for brain ... |
13befda6728c03a6e9bcb7f50531deb4d880abc2278b4a00ed1febb577c02a99 | Shell | 2,828 | 90 | #!/bin/bash
# $1: file containing arguments for batch-consistency-analysis.r
# File has 3 tab-delimited fields
# [peakFile1]\t[peakFile2]\t[pairOutFilePrefix]
# Rscript batch-consistency-analysis.r [peakfile1] [peakfile2] -1 [outfile.prefix] 0 F signal.value
if [[ "$#" -lt 1 ]]
then
echo 'submit.idrpair.lsf.sh:' 1>&... |
da70a596a069b3b2008e9056fed2a6c3b191d5d45f507cd01f1b933c7c92e3b5 | Shell | 2,835 | 94 | #!/bin/bash
#SBATCH --partition=cpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=soff_bulk_cts
#SBATCH --error=error_%x_%j.txt
#SBATCH --output=output_%x_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
# set environment
#PATH_BCL2FASTQ=/gpfs/scic/software/biot... |
1747d92c56c4b331573bd775ff5a16ecb1f154410473a062681ea08d8b101ab1 | Shell | 2,839 | 60 | #!/bin/bash
# this function computes the PFM for all models used in our paper
#
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
pred_results_dir=$1
PFM_outdir=$2
#########################################################################################... |
d994f91b29403a05ec6c8e9d5c0321b74af1d7db9b5a25758ebd1a3d03ec94e6 | Shell | 2,840 | 69 | # Author: Javier Gonzalez-Castillo
# Date: January 23th, 2023
#
# Description:
# This script takes two input parameters: subject and run name
#
# This script will extract representative timeseries for the default atlas used in this work
set -e
echo "++ Load AFNI"
module load afni
# Unset DISPLAY variable
# ----------... |
645801194b9ad541028835dc35d0a7b2ca1c7850ee78b697d73157ec3ab5aa2d | Shell | 2,841 | 91 | #!/bin/bash -e
## V3: identify 10X samples, faster processing with tuned fasterq-dump & pigz
PARSED=$1
SRA=`grep -w "SRA$" $PARSED | cut -f1 | head -$LSB_JOBINDEX | tail -1`
SIF="/nfs/cellgeni/singularity/images/reprocess_10x.sif"
CMD="singularity run --bind /nfs,/lustre $SIF"
WL=/nfs/cellgeni/STAR/whitelists
CPUS=... |
518d8eb24c296c7c37b8e2e92026689bc9782785a01d10474b93085fea04c0fb | Shell | 2,845 | 119 | #!/bin/bash
set -e
function usage ()
{
echo "Usage: $0 [-s <source dir>] [-d <cobertura dir>] [-h <history dir>] [-o <output dir>] [-l <license>]" 1>&2
exit 1
}
source="$(pwd)"
directory="$(pwd)"
history="$(pwd)/history"
output="$(date -Id)"
while getopts ":s:d:h:o:l:" key; do
case "${key}" in
s... |
39d012a06598b0a54eb0adf53988e5e0f24bf727c9f190ee7c95aa7c58b82c5f | Shell | 2,878 | 69 | #!/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... |
64c238b25030c422b47e79b65d077b1cf0df0922c28fffd9c12e421477f7e139 | Shell | 2,878 | 77 | #!/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... |
7036f473ce1c2c50e651ea07d0486fdc9588d744bba766ac7a9e8529105800d1 | Shell | 2,887 | 72 | ## Setting up base directory values
user_dir="/data/nsm/velottalab/riley/manuscript_pipeline"
tmp_dir="${user_dir}/data/tmp"
mkdir -p ${tmp_dir}
scripts_dir="${user_dir}/scripts/analyses"
bin_dir="${user_dir}/bin"
data_dir="/data/nsm/velottalab/riley/manuscript_pipeline/data"
reference="/data/nsm/velottalab/public_res... |
fd635524ecf104ed3074a5bedba371e9ae779ca8a4e0e28ab9bbbaaf9d242956 | Shell | 2,888 | 63 | #!/usr/bin/env bash
# Create the k3d cluster used by Tilt for local dev and CI, if it does not
# already exist. The cluster name and k3s node image are overridable so CI can
# pin a Kubernetes version.
set -eu -o pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
REPO_ROOT="$(cd "${SCRIPT_DIR}/../.." ... |
fcbd3ccb11fb9e1aa7d81cfe1e15d62d513f1c8b7ac097d5a8e074753a52820e | Shell | 2,889 | 80 | #!/bin/bash
# =============================================================================
# STARsolo CLI - inDrops platform
# =============================================================================
# CB_UMI_Complex with 2 barcode segments, adapter sequence, and 6 bp UMI.
# ======================================... |
f356288df080d2e784154f711187fcb97eb57bb52378a03cda520a4cf740894c | Shell | 2,891 | 81 | #!/bin/zsh
# This script assumes you already have run the experiments below,
# and the training artifacts are stored in pisces2/results subdirectories:
# Usage: ./make_all_plots.sh [--reset]
# --reset: delete all existing PNG files in final_figures/ before generating
RESULTS_DIR="./results"
FIGURES_DIR="./final_figur... |
f5dc4ffd6ced82dbb31c619fd6be64b67f9e747fe2c4210fba67885ab7985da0 | Shell | 2,896 | 87 | #!/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
#... |
2c131cb52be2e93224a1d6ccac3cdd14619e5f9e9e2e498d854de54f60972c49 | Shell | 2,912 | 83 | #!/bin/bash -e
# Part of STARE: https://github.com/SchulzLab/STARE
# Small bash script to ease the normalization of .hic-files with Juicebox (https://github.com/aidenlab/juicer/wiki/Data-Extraction)
help="\n
Usage: ./Juicebox_KR_normalization.sh [-h hic-file to normalize]\n[-j path to the jar-file]\n
[-d folder to wr... |
bb4ce53b6a94f89e72f8b8fcdc48f1499e6fab2b3d59384c693942cf55a579b6 | Shell | 2,916 | 114 | #!/bin/bash
# see the README file for usage etc.
#
# ------------------------------------------------------------------
# This file is part of bzip2/libbzip2, a program and library for
# lossless, block-sorting data compression.
#
# bzip2/libbzip2 version 1.0.6 of 6 September 2010
# Copyright (C) 1996-2010 Julian S... |
ff740d94fd1667ba56605efbf44665975a96850c23ecc4da135475655b31f963 | Shell | 2,917 | 45 | #!/bin/bash
#BSUB -J VAL_UMi
#BSUB -o ./VAL_UMi_%J.out
#BSUB -e ./VAL_UMi_%J.err
#BSUB -W 68:00
#BSUB -q general
#BSUB -n 1
#BSUB -u pasteris@miami.edu
#BSUB -M 6000
#BSUB -R "rusage[mem=6000]"
#
module purge
module load hihg-analysis java/1.8.0_60 R/4.1.0 perl/5.18.1 samtools/1.3 intel/13.0 impi/4.1.1.036
#
for PHENO... |
75ee6b2669ae2f6f1aeffcf24f3d06c443b6012bcae1eb675daad09a28b492e7 | Shell | 2,918 | 67 | #!/bin/bash
#SBATCH --job-name=SupBigFLICA # Job name
#SBATCH --output=%x_%j.out # Standard output file name (%x: job name, %j: job ID)
#SBATCH --error=%x_%j.err # Standard error file name
#SBATCH --cpus-per-task=2 # Number of CPUs per task (reduced based on low CPU utiliza... |
cbe502a3b79ddd98e36845c59031244f1149a2c3de6e015a3eb39cc4bc129429 | Shell | 2,919 | 117 | #! /bin/bash
CORE_NUM="8"
tgt="target.tif"
sbj="subject.tif"
output="out"
channel="1"
log="log"
if [ "$#" -eq "1" ]
then
output=$1
fi
if [ "$#" -eq "3" ]
then
tgt="$1"
sbj="$2"
output="$3"
fi
if [ "$#" -eq "4" ]
then
tgt="$1"
sbj="$2"
output="$3"
channel="$4"
fi
# check existence
if [ ! -e "$tgt" -o ! -e "$s... |
1b87c5ba8333f908a143e2168763850bf6a9afed7991f3620ff19d308aafd6b1 | Shell | 2,920 | 73 | #!/bin/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"); yo... |
810a9e63105b74d8e2352d3a80443ed6036f2fa45d827732dc2cb1814b7972a8 | Shell | 2,921 | 72 | #!/bin/bash
#SBATCH --job-name=roinet_train
#SBATCH --account=kempner_rhakim_lab
#SBATCH --partition=kempner_requeue
#SBATCH --constraint=h100
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=24
#SBATCH --mem=374000M
#SBATCH --time=3-00:00:00
#SBATCH --requeue
#SBATCH --open-mode=append
## --------------------------------... |
13e8c1b57471bc6e1ff101402ebc78ae7efe5a12ade8384c1200fd9df5b2c75a | Shell | 2,927 | 74 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO IMAGE REGISTRATION (FLIRT/FNIRT)
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATIONS*****!!!!!
##
## R-fMRI master: Xi-Nian Zuo. Nov. 27, 2015, Institute of Psy... |
2602d33b2d4ac9c680a3b4048640026c97de4e4cc3d26fececac8897f3ad4df5 | Shell | 2,928 | 59 | #!/bin/bash
#####
# This script generates the connectome from the tractogram. Additionally fits a DTI model and generates the
# average of DTI indices over each connection from ROI A to ROI B.
#
# Written by Leon Ooi and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#####
########... |
6e059adabd74d59d0c89cf56b05de006f05d18ace8e9974a3553d065a546eefd | Shell | 2,929 | 122 | #!/usr/bin/env bash
################################################################################
#
# WARNING: THIS SCRIPT IS UNSUPPORTED!
# USE AT YOUR OWN RISK
#
# DESCRIPTION:
#
# This script will give you the overlapping encode gene entries for a given
# reference and genomic position.
# It must be internally ... |
ac97ed7918e2e5615bcb4714e6e09b4f8a27b82fdbe6efd53fc1b703a464f74a | Shell | 2,930 | 102 | #!/bin/bash
read -p "Do you want to extract ROI values? (y/n): " extract_answer
if [[ "$extract_answer" =~ ^[Yy]$ ]]; then
while true; do
echo "Enter the parent folder location: "
read parent
if [ ! -d "$parent" ]; then
echo "Error: Parent folder '$parent' does not exist."
... |
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