sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6980dc879a8ef61fb0ca89c1ecaca3a519190cfc44d9fd8bc58705da2141f7df | Shell | 4,758 | 153 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : system.sh
# Simulator : Aldec Active-HDL Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source fi... |
32d12f46dafe0d2f5674054f02edde02f5a800dfc10b424626802dcb5a591d90 | Shell | 4,767 | 136 | #!/bin/bash
#
# Gokberk Alagoz, March 2022 - updated Nov 2022
#-----Munge Sumstats-----
# Reformat GWAS summary stats before computing LDSC intercept
# munge_sumstats.py is from github.com/bulik/ldsc
# Based on the tutorial at github.com/bulik/ldsc/wiki/Heritability-and-Genetic-Correlation
# After final updates on th... |
47dba150c044aa8a7996b8e407b9455809d2a586e4adab38b32c392add47f89e | Shell | 4,777 | 145 | #!/usr/bin/python3
"""
Bias Field Correction via SPM.
Also ouputs the 5 segmented classes.
Currently only supports nii and nii.gz inputs.
Daniel Gomez 2021.03.25 -- initial version
Daniel Gomez 2021.05.08 -- add support for segmentation classes.
"""
import argparse
import os
import os.path as op
import string
import ... |
56d479c75269c2a0eba0e6f4dea48dd711e3c1f1c69a6b2e00e92958485de1f2 | Shell | 4,791 | 95 | #!/usr/bin/env bash
# Spike (Phase 0, plans/06132026_aligner-hisat2-multicore) — HISAT2 `-p N` determinism for Approach B.
#
# QUESTION: Does Bismark `--hisat2 -p N --reorder` (one instance, whole read set, N>=2) produce
# decompressed-BAM content IDENTICAL to the bare-no-`-p` single-core run, deterministically
# run-t... |
76fb2862a44d155ba7fa141b3cfb3c02f6e448e116741185aff96b3b64f3c2f3 | Shell | 4,814 | 95 | #!/bin/bash
# This script will create the necessary input files
# for MAGMA annotation, gene analysis and gene-set
# analysis.
# Gokberk Alagoz, 11.10.22
##########################
# Set Paths
genSEM="/data/clusterfs/lag/users/gokala/beat-dyslexiaevol/results/gSEM/"
geneLoc="/data/workspaces/lag/workspaces/lg-genla... |
c95035bfe3c183ce7b3a4b10d383b568f170d26c7ef3182840d504ae6bf8be57 | Shell | 4,835 | 134 | #!/bin/bash
#Purpose: Determine which subjects have which number of runs available and create lists accordingly for MSHBM Step3.
#Inputs: Generate_data_step_2.5 sess_lists output.
#Outputs: Text lists with corresponding subjects for each number of sessions.
#Written by M. Peterson, Nielsen Brain and Behavior Lab und... |
9621df8a5120e00441af36d6ed9f006f8039ba2931bbfb6c66dae44821d0940c | Shell | 4,838 | 139 | #!/bin/sh
# This function replicate the linear ridge regression results in the HCP 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... |
61bbdc24dc9a5fc785f6f2cd66c1e3c874fd5c918b7835c6756274f117ea2ed5 | Shell | 4,849 | 134 | #!/bin/bash
#Purpose: Determine which subjects have which number of runs available and create lists accordingly for MSHBM Step3.
#Inputs: Generate_data_step_2.5 sess_lists output.
#Outputs: Text lists with corresponding subjects for each number of sessions.
#Written by M. Peterson, Nielsen Brain and Behavior Lab und... |
7aa8901c04f49c76c92200e78aa2669f37d5bea5f33bba8dad3cff7008852738 | Shell | 4,857 | 142 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
c86c262ac9e995130793d9246774444d9fa15cfa7b7814001cb06821893e0a88 | Shell | 4,862 | 167 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_0.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
3f932695a3d968100308df11e27e9859e1fbc787586a55c0ec6b844af8561201 | Shell | 4,872 | 136 | #!/usr/bin/env bash
## build.sh: compile manuscript outputs from content using Manubot and Pandoc
set -o errexit \
-o nounset \
-o pipefail
# Set timezone used by Python for setting the manuscript's date
export TZ=Etc/UTC
# Default Python to read/write text files using UTF-8 encoding
export LC_ALL=en_US.UTF-... |
49774611df5d9e604d9b37c765fe9a3e3477288ff9fcc4bdea1e7e1316426eef | Shell | 4,876 | 160 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : fifo_generator_0.sh
# Simulator : Mentor Graphics Questa Advanced Simulator
# Description : Simulation script for compiling, elaborating and verify... |
f6235bd9589b8c4f442710459450cbdab3d57aab2bf02d4521561831d69d7096 | Shell | 4,890 | 121 | #!/usr/bin/env bash
# Create or verify the project environment, then start the Observatory.
# ./scripts/launch_observatory.sh CUDA GUI (default)
# ./scripts/launch_observatory.sh --cpu explicit CPU validation
# ./scripts/launch_observatory.sh --replay F offline replay, no model weights
# Any other... |
5e2245cb73d472f0dc7348d892e2f7f998c8a9ce71206ce8c9f7031253f9adb8 | Shell | 4,904 | 161 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_4.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
7859630cc8824f54fb771bed4a7c987d6718cca5f68fae3806fdaa54eb9f127c | Shell | 4,904 | 161 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_1.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
8b82e207d5fa1934320d02590cf8d483ece6806fc4e87fe3609badb06148870d | Shell | 4,904 | 161 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_2.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
8d74b103badbeaf4f891275742dace052882c88187f2fdbfe401d6abef321e78 | Shell | 4,904 | 161 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_3.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
94905e0441cd08110d13afa19deaeff427f913217f462957d62ad463f78f711b | Shell | 4,904 | 167 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : system.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the project s... |
b99086227ed7a0a58005659102f9ce18d5d44d58a2b6175d16031dee64b579d4 | Shell | 4,904 | 161 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : vio_0.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
21f811f7430044a623c487ee5dcdfc8add7806134d8757cb98913d4ed97893e1 | Shell | 4,918 | 137 | #!/bin/bash
# Clean out any old sandbox, make a new one
OUTDIR=sandbox
rm -fr $OUTDIR; mkdir -p $OUTDIR
# Check for os
SEP=:
case "`uname`" in
CYGWIN* )
SEP=";"
;;
esac
function cleanup () {
kill -9 ${PID_1} ${PID_2} ${PID_3} ${PID_4} 1> /dev/null 2>&1
wait 1> /dev/null 2>&1
}
function countData... |
68ca83f4201eae846d373db65249746ac63005f9e82599c705749c1ce7400ec3 | Shell | 4,918 | 118 | #!/bin/sh
# This function replicates the variance component model results in the HCP dataset shown in Li et al., 2019
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################
# setup for CIRC cluster
########################
curr_dir=$(p... |
d0b272553a3e63610391ad5e47c9870ecdc99dd1ab4ab49d527f238d1f463db3 | Shell | 4,919 | 92 | #!/bin/bash
# Data downloaded from https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6814
input_dir=/media/NAS1/Sammi_NAS1/Processed_Reads/OrganDevelopment/human
samtools_tmp_dir=OrganDev_v1
mkdir -p $samtools_tmp_dir/fixmate
mkdir -p $samtools_tmp_dir/possorted
mkdir -p $samtools_tmp_dir/markdup
mkdir -p... |
73047bef1510d9027b2390e9ffdc917160f878a200f6d4b3fa7c71cc379627ae | Shell | 4,956 | 156 | #!/bin/bash
# author : sjn
# date : Aug 22, 2022
# histogram of nucleosome lengths
# report stats: median length of 80-220 bp nucs
# (#80-220bp)/(#250-450bp) mono vs. di-nucleosome ratio
set -euox pipefail
if [[ $# != 4 ]]; then
printf "Expect $0 <sample-name> <input-file> <output-pdf> <output-stat... |
10ffe0f9a2ba8f791b48fdc575b338e108f6b3b679bd764fec326c6b6684399a | Shell | 4,966 | 174 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_0.sh
# Simulator : Mentor Graphics Questa Advanced Simulator
# Description : Simulation script for compiling, elaborating and verifying the pro... |
1844b661e27bd1fb206c869e564fdf2c217e3a32bf01ad039cbf14309fea2f31 | Shell | 4,991 | 152 | #!/bin/bash
set -e
# Build script for creating XCFramework for iOS and macOS
# This script builds the Kiwi library for multiple platforms and architectures
# and combines them into a single XCFramework
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
PROJECT_ROOT="$(cd "$SCRIPT_DIR/../../.." && pwd)"
SWIFT_... |
a49a5b553657901aa46e7979ec59f4dcfc095147ab4f434b2fe86d26f3131b03 | Shell | 5,008 | 174 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : system.sh
# Simulator : Mentor Graphics Questa Advanced Simulator
# Description : Simulation script for compiling, elaborating and verifying the pr... |
33928890de0364fa3edec214d16b55f4d417264d2055b9aaca0e0cce27888cd6 | Shell | 5,047 | 161 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : fifo_generator_0.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the... |
93294bb8813fcfe3211f3b9a525d5a546e2287fd21afec59ca9a4c770921e119 | Shell | 5,054 | 82 | #!/usr/bin/env bash
# Phase 0 determinism spike — Rust bismark-aligner port.
#
# Question: is Perl Bismark v0.25.1 -> Bowtie2 2.5.5 deterministic enough that a
# faithful Rust reimplementation can be byte-identical? (SE directional.)
# Criteria: C1 two full Bismark runs -> identical records + header
# ... |
9b36440e17bd0d022faf99f3d2854559ef86f74d009b6e1f5d27c2887a4a5e64 | Shell | 5,120 | 168 | #!/bin/bash
## All original files have to be in an original folder
## to modify interactively
##MY_MAINDIR="/mnt/2T/Insync/ONEDRIVE/REINSTALLED/projects_vault/Projects/2023/1_AvianInfluenza/12302_Avian_influenza_2023/data/sea_eagle_consensus/data_2_ok/H5N1"
##MY_STRAIN="H5N1"
##MY_ARTICLE="SEP"
##MY_DATASET="NVI2"
##... |
c91bebedbc8b8e2126b30a296976e648dda5d2aa4374e1b2d56df6c5320e66df | Shell | 5,132 | 93 | #!/bin/bash
# This script will generate bed files for magma gene-set analysis.
#
# Gokberk Alagoz - 04.08.2022 - last updated on 08.08.2022
##########
# PATHS
resources="/data/workspaces/lag/workspaces/lg-genlang/Working/23andMe/Dyslexia2/Evolution/dys_rhy_pleiotropy/resources/"
annots="/data/workspaces/lag/workspac... |
26b46886e54c8783c0da8f5bb65eb05d0e653e956b13074d1b317e48759d00ee | Shell | 5,173 | 114 | #!/usr/bin/env bash
# oxy B-faithful gate — Rust `bismark_rs --hisat2 --multicore N` must be byte-identical
# (decompressed BAM body) to Perl `bismark --hisat2 -p N` for the matching N. The remap
# routes `--multicore N` → ONE HISAT2 instance with `-p N --reorder`, so the oracle is
# Perl's `-p N` mode (NOT single-core... |
1a2b51044fcd0dae3c4e9cdefc6f954767863aae1782ba688e217abd178752e5 | Shell | 5,199 | 224 | #!/bin/bash
# file: tests/test-utils-semaphore.sh
if [ -f tests/test-helper.sh ]; then
. tests/test-helper.sh
elif [ -f ./test-helper.sh ]; then
. ./test-helper.sh
else
echo "no test-helper.sh in tests dir or current dir."
exit 1
fi
SHUNIT2_SRC_DIR=/mp/nas1/share/lib/shunit2
SEM=utils/semaphore/semaph... |
88eb5f5e91d80d00e3eb84b1c994045beae3a82500ca60f45dba04470df6e36a | Shell | 5,290 | 228 | #!/bin/bash
# Setup Manubot
# Based on https://github.com/manubot/rootstock/blob/main/SETUP.md
# This is designed to be run from the bash terminal
# Stop on first error.
set -e
usage() {
echo "Usage: $0 [--owner text] [--repo text] [--yes]"
echo "Guides the user through the creation of a new Manubot repository for th... |
bbd0f2377b6e0ad1346bcb44057e75a5179f30be206b917848f831cdb09cdf89 | Shell | 5,300 | 132 | #!/bin/bash
# This script will generate example input data for two examples:
# 1) group priors estimation
# 2) indidividual parcellation generation
# The user need to specify the output directory, which will later contain two folders:
# 1) estimate_group_priors
# 2) generate_individual_parcellations
# Written by Ru(by... |
622267219e53b349b4eb9a42d6c3bcb98cfa1add37691e6841c106efa1a087e0 | Shell | 5,303 | 202 | #!/bin/bash
set -e
set -u
function showHelp() {
#
# Display commandline help on STDOUT.
#
cat <<EOH
===============================================================================================================
Usage:
$(basename $0) OPTIONS
Options:
-h Show this help.
Required:
-i inputfile (final report f... |
c0bca5ee965936666e806d35181faa2c1b6198cfd4093ce22e2f0ee011cbda40 | Shell | 5,330 | 107 | #!/bin/bash
# Phase-2b oxy PE byte-identity gate (HISAT2 backend, single-core).
# Runs Perl bismark v0.25.1 --hisat2 + HISAT2 2.2.2 and the Rust bismark_rs
# --hisat2 with IDENTICAL argv into the SAME -o (Perl moved aside), then diffs
# DECOMPRESSED SAM (samtools @PG filtered) + the _PE_report.txt (wall-clock
# filtere... |
4f21081a15be97dfefb803180b1adb15be8f837714221d43df247e116db9a430 | Shell | 5,354 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_2.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying the project... |
579f5c97a59556fba87dd3b1c668ac4c0a73daba0203ad4ff1fab75ccc045546 | Shell | 5,354 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_4.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying the project... |
affcf9224f8c7eaef06896f93ebbcfa21134cfcbbed95a4b11837258ec870e73 | Shell | 5,354 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_3.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying the project... |
b12039c3e9e8601b59638b5c1d84c56f2412884f7adc36f2af58ce7a7abc2368 | Shell | 5,354 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : vio_0.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying the project... |
fdc433f5d54f60eab452187cbf29ce54e52c0564ab7b24c771813c45af334217 | Shell | 5,354 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_1.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying the project... |
032fc49346f715185ab3dc710071c4e4fafda4f822137c5fc3cbe5e5fa4ddd1c | Shell | 5,363 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_1.sh
# Simulator : Cadence Xcelium Parallel Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
59ec5844651be9a06e9e1952d72e0967a7218749c1c879f23696273382d7a742 | Shell | 5,363 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_2.sh
# Simulator : Cadence Xcelium Parallel Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
77d17c893a9b556b810d63fad93f8d67d8e076ba9121c4e94b3795a598f11da8 | Shell | 5,363 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_3.sh
# Simulator : Cadence Xcelium Parallel Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
d6e2cf6ead4e120f1b13692bc421c3651f7e16e4f6832d737ae245b9acde90d8 | Shell | 5,363 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : vio_0.sh
# Simulator : Cadence Xcelium Parallel Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
e16720c9be78ad92c7eac1d7ff6ea708f4b528b0b7ebe84208baa080dfd27f9a | Shell | 5,363 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_4.sh
# Simulator : Cadence Xcelium Parallel Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
06544faf2e0f4ebf14512b1e4feed26b24c433c8718c4fe9bc565ead31e21d5c | Shell | 5,388 | 131 | #!/usr/bin/bash
##########################
##### Download fastqs ####
##########################
# E14.5 NEUROD2
module load SRA-Toolkit
prefetch SRR1951389
fasterq-dump SRR1951389 -o e14.5.neurod2.1.fastq
prefetch SRR1951390
fasterq-dump SRR1951390 -o e14.5.neurod2.2.fastq
prefetch SRR1951392
fasterq-dump SRR195139... |
f09ba5921057046a22042214e86a9d0212fe06188617e0eb1d6375c89011179d | Shell | 5,392 | 108 | #!/bin/bash
#SBATCH -J snakemake
#SBATCH --time=12:00:00
#SBATCH --partition short
#SBATCH -N 1
#SBATCH -n 2
#SBATCH --mem=4G
#SBATCH --account # Specify the SLURM project to charge the job. If you don't have, remove the line
#SBATCH --mail-type=ALL
#SBATCH --mail-user= # Email address to send notific... |
936df93e7fc2c8872634234357b9fca23b8199f5c4889702b50c3e6aa80334a5 | Shell | 5,431 | 162 | #!/bin/bash -f
# Vivado (TM) v2015.4 (64-bit)
#
# Filename : clk_wiz_0.sh
# Simulator : Mentor Graphics ModelSim Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files.
# The script will automatically create the design libraries sub-directories i... |
02fbaa38543282b4fb27a4daedfda5b69f147a646684fc1630e3b0006a61b9c9 | Shell | 5,462 | 113 | #!/bin/bash
# Phase-2a oxy SE byte-identity gate (HISAT2 backend).
# Runs Perl bismark v0.25.1 --hisat2 + HISAT2 2.2.2 and the Rust bismark_rs
# --hisat2 with IDENTICAL argv into the SAME -o (Perl moved aside), then diffs
# DECOMPRESSED SAM content (samtools @PG filtered) + the report (wall-clock
# filtered). Cells: SE... |
66c42afc81b941232a6c9b3293faa81edb0bf5547493826e0972815f41b38484 | Shell | 5,483 | 88 | #!/usr/bin/env bash
# oxy byte-identity gate — Rust `bismark_rs --hisat2 --local` must be byte-identical
# (decompressed BAM body) to Perl `bismark --hisat2 --local` for the matching cell.
# HISAT2-local = drop `--no-softclip` (soft-clip allowed) + L-form `--score-min L,0,-0.2`
# + local ln() MAPQ, no `--local` flag. R... |
be3965ac178229926de55c4e25a225b76573b4976bf470b6fe454a8f0fdce6a8 | Shell | 5,490 | 161 | #!/usr/bin/env bash
MetadataFile=${1}
FastqDir=${2}
# Check if input arguments are provided
if [[ -z ${MetadataFile} || -z ${FastqDir} ]]; then
echo "Usage ${0} DRE_metadata.tsv /path/to/fastq/dir"
exit 1
fi
head ${MetadataFile}
# Step 1: Read metadata file and store [ProjectSeqBatch]-[Barcode]-[SampleName] mappi... |
a0e0673ca2f180532a1e7dc2c000fe3a9be0cc1d7cfe72dbf5f9ac9de2c3c01b | Shell | 5,508 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : fifo_generator_0.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying ... |
f96063d7a7afc463a64fdf4a6e067e755bbee96b323f518fd2bdde57f3bb24a4 | Shell | 5,517 | 173 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : fifo_generator_0.sh
# Simulator : Cadence Xcelium Parallel Simulator
# Description : Simulation script for compiling, elaborating and verifying the... |
41892079e4bf850802bcbdb5cce03c40c9719a712331c6a401bfaad56930327e | Shell | 5,525 | 31 | #!/bin/bash
#for run in 1.1.1_C1 1.1.2_C1 1.1.3_C1 1.1.4_C1 1.1.5_C1 1.1.6_C1 1.1.7_C1 1.1.8_C1 1.1.9_C1 1.1.10_C1 1.2.1_C1 1.2.2_C1 1.2.3_C1 1.2.4_C1 1.2.5_C1 1.2.6_C1 1.2.7_C1 1.2.8_C1 1.2.9_C1 1.2.10_C1 1.3.1_C1 1.3.2_C1 1.3.3_C1 1.3.4_C1 1.3.5_C1 1.3.6_C1 1.3.7_C1 1.3.8_C1 1.3.9_C1 1.3.10_C1 2.2.1_C1 2.2.2_C1 2.2.... |
bdaf31f9b41e132a36090ce17eec80bedcc852f64fd3eb628762e9cd0af269d8 | Shell | 5,534 | 177 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_0.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying the project... |
340835fa42135e140386f620fed50ea821d38e7efe1cb111348beae511fe428a | Shell | 5,541 | 169 | #!/bin/bash -f
# Vivado (TM) v2015.4 (64-bit)
#
# Filename : clk_wiz_0.sh
# Simulator : Mentor Graphics Questa Advanced Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files.
# The script will automatically create the design libraries sub-direct... |
60b675bdd6d0ac47bab37c4713c48ff46173911560c7461a76e5d7b23b252940 | Shell | 5,543 | 177 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_0.sh
# Simulator : Cadence Xcelium Parallel Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
da43501baa3adf2ea24d0883388e38d588d27111dc9c135cd77dbd6e1d4b8858 | Shell | 5,555 | 55 | aws s3 sync --no-sign-request s3://openneuro.org/ds000030/sub-10299/anat ds000030-download/sub-10299
aws s3 sync --no-sign-request s3://openneuro.org/ds000030/sub-10316/anat ds000030-download/sub-10316
aws s3 sync --no-sign-request s3://openneuro.org/ds000030/sub-10428/anat ds000030-download/sub-10428
aws s3 sync --no-... |
7a69328775e6d3719f77d7542d21bcb448548cc1ba8e7f3183dd109367752eb9 | Shell | 5,558 | 197 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_1.sh
# Simulator : Xilinx Vivado Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files.... |
c338a1f8a5cd513843ee7f7ac1506626e5f32376f3727933577d469abba049f3 | Shell | 5,558 | 197 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_2.sh
# Simulator : Xilinx Vivado Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files.... |
dff0fd338dfde6b4fbad0461f01731621b4e91529c4ba355acec9f22800cac77 | Shell | 5,558 | 197 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : vio_0.sh
# Simulator : Xilinx Vivado Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files.... |
e4568600af4ad2174adcba25a9bc12d0066495fe00f0472d3f9f450d3bb89dc1 | Shell | 5,558 | 197 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_4.sh
# Simulator : Xilinx Vivado Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files.... |
f6a7bc53fa4f19eeaf31b34aaa41d0da007302517ed7cf48584cd7c288316200 | Shell | 5,558 | 197 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_3.sh
# Simulator : Xilinx Vivado Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files.... |
728f0ac59e9718135045cf0e23ce70b5ddfc6bbbdbd4e30def46306648d69b25 | Shell | 5,562 | 32 | #!/bin/bash
#for run in 1.1.1_C1 1.1.2_C1 1.1.3_C1 1.1.4_C1 1.1.5_C1 1.1.6_C1 1.1.7_C1 1.1.8_C1 1.1.9_C1 1.1.10_C1 1.2.1_C1 1.2.2_C1 1.2.3_C1 1.2.4_C1 1.2.5_C1 1.2.6_C1 1.2.7_C1 1.2.8_C1 1.2.9_C1 1.2.10_C1 1.3.1_C1 1.3.2_C1 1.3.3_C1 1.3.4_C1 1.3.5_C1 1.3.6_C1 1.3.7_C1 1.3.8_C1 1.3.9_C1 1.3.10_C1 2.2.1_C1 2.2.2_C1 2.2.... |
dd026e8d303e3822e662428814ac941fe2f3f7e3dafe2543c5b328c157de9f06 | Shell | 5,582 | 200 | #!/bin/bash
### 1. set paths ###
## set parameter parsings for user-specified paths ##
usage="## this script calculate window nucleotide diversity.\n
usage: bash $0 [-h/--help] [-w/--work_directory <path>] [-s/--dir_snp <path>]\n
[-m/--dir_mpileup <path>] [-c/--chr_assignment <path>] [-a/--sample_size <path>] [-r/--in... |
03ff5f1d9c4a1c36a3d88313bf8ff1979f8a8644255b8229accbef1ff035e417 | Shell | 5,598 | 179 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This function warps an input volumes to a target volume space with specified ANTs warp or inverse warp files
###########################################
# Main commands
###############... |
6995877fc8be9a0890a0ef32d0ded362097a6a49ea85ae6eaeb4645d5808cbe7 | Shell | 5,609 | 151 | #!/bin/bash
# ==============================================================================
# == Launch analysis
# ==============================================================================
# ------------------------------------------------------------------------------
# -- Variables
# -------------------------... |
86f7ba0afc282699b0cbb88383d828dc409e3d9a0e9ad1ddca0b2c4ef3b0faed | Shell | 5,625 | 171 | #!/bin/bash
set -x
## Clean data in output directories used for testing/tutorials
## TEST
echo $PWD/
if [ -d $PWD/code/tests/results ]; then
rm -rf $PWD/code/tests/results/*
else
mkdir $PWD/code/tests/results
fi
## TUTORIAL exp_ssmb
# tracing
if [ -d $PWD/data/tutorials/exp_ssmb/tracing/mb_single/graph/cyto ]; th... |
ef10746fc548cc795e0520aedf60f9c17ffc6355e380d32f5ffff5151e47422a | Shell | 5,626 | 158 | #!/bin/sh
# This function replicate the kernel ridge regression results in the HCP dataset shown in Li et al., 2019
#
# Written by Jingwei Li and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################
# setup for CIRC cluster
########################
curr_dir=$(pwd... |
20137f8fa8ac56758026ab2385e9532ccfe4410965daa23dd328144cc5b8f6aa | Shell | 5,643 | 146 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#This script projects fsaverage surface data to MNI152 volume space using Freesurfer baseline approaches
###########################################
#Define paths
#######################... |
b0cd76ab7873c62dc7adfdb04fbf5cd0bad307fc779380ffdf7d4e3c438eb057 | Shell | 5,701 | 197 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : fifo_generator_0.sh
# Simulator : Xilinx Vivado Simulator
# Description : Simulation script for compiling, elaborating and verifying the project so... |
54b48cc06664d1c09583bf4d6a0fc6dcfe6c4f875197be2cd31a0eb39f077b11 | Shell | 5,716 | 125 | #!/bin/bash
# Argument parsing
if [ "$1" = "jacoco" ]
then
JACOCO_ENABLED=true
else
JACOCO_ENABLED=false
fi
# Clean out any old sandbox, make a new one
OUTDIR=sandbox/single
MKDIR=mkdir
SEP=:
case "`uname`" in
CYGWIN* )
MKDIR=mkdir.exe
SEP=";"
;;
esac
rm -fr $OUTDIR
$MKDIR -p $OUTDIR
f... |
ef3c55ed10142cc832367c58e54eed7bf15f4bd36ffb55b76d9d6e6006c08357 | Shell | 5,763 | 174 | #!/bin/bash
#Package loading required before running
#apt-get install dcm2niix
#apt-get install jo
#apt-get install jq
#set -e
# setting your dataset path here
homedir=/home/amax/CPP/data/
dcmdir=${homedir}/HCRAW
niidir=${homedir}/HCBIDS
if [ -d ${niidir} ];then
rm -r ${niidir}
fi
mkdir ${niidir}
jo -p "Name... |
08c9201de998481ee1005a382a09384012f287bf9f879bf371ca9aadf3925349 | Shell | 5,779 | 188 | #!/usr/bin/env bash
set -euo pipefail
REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)"
NEXTFLOW_ROOT="${REPO_ROOT}/nextflow"
param_value_from_args() {
local key="${1}"
shift
local arg=""
local next=""
while [ "$#" -gt 0 ]; do
arg="${1}"
next="${2:-}"
if [ "${... |
6a4674e3f1d4d42648b2bde037baf15364837eae7ffc82deb2a8ec50ecc91f9e | Shell | 5,819 | 152 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#This script computes average mapping from MNI152 to fsaverage across a specified number of GSP subjects, for a specified RF approach (by supplying the corresponding input prefix)
######... |
40eeaff4f6ff12662125494eb6a3c4a01d2c071a859349d309552ed814e47f8a | Shell | 5,835 | 111 | #!/usr/bin/env bash
#
# byteid_run.sh — full-scale byte-identity (PARITY-with-Perl) gate for one dataset.
# Part of plans/05302026_extractor-fulldata-validation/PLAN.md (Phase 1).
#
# Two checks per dataset:
# (1) Rust-vs-Perl PARITY — runs scripts/phase_h_smoke.sh at --parallel 1 (Perl
# --multicore 1, determi... |
96bf2a77be110d71d582ab1e47a9881d86d5b5eca69745cbc6e93b167b958925 | Shell | 5,856 | 55 | #!/bin/bash
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
22b64c45bd9d8288414d96d196b2e03ff9fc0d744da883ad2baeb24e19ee0284 | Shell | 5,896 | 200 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_1.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying the project s... |
5d1f86d23ecb7a9641bec7b9cfa9163eeb6648437d7816b8c9a846b0cbc1e378 | Shell | 5,896 | 200 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_4.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying the project s... |
899a97dc9c07370d4274dfeaa34ffe68de27ee7500e6ef74e5c6e271957f2894 | Shell | 5,896 | 200 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_3.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying the project s... |
a58bf5111b6752607f365b46171dc4e8b48272b5f1101a2160a76d7c7b179ea7 | Shell | 5,896 | 200 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_2.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying the project s... |
d1cf445430d16008a8adb1f9e771cc45b6716b9e5523e79e01413354d65e9b0e | Shell | 5,896 | 200 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : vio_0.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying the project s... |
bd93bc16eb260c4085bccdf58ecc4e84fb4f637ed39c71ed22fc12ec253dd81a | Shell | 5,963 | 154 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This function runs RF-ANTs vol2surf mapping creation and projection using 1 subject
RF_DIR=$CBIG_CODE_DIR/stable_projects/registration/Wu2017_RegistrationFusion
RF_VOL2SURF_DIR=$RF_DIR... |
14abf3b03cd4a5717ab29e2eb3ca4c94fead497f38c1f4bb109ea73f745b5c16 | Shell | 5,968 | 150 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#This script uses the mappings generate using Registration Fusion approach to project batch data in a volumetric space to fsaverage surface
###########################################
#S... |
2df940434cfa063ba05d7ed94bddf3436302925f080fc7c8644bb1fb43debc51 | Shell | 5,991 | 196 | #!/bin/sh
# This script serves as a toy example of using the code in folder step1_FC2doc
# and step2_polarLDA in Tang2020_ASDFactors
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#############################################
# Specify output director... |
dbd03f13c6c2ed578c0993b9793d539cddb6f15c7c790d1a302705fa101b7ba6 | Shell | 6,038 | 211 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : ila_0.sh
# Simulator : Xilinx Vivado Simulator
# Description : Simulation script for compiling, elaborating and verifying the project source files.... |
b668c87135acaeb6a14cb9aa5d28ed90a98b825ca0492e909c32e33215fde1f7 | Shell | 6,061 | 200 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : fifo_generator_0.sh
# Simulator : Synopsys Verilog Compiler Simulator
# Description : Simulation script for compiling, elaborating and verifying th... |
30e62084e6bf74b5b3b88031caac187946924a43234978de579e043b7b066bb6 | Shell | 6,072 | 161 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This function runs RF-ANTs vol2surf mapping creation and projection using 5 subjects
RF_DIR=$CBIG_CODE_DIR/stable_projects/registration/Wu2017_RegistrationFusion
RF_VOL2SURF_DIR=$RF_DI... |
b456b9782c6992618da698e0fa38404ca5c93c5b05b133219004c911dbe303ba | Shell | 6,104 | 149 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#This function uses the mapping generated using Registration Fusion approach to project batch surface data in fsaverage to a volumetric atlas space
######################################... |
3b3e6bf1f5ee4fea8302cb744d6ad41b4074258d9c72452906fd7063396569f3 | Shell | 6,140 | 63 | #! /bin/bash
################################################################################
# bash script for ASL analysis for K6. Written for Unix, FSL v6.0 #
# Author: Sofie Tapper, IMT, Linkoping University, sofie.tapper@liu.se #
# October 2023 ... |
99cbe1e42281b877d029925db1dc6b3ef76136cf76a3563fc05314bec23141fb | Shell | 6,204 | 129 | #!/bin/bash
# Argument parsing
if [ "$1" = "jacoco" ]
then
JACOCO_ENABLED=true
else
JACOCO_ENABLED=false
fi
# Clean out any old sandbox, make a new one
OUTDIR=sandbox/single
MKDIR=mkdir
SEP=:
case "`uname`" in
CYGWIN* )
MKDIR=mkdir.exe
SEP=";"
;;
esac
rm -fr $OUTDIR
$MKDIR -p $OUTDIR
f... |
48228abd4a8671793ec4e1a3bb1596613c891dbcb39228b0dc6423a2f93bec1e | Shell | 6,285 | 259 | #!/bin/bash
# Latest version of this script can be found at:
# https://github.com/NanoComp/meep/blob/master/contrib/build-meep.sh
help ()
{
cat << EOF
$1: Download MEEP sources and dependencies, compile, and install
Usage: $1 [options]
EOF
sed -ne 's,[ \t]*\(-[^ \t]*\))[^#]*#[ \t]*\(.*\), \1 \2,p' "$1"... |
6575617588d565fad47bb4df533bd2793f6ac30623f2f1c93bf006ca6a97bfd3 | Shell | 6,297 | 113 | # AIM: Run BetaScan on high-quality SNPs for all chromosomes
# Use VCF file as input, with genotypes having less than 4 read depth recoded as missing
# Follow the example provided in the tutorial here:
# https://github.com/ksiewert/BetaScan/wiki
##################################################
# STEP 1: Insta... |
b68ce92fa2b2a883e909ec4f46deefd84bfb5859db5feaee6ac156655ee56aa0 | Shell | 6,307 | 57 | #! /usr/bin/env bash
# BF-C2DL-HSC
# python /opt/elephant/script/train.py --baseconfig /opt/elephant/script/base_train_seg.json seg /opt/elephant/script/BF-C2DL-HSC_seg_GT.json
# python /opt/elephant/script/train.py --baseconfig /opt/elephant/script/base_train_seg.json seg /opt/elephant/script/BF-C2DL-HSC_seg_ST.json
#... |
3a787455fd73cabeb07fa9f6b0c7dea10fd8b929dcc1e82cc29e9c66fe26f15b | Shell | 6,327 | 188 | #!/usr/bin/env bash
set -euo pipefail
REPO_ROOT="${REPO_ROOT:-$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)}"
MOCHI_REPO="${MOCHI_REPO:-${REPO_ROOT}}"
MOCHI_VENV="${MOCHI_VENV:-${MOCHI_REPO}/.venv}"
PYTHON_BIN="${PYTHON_BIN:-${MOCHI_VENV}/bin/python}"
MOCHI_ENTRYPOINT="${MOCHI_ENTRYPOINT:-${MOCHI_REPO}/pymochi/b... |
822be6e8cdc1235f08576f67216134418c1d659acfdb7072ea363dd17926ced7 | Shell | 6,358 | 200 | #!/bin/sh
#
# Example:
# sh ./CBIG_ASDf_unit_test.sh ~/storage/Temporaray/CBIG_ASDf_unit_test
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################################
# Set paths and create log file
#######################################... |
69739c7c97c467ef3ea8d72f3261340d84fe4a876d7b9b4547a30a987b9106d2 | Shell | 6,360 | 182 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : system.sh
# Simulator : Cadence Incisive Enterprise Simulator
# Description : Simulation script for compiling, elaborating and verifying the projec... |
fb40f3a1088c9fc8f2eea2f8e7e01e42c687f8b579adf4fe97e8021c3b6e5153 | Shell | 6,369 | 182 | #!/bin/bash -f
#*********************************************************************************************************
# Vivado (TM) v2018.2 (64-bit)
#
# Filename : system.sh
# Simulator : Cadence Xcelium Parallel Simulator
# Description : Simulation script for compiling, elaborating and verifying the project s... |
f4487462acdffe2ed508c8cdcb7d4e5b64cf24f8197968b258ef24626089f768 | Shell | 6,370 | 210 | #!/bin/sh
#
# Example:
# sh ./CBIG_ASDf_replication.sh ~/storage/Temporaray/CBIG_ASDf_replication
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################################
# Set paths and create log file
###################################... |
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