sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
323349f7433c3ed505088d9ea212a0059da107ad7ef3c8552320df5164cacade | Shell | 1,891 | 56 | # conda activate scrna-seq
# bash /data/private/psurana/TSpDNA2/src/3_attention/2B_meme.sh
#!/bin/bash
res_pdir="/data/projects/dna/pallavi/DNABERT_runs/DATA_RUN/dnabert2_FineTune_Zhihan_attention_extracted/july_2025_mmseq/RESULT/lr3e-5_ep10/"
dir="TSp_vs_nonProm_3k_tsptestis_nonPromHu"
full_fasta_file="$res_pdir/$di... |
82c8fb0a2c4c08e8816cc8de13e86fb46272c02d79fc7c558e044f796f752ee8 | Shell | 1,892 | 83 | #!/bin/bash
CHROMFA=$1
OUTFILE=$2
TRF=$3
NUMPROC=$4
MAXCHR=$5
TMPPREF=$6
BASE=$(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)
... |
bb5a73351ac45560436d264a392924352d6d9da2b9b7e145501d52bed186f0fc | Shell | 1,898 | 45 | #!/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
# "Li... |
22a37ba593f742a83013e96a4108804b45247c88e689c21f135a954caef5f22a | Shell | 1,900 | 53 | #!/bin/bash
#SBATCH -o logs/fastp/fastp-%j.out
#SBATCH -e logs/fastp/fastp-%j.err
#SBATCH --time=3:00:00
#SBATCH --mem=4G
#SBATCH --cpus-per-task=6
module load cesga/2020 gcccore/system fastp/0.22.0
# This script takes three positional arguments:
# 1. the directory where the fastq files are located
# 2. the r1 fastq ... |
dd8aebdb5ac454405d6e8d9115c024161277c1700dd1f605af64804c080193f9 | Shell | 1,900 | 62 | #!/bin/bash
#
# A script that takes a prebuilt docker image, and pushes it to the GATK release repositories on
# dockerhub and GCR
#
# Usage: release_prebuilt_docker_image.sh <prebuilt_image> <version_tag_for_release>
#
# If the prebuilt image exists locally, this script will push the local version. Otherwise,
# it wil... |
75d78df8bf6f7baeaeea0a673569f1355fba78aeeacf5d21795408a4e69ac5de | Shell | 1,903 | 46 | #!/bin/bash
# Elastix affine
# Use corresponding points to drive the alignment (ignoring two pairs
# at the start of the neck connective which will be used in Bspline).
# Use a mask to only pay attention to image correlation in the central
# brain (though image correlation isn't that important anyway when
# correspond... |
57f8d5e316af7bc29ddcfe33cb71adc307ae33ca4486d5cfe285bea289e157da | Shell | 1,904 | 76 | #!/usr/bin/env bash
set -e # stop immediately on error
umask u+rw,g+rw # give group read/write permissions to all new files
#--------------------------------------------------------------------------
# General dimension swapping for imaging files and vectors. This version created
# after discussion with Paul McCart... |
1dda2d1627660694b32d119b01ee1650dfc3f2f9c815a1b8f52fee6b59837c44 | Shell | 1,905 | 44 | #!/bin/sh
# Last successfully run on Oct 29, 2020 with git repository version v0.17.2-CBIG_preproc_spatial_distortion_correction
# Written by Pansheng Chen 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 ex... |
e067eb58e25c919316b07c02d525d42deaf16505a3f5a30de13b1ce38d6ade2b | Shell | 1,907 | 60 | #!/bin/bash
# SegVol Zero-Shot Evaluation Pipeline for KiTS23
#
# Evaluates the pretrained SegVol model (BAAI/SegVol) on KiTS23 using
# text-prompted zero-shot inference. No training required.
#
# Environment: conda activate segvol
# -------------------------------------------------------------------
set -e
KITS23_DI... |
bf73af7edac4ab8f29c5bb185289f420bedf521003f4e587ff70f445294b491f | Shell | 1,909 | 48 | #!/bin/bash
# Name for the job that will be visible in the job queue and accounting tools.
#SBATCH --job-name count_ferret_rxn2
# Name of the SLURM partition that this job should run on.
#SBATCH -p 256GB # partition (queue)
# Number of nodes required to run this job
#SBATCH -N 1
# Time limit for the job in t... |
832f7d2c26c281fd8a2999729c22d87bbd2bef62f254f5ad1b2fc06e383fef15 | Shell | 1,912 | 81 | #!/bin/bash
Usage() {
echo " "
echo "Usage: `basename $0` [options] -i <BrainT1 image> "
echo ""
echo " Compulsory Arguments "
echo "-i <T1.nii.gz> : Image must include nii or nii.gz file extension "
echo " Optional Arguments"
echo " -o <output_directory> : Outp... |
1c6d15baa225a403f49ba45591c3d48b07ab686daadb87ecd39f2cffc4e48d48 | Shell | 1,913 | 47 | #!/bin/bash
###################################################################
#created by Davit Bzhalava on 2014-07-08 #
#compares sequence database with itself using ncbi blast #
###################################################################
#sudo nohup /media/StorageOne/HTS/... |
e5d56bc45e170aa495951b7440ae3a4e39dd7fb84eae847fb0ae2893b8219ba2 | Shell | 1,915 | 6 | #!/usr/bin/env bash
C:/Users/Niflheim/Documents/GitHub/SpikeGLX_tools/CatGT-win/CatGT.exe -dir=//oak-smb-giocomo.stanford.edu/groups/giocomo/export/data/Projects/JohnKei_NPH3/AO1 -run=AO1_231221_postop_day9_dark01 -g=0 -t=0,0 -prb=0 -ap -ni -gblcar -gfix=0.4,0.10,0.02 -prb_fld -out_prb_fld -apfilter=butter,12,300,10000... |
8c7278c327431a70a36df34cc22b78d60827c98699a3866399110dd36404eb38 | Shell | 1,917 | 54 | #!/bin/bash
# This script submit a job to HPC for CBIG_fMRI_Preproc2016 single subject unit test within a Singularity container.
# Written by Fang Tian and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# First, define the directory to store the Singularity image
IMG_DIR="$HOME/sto... |
2195d84b17c9f8673b97bf8e2dbb72dcb3db1735279838d648c1812925239d13 | Shell | 1,919 | 90 | #!/opt/homebrew/bin/bash -i
# Find working directiory
# Function to display script usage
usage() {
echo "Usage: $0 [OPTIONS]"
echo "Options:"
echo " -h, --help Display this help message"
echo " -i, --read1 File path to read 1"
echo " -o, --out File path to output"
}
has_argument() {
[[ ("$1" == *=*... |
4c53c78d43694dc19c4e8249ecc1b7c8b6fbf9312c92a82cdfffd78f0c5d74d8 | Shell | 1,919 | 49 | #!/bin/bash
#SBATCH -c 8
#SBATCH -t 5-00:01
#SBATCH -p long
#SBATCH --mem=249G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_ntac_rerun_%A_%a.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_ntac_rerun_%A_%a.err
#SBATCH --array=0-2
###############################################################################
#... |
404437d4de92ee13c54e25ce3b8cd6e08834dc35a6f5bcf0778b80b0c8e968e0 | Shell | 1,928 | 47 | #!/bin/bash
set -xe
echo "Activating test environment:"
conda activate testenv
if [[ "$PYTHON_VERSION" == free-threaded* ]]; then
# This is needed because for now some C extensions have not declared their
# thread-safety with free-threaded Python, for example numpy and coverage.tracer
export PYTHON_GIL=0... |
c29616f7ff9d4ee9d297c9ab1419865da0cc73508f3bc5ab7574a92c1d6a985c | Shell | 1,931 | 67 | #!/bin/bash
# Set directories
BASE_DIR=""
OUTPUT_DIR=""
CSV_FILE=""
WMH_MASK_FILE=""
export FREESURFER_HOME="PATH/TO/FREESURFER"
export SUBJECTS_DIR=${BASE_DIR}
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export FSLDIR="PATH/TO/FSL"
export FS_LICENSE="FREESURFER/LICENSE.txt"
source $FSLDIR/etc/fslconf/fsl.sh
# Create ... |
009def2f0aeb5f3db32ca59f71586fffc858b07021342b32718a96088880de87 | Shell | 1,933 | 63 | #!/bin/bash
#PBS -l walltime=8:00:00
#PBS -N fmriprep-nightowls
#PBS -q normal
#PBS -l nodes=1:ppn=14
# load modules and go to workdir.
umask 0000
module load singularity
cd $PBS_O_WORKDIR
# ensure paths are correct
projectname=night-owls
maindir=/gpfs/scratch/tug87422/smithlab-shared/$projectname
scriptdir=$maindir/... |
e2c5b39d5e38421e21999e25bc9c0436f297c560d564cf5321bec2f266920aa3 | Shell | 1,933 | 41 | #!/bin/bash
basedir="/mnt/y/PROJECTS/GMmicrostructure/DATA/Longitudinal_VIPD/SESSION1"
cd ${basedir}
mapfile -t allsubs < /mnt/y/PROJECTS/GMmicrostructure/DATA/Batch.txt
template=/mnt/y/PROJECTS/GMmicrostructure/DATA/fsaverage/fsaverage_brain.nii.gz
for sub in ${allsubs[@]}; do
subdir=$basedir/$sub
cd $subdir
... |
28790a545feea4e3d710ea5a47a03d2cbf91c9d71c5b0a88ebd743d27ae4906c | Shell | 1,934 | 61 | #!/bin/bash
#
# Collects the pull-requests since the latest release and
# arranges them in the CHANGES.txt file.
#
# This is a script to be run before releasing a new version.
#
# Usage /bin/bash update_changes.sh 1.0.1
#
# Setting # $ help set
set -u # Treat unset variables as an error when substituting.... |
f69f25e714fb8f980af53cba52b02c050b91377fe84a2b4bd3d68d191a9612ff | Shell | 1,934 | 60 | #!/bin/bash
#
# A script that takes a prebuilt GATK base image, and pushes it to the GATK release repositories on
# dockerhub and GCR. Use the build_docker_base_cloud.sh or build_docker_base_locally.sh scripts to
# build the image before running this script.
#
# Usage: release_prebuilt_base_image.sh <prebuilt_image> <v... |
551f7d7e394ffbf09959dd9e761a9c82366db0b7fe688897d71c4720552d0a0d | Shell | 1,938 | 61 | #!/bin/bash
# 1. Easy to Classify Wake. Used as a baseline model.
# This provides CSV rows with train set = test set, for comparison later.
# It also provides AUROC baselines
python run_config.py \
-pc config/processing/frequency_sum.json \
-mc config/models/etc_model.json \
-cvc config/cv/tr_h_test_... |
b48c1fe53cb589032c7316ad58f872ce0bcab49e59cf89cca2d5e37ccb9cd15e | Shell | 1,938 | 35 | # ===========================================================
# 1d normalized surface for VGG-9
# ===========================================================
mpirun -n 4 python plot_surface.py --x=-1:1:51 --model vgg9 \
--model_file cifar10/trained_nets/vgg9_sgd_lr=0.1_bs=128_wd=0.0_save_epoch=1/model_300.t7 \
--mpi -... |
20bdd19e566bb7a0fd14faea6da4f6ecd12b5e57104f7300fa1fe0835f56e10c | Shell | 1,941 | 65 | #!/bin/bash
#SBATCH --account=def-pbellec
#SBATCH --time=24:00:00
#SBATCH --job-name=shi_mvpa_seslvl
#SBATCH --output=logs/slurm/%x/%x_%j.out
#SBATCH --error=logs/slurm/%x/%x_%j.err
#SBATCH --mem=256G
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40
# Arguments from task launcher:
# $1 = subject (e.g., sub-01)
# $2 = sc... |
2241d40f98ce2741510c8fcf3379472e7a38e927d34d15176093af2277b1a2f4 | Shell | 1,941 | 87 | #!/bin/bash
CHROMFA=$1
OUTFILE=$2
TRF=$3
NUMPROC=$4
MAXCHR=$5
NONNUMCHR=$6
TMPPREF=$7
$NONNUM=${NONNUMCHR//,/ }
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 ... |
fa20913bffbd1a2934aa2cacd9a8058e5d20ddea4ae712445cf3834400550a7d | Shell | 1,942 | 53 | #!/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... |
7b25201810a090e3e269e09572aae4e55034ee0c65103c349108557a01d1c5e3 | Shell | 1,944 | 53 | #!/bin/bash
#SBATCH -c 8
#SBATCH -t 2-12:00
#SBATCH -p priority
#SBATCH --mem=250G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_ntac_v888v2_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_ntac_v888v2_%j.err
###############################################################################
# WB NTAC run on v888... |
889cbe298f00ab6665554da6cf6a65dad25df6b1d59db1e6640a4a25807c7154 | Shell | 1,948 | 57 | #!/bin/sh
# how to build from just the cvs sources
# takes us only to the distribution level.
# must still run a ./configure commmand (see examples after autoconf command)
########################################
########################################
# the following commands must be executed in this directory
sh gi... |
41344c45e0901e592e43546e37b40a8e6c82b50901b28253d5dd357c071b830c | Shell | 1,950 | 56 | #!/bin/bash
# Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is 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... |
812379aca22aa342cfb561d42ae0f18a8c792668770a76cd730ce854e6e9e92e | Shell | 1,951 | 66 | #!/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
# ------------------------------ #
# Help
# ------------------------------ #
usage() {
cat <<EOF
rsn_swapdim.sh: Swap the d... |
e254cac7e6c83051ba148179a5ba27b94f2892cd8e57531a74df6303d3370e53 | Shell | 1,952 | 18 | CUDA_VISIBLE_DEVICES=0 python train_aba.py --model AVresnet18 --node-type ReLUNode --dataset KineticSound --epoch 100 --batch-size 32 --num-classes 31 --step 1 --modality audio-visual --alpha 0.8 --modulation OGM_GE --fusion_method concat --seed 2025 --inverse --inverse-coef 0.1 --output ./exp_aba&
PID1=$!;
CUDA_VISIB... |
f17a399e69afe7cf4de24dbc8847b5337a069f3cef0a02b050af548a0c44a2a6 | Shell | 1,954 | 61 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=soffDNA
#SBATCH --error=joblog_error_%j.txt
#SBATCH --output=joblog_output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
function getSampleName {
local fil... |
871519145c9ac870853201c60a4db0545e4a14754f754e3354e3f1c528897b59 | Shell | 1,959 | 51 | #!/bin/bash
########################################################################
# #
# This pipeline is only for processing the multicenter diffusion data. #
# From Qiqi Tong, CBIST, Zhejiang University. #
# ... |
95370d8431012bba02439d4785ccfcbcd30fe41c7354b7dd4732a0a96d3d87e5 | Shell | 1,959 | 47 | #!/bin/bash
#SBATCH -c 1 # Request cores
#SBATCH -t 1-12:00 # Runtime in D-HH:MM format (actual ~27h)
#SBATCH -p medium # Partition to run in
#SBATCH --mem=48G # Total memory (bumped from 12G after recurring OOMs 2026-05-... |
26990b277b98c0433b571bc3ed160fa62fda6abf8300cd4ebb6cbf5b231b0e2c | Shell | 1,962 | 54 | #!/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... |
b5cb826ecd67cc57356947d933ddd0913366161eae8962edb699f2cb4812be8f | Shell | 1,962 | 51 | #!/bin/bash
#########################################################################################
# BWA_NR
# Copyright (c) 22/08/2013 Davit Bzhalava
##########################################################################################
#
# Alligns row anassembled pairend sequences to quey fasta and estima... |
52833695f18d81dcea0390d87dea235546fae43baccf4920388eb753a6ce9c87 | Shell | 1,966 | 66 | #!/bin/bash
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
set -e
PYTORCH_NIGHTLY=false
DEPLOY=false
CHOSEN_TORCH_VERSION=-1
CHOSEN_TRANSFORMERS_VERSION=-1
while getopts 'ndfv:t:... |
b1d048cbc898628c3fb15aef96703850dd4565a3341e289294ecc7dab8d5bd1f | Shell | 1,968 | 83 | #!/bin/bash
# Extract druggable targets from a somalogic platform dataset. All targets in a
# separate file
DATA_FILES="$1"
DATA_SET="$2"
FLANK="${3:-1000000}"
TMP="/data/tmp"
DATA_TYPE="pqtl"
TISSUE="blood"
TECHNIQUE="somalogic"
TARGET_FILE="/gwas_atlas/merit/target_list_grch37.txt"
OUTDIR="/gwas_atlas/merit/druggable... |
23ddb8ddaaacc3fa78b90a7b4a7ac5cd92c434b938fcad1430025980627bfd09 | Shell | 1,969 | 57 | #!/bin/bash
# Usage: ./submit_all_single_jobs_in_run.sh Run1_Figures
if [ $# -ne 1 ]; then
echo "Usage: $0 <RunDirName>"
exit 1
fi
RUN_DIR_NAME="$1"
# User specific variables
CURRENT_USER=$(whoami)
USER_FIRST_LETTER=${CURRENT_USER:0:1}
if [ "$CURRENT_USER" = "rwollman" ]; then
BASE_RUNS_DIR="/u/home/r/rw... |
773e86d9575e042417d10252eff2a552f1cbe0660dcf51e3c3468d30d2653757 | Shell | 1,974 | 49 | #!/usr/bin/env bash
##########################################################################################################################
## CCS SCRIPT TO DO IMAGE REGISTRATION (FLIRT/FNIRT)
##
## !!!!!*****ALWAYS CHECK YOUR REGISTRATIONS*****!!!!!
##
## R-fMRI master: Xi-Nian Zuo. Dec. 07, 2010, Institute of Psy... |
5d3dd4c1dab9fe042c9d565e9f188e0465ef26cd78fc19ab83178d134125a3b0 | Shell | 1,979 | 46 | #!/bin/sh
#####
# This is a wrapper script to run prediction algorithms in the ABCD dataset.
#
# EXAMPLE:
# CBIG_ME_ABCD_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=$CBIG_COD... |
041d8af891468f43c3f7064665d293834772dc32bcfa0ab3d6e25d15faca4dec | Shell | 1,981 | 21 |
export UCRTContentRoot='C:\Program Files (x86)\Windows Kits\10\'
export INCLUDE='C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE;C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt;C:\Program Files (x86)\Windows Kits\8.1\include\shared;C:\Program Files (x86)\Windows Kits\8.1\include\um;C:\P... |
40a8800f14bf2f500f3bd4b2ccdb14c8f93d5079ea0e41a3e7dd1ddac81b94a2 | Shell | 1,982 | 57 | #!/bin/bash
#SBATCH -c 4
#SBATCH -t 0-01:00
#SBATCH -p short
#SBATCH --mem=32G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_optic_prep_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_optic_prep_%j.err
###############################################################################
# Optic lobe alignment prep (loca... |
a5bc3a35985e60fe298898089a7a1936dad2d0fd0df40196262a86b40357358f | Shell | 1,984 | 56 | #!/bin/bash
#SBATCH --job-name=soSEQKIT
#SBATCH --partition=gpus
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=32G
#SBATCH --error=joblog_error_cleanMito_%A_%a.txt
#SBATCH --output=joblog_output_cleanMito_%A_%a.txt
#SBATCH --array=0-10
#### source library
path_script="/gpfs/scic... |
7f4682f87d034312519a392649d1be98b416657ef7ea29ce4739ee7ae20809f9 | Shell | 1,985 | 47 | #!/bin/bash
# Copyright 2018 Google LLC.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following dis... |
d2d9595e282b95ff4775cfad390d675d41cedc47f57960383fb15d036461bb9e | Shell | 1,988 | 59 | #!/bin/bash
# define project directory and working directory
pd=/your/project/directory/
input_dir=$pd/data/validations/nanopore_FASTQ
output_dir=$pd/data/validations/nanopore_BAM
mkdir -p $output_dir
# map human samples
for i in `ls $input_dir/human*.fastq.gz| xargs -n1 basename`;
do
sample_name=`cut -d _ -f... |
040f3469c8803617cceeffe30f06a230ae5df49e7b0fe76afd000cd7d0c90f3d | Shell | 1,991 | 36 | #!/bin/bash
# fmriprep was used to align MNI152NLin6Asym 1mm T1 images (non-skull stripped) to the MNI152NLin2009cAsym:res-01 space,
# which is 1mm space in templateFlow that fmriprep uses to pull its templates. This produced ants format *.h5 files which
# are composite affine/warp files.
# these files were created by... |
ab12d5e60f07af764c208d8f32603da0dd6a61574b4b893c769d8aa589eef4b8 | Shell | 1,994 | 44 | #! /bin/sh
# Last successfully run on July 13, 2021 with git repository version v0.20.0-Kong2022_ArealMSHBM
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# DO NOT CHANGE: This clears old freesurfer variables if they previously exists
if [ -n "$FREES... |
0cf0767def17a788e79642e7ba3e70b3d3cfffd4b64e581bebe9c70ddf781e65 | Shell | 1,997 | 50 | #!/usr/bin/env bash
# Download data
python ../src/download.py single \
--variable orography land_sea_mask soil_type \
--level_type single \
--output_dir /media/rasp/Elements/weather-benchmark/raw/constants \
--years 1979 \
--month 01 \
--day 01 \
--time 00:00 \
--custom_fn constants_raw.nc
# Regrid data to 5.625 degr... |
6ffcff1abd49c4a390f9c93b8f3b3044159886e7d0d138f49d40ff65491bb847 | Shell | 1,998 | 35 | # ===========================================================
# 1d normalized surface for ResNet-56
# ===========================================================
mpirun -n 4 python plot_surface.py --x=-1:1:51 --model resnet56 \
--model_file cifar10/trained_nets/resnet56_sgd_lr=0.1_bs=128_wd=0.0_save_epoch=1/model_300.... |
6c16d563599d192be3ec3fdfc1c1463f55025cf4bd10c324bba48b7c36f4f15a | Shell | 2,012 | 56 | #!/bin/bash
# This script sets up CBIG's Python environment for containers.
# Compared to the original version ($CBIG_CODE_DIR/setup/python_env_setup/CBIG_python_env_generic_setup.sh):
# 1. This script removes redundant codes for containers (e.g., checking the existence of CBIG_py3).
# 2. This script creates the envir... |
3c0ba9f5e66dd3ff55e2afe618bc6eaf5aa72b7ad787124ee0917dc47e6211b7 | Shell | 2,014 | 50 | #!/bin/bash
# this version was based on fmriprep output
ROOT=/dartfs-hpc/rc/lab/C/CANlab/labdata/projects/bogdan_atlas
RES_DIR=$(readlink -f $ROOT/_resources)
NPM_DIR=/dartfs-hpc/rc/lab/C/CANlab/modules/Neuroimaging_Pattern_Masks
#make subcortical mask
# we doubly dilate it so that it encompases the subcortex in th... |
2e44f320e57a8e835949415cff5aac89c6b132c64e23051386fd90244dcc26a1 | Shell | 2,015 | 59 | #!/bin/bash
#
# CREATED USING THE BIOHPC PORTAL on Fri Jun 21 2019 22:56:40 GMT-0500 (Central Daylight Time)
#
# This file is batch script used to run commands on the BioHPC cluster.
# The script is submitted to the cluster using the SLURM `sbatch` command.
# Lines starting with # are comments, and will not be run.
# L... |
756ecb59ec5410066b4f8249dc9639100ab43550c609a26b8eae4bb367755f19 | Shell | 2,015 | 67 | # This scripts sets necessary environment variables for external tools.
# It should be sourced, not executed!
# e.g. source tools/setenv.sh
# get the current shell
shell=$(ps -p $$ | tail -n 1 | awk -F' ' '{ print $4 }')
if [[ "${shell}" == *"bash"* ]]; then
# get the path to this script
basepath=$(dirname $(r... |
aca93acec99dfeeedf982d527a4392946a2c5ad5952b9f2dc301ae86defe3ed4 | Shell | 2,016 | 63 | #!/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... |
4fcdd501236773e8d860563cf27af32eb4222fcbd95c155cf04b7d92d667ac38 | Shell | 2,019 | 43 | #!/bin/bash
# this function runs all the kernel regressions in Chen & Tam 2021 paper
#
# Written by Jianzhong Chen and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
pred_results_dir=$1
perm_out_dir=$2
################################################################################... |
89a4961abe4eb0374238493f27a503a25fbba421dd8c2cdbebf2600dad226977 | Shell | 2,024 | 68 | #!/bin/bash
# Ensure the script stops on first error
set -e
# Get the directory of the current script
SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
# Function to print log messages with timestamp
source "$SCRIPT_DIR/utils/_log.sh"
source "$SCRIPT_DIR/utils/_colors.sh"
# Ask the user fo... |
950b30e3fdd665b6d8f62822afccfb6e0788a54a46311d2db4ff6b7dcdf7597f | Shell | 2,037 | 97 | #!/opt/homebrew/bin/bash -i
# Function to display script usage
usage() {
echo "Usage: $0 [OPTIONS]"
echo "Options:"
echo " -h, --help Display this help message"
echo " -i, --read1 File path to read 1"
echo " -I, --read2 File path to read 2"
echo " -o, --out File path to output"
}
has_argument() {
... |
d4d0c3feb6ed4dd4b671bed7cd504f48624d344e9b833e706a4e9fcc4996edd2 | Shell | 2,037 | 67 | #!/bin/bash
### basically a script to keep downloading things for as long as it is necessary
### step 0: start downloading everything using transfer queue
SERIES=$1
if (( $# != 1 ))
then
>&2 echo "USAGE: ./continuous_download.sh <series_id>"
>&2 echo
>&2 echo "(requires bsub_transfer.sh, cleanup_wget_download... |
c59261c04e1792e6eb0c0c14a9177f54d26c8b0546e2aabd51a8d22feeac1843 | Shell | 2,039 | 61 | #!/bin/bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... |
cc0290d786e12d71f71527bec4256425b5f2d8e4394552b914a72a3ae8c82ef0 | Shell | 2,040 | 71 | #!/bin/bash
#$ -cwd
# error = Merged with joblog
#$ -o job_logs/job_log.$JOB_ID
#$ -j y
## Edit the line below as needed:
#$ -l h_rt=24:00:00,h_data=48G
## Modify the parallel environment
## and the number of cores as needed:
#$ -pe shared 12
# Get the current username
CURRENT_USER=$(whoami)
echo "User identified as $... |
eefda888974f90216e25703b0f8b4ecabbf630d51f458b00694d70803d64d336 | Shell | 2,041 | 56 | #!/bin/bash
#SBATCH -c 8
#SBATCH -t 0-04:00
#SBATCH -p priority
#SBATCH --mem-per-cpu=12G
#SBATCH -o /home/ab714/bancpipeline/jobs/banc_wb_prep_v888v2_priority_%j.out
#SBATCH -e /home/ab714/bancpipeline/jobs/banc_wb_prep_v888v2_priority_%j.err
############################################################################... |
0017382f280ad9e487474200006e60bbbd2f78ce13d7ac7bff6b10f7b8443247 | Shell | 2,043 | 54 | #!/bin/bash
#SBATCH --job-name=hi7
#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... |
5d4f66671a72ac1b8223647dec10c5ced5574c690456c2138e620d2bf08730ed | Shell | 2,043 | 54 | #!/bin/bash
#SBATCH --job-name=hi8
#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... |
8cb97ea3e48fe8882af10e80f9b28ede0181a24e42d73b30667e5b051e0df857 | Shell | 2,043 | 54 | #!/bin/bash
#SBATCH --job-name=hi6
#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... |
a5618382f1653005a1ec4ea3e8884182507973c88c5d3e912720f46e2fa7724e | Shell | 2,043 | 54 | #!/bin/bash
#SBATCH --job-name=hi3
#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... |
c90e6b62bb4578702df83ff071cd95d27e73bed7bb8761eee58e3d0194c88a6d | Shell | 2,043 | 54 | #!/bin/bash
#SBATCH --job-name=hi4
#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... |
eff26b434e3412290bd6a7438c67e37c101aac0ad623c32c59975b830b3b450b | Shell | 2,043 | 54 | #!/bin/bash
#SBATCH --job-name=hi5
#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... |
bdb7a276c1520fe98c66b0a3dfac5cc49739bc83c7f309d5e2d406f8e1a4e379 | Shell | 2,045 | 24 | #!/bin/bash
export path_htsa_dir=$1
export path_pipeline=$2
export project_work_dir=$3
export work_fasta=$4
echo "pfam $work_fasta"
filename_extention=$(basename $work_fasta)
extension="${filename_extention##*.}"
filename="${filename_extention%%.*}"
$path_htsa_dir/$path_pipeli... |
e102a7ca6dd7a7942235fe667bf9b1644190bba27c42c1f06989480dcc7494c4 | Shell | 2,046 | 50 | #!/bin/bash
source /home/h.bi/anaconda3/etc/profile.d/conda.sh
conda deactivate
conda activate new_autogluon
# Set the environment variables
export MKL_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1
# Define feature combinations and targets
feature_comb_list=("Sleep... |
aa804056ad0960b8e364b3a6035d0008b03053189f4e8411d94aedde4370e2ab | Shell | 2,048 | 57 | #!/bin/bash
### apply dual threshold to a WM probability/posterior image
### strict threshold outside a region mask, lenient inside it
### use to rescue under-called WM in difficult regions (e.g. temporal pole)
### without over-claiming WM elsewhere
### output goes to <precon_dir>/mri/wm_hand_edit.nii.gz
usage() {
... |
2ee9fe44cd3866691fc1765622429fe7132a2fae421f3ba9d359ec0aa29f5fdc | Shell | 2,051 | 79 | #!/bin/bash
path=/mnt/d/data_analysis/TN
cd ${path}
#rm -rf cortex_ts_TN_E
#mkdir cortex_ts_TN_E
cd cortex_ts_TN_E
for sbj in 20
#for sbj in {1..30}
do
rm -rf ${sbj}
mkdir ${sbj}
cd ${sbj}
#3dresample -input ${path}/TN_E_xcp_out/sub-${sbj}/ses-ST0/func/sub-${sbj}_ses-ST0_task-rest_space-MNI152NLin2009cAsym_desc-deno... |
057afd6120a18111c323553dfcb88d864557c4e00d1f01934a07194b4e7d5fb0 | Shell | 2,053 | 54 | #!/bin/bash
#SBATCH --job-name=hi17
#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-Second... |
08ef12a91b56d4c5d8589526a46b3830daa7660f1b55d25d7c5088db11c3e550 | Shell | 2,053 | 54 | #!/bin/bash
#SBATCH --job-name=hi16
#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-Second... |
0d286fc749e5eab2dc1c12e75544b8437661c6f1b938b942ceda3c24b58bb485 | Shell | 2,053 | 54 | #!/bin/bash
#SBATCH --job-name=hi11
#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-Second... |
1639caa332b36ce616b41d9dde44ac377e8d4085b574cc4dfa363871ae0055c0 | Shell | 2,053 | 54 | #!/bin/bash
#SBATCH --job-name=hi13
#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-Second... |
318bd5e168c14758afb5e36cf3d2dd7276c5e38f2e7c172b7ada99881f9b8a5f | Shell | 2,053 | 54 | #!/bin/bash
#SBATCH --job-name=hi18
#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-Second... |
3678f1717dc178ee0c8c297da394f1db58f03451e837565c7bae6b8b4130ea0d | Shell | 2,053 | 54 | #!/bin/bash
#SBATCH --job-name=hi12
#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-Second... |
9ea381d0a5f0ce49ab03ed4ef2034dea03d4ac1ef67fbaac233b7a3e1212b773 | Shell | 2,053 | 67 | #!/bin/bash
#SBATCH --nodes 1
#SBATCH --ntasks 60
#SBATCH --job-name WGBS
#SBATCH --mem 400G
#SBATCH --time=3-00:00:00
#SBATCH --output WGBS_%j.out
ulimit -n 10000
module load gcc
source /work/upzenk/miniconda3/bin/activate
conda activate snakePipes
# This script is for running the WGBS pipeline using snakePipes
use... |
3566247f0c5b88e3e014004375748c81a7ea697f02e05f0e71333a9caf5b33ef | Shell | 2,054 | 44 | #!/usr/bin/env bash
# Download all required data for genomes and store in HDFS. Use this for non-GCS clusters.
TARGET_DIR=${1:-q4_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 dire... |
a91d170fcc718c52bd291a6a69a11d43f0bd43c3c38a029aad37cb4ee3d9b26a | Shell | 2,054 | 59 | #!/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 directory... |
5a6b1e0ae7c83e511166e0ff8030cc84cfd8c625ce8591a0b35067815d12aa2b | Shell | 2,055 | 67 | #!/bin/bash
#$ -cwd
# error = Merged with joblog
#$ -o job_data_format.$JOB_ID
#$ -j y
## Edit the line below as needed:
#$ -l h_rt=1:00:00,h_data=64G
## Modify the parallel environment
## and the number of cores as needed:
#$ -pe shared 1
# Get the current username
CURRENT_USER=$(whoami)
echo "User identified as ${CU... |
78a1f0bbe47d608ad8173358f3a0971ba61a20b1f61b34e05e572b360d45b3fa | Shell | 2,057 | 49 | #!/usr/bin/env bash
# Builds a manifest of bgen chunk genomic bounds (chrom, first/last variant position) by reading
# each chunk's local .bgi index via bgenix -list (index-only, no genotype data touched -- cheap even
# for hundreds of chunks). Runs in parallel across all local CPUs.
#
# Output paths are rewritten from... |
5e454e33bf43d0ed60b8125053a0cbef4b973125861144ecb5216fd1bf7cde66 | Shell | 2,063 | 57 | #!/bin/bash
basedir="/mnt/y/PROJECTS/GMmicrostructure/DATA/"
cd ${basedir}
mapfile -t allsubs < /mnt/y/PROJECTS/GMmicrostructure/DATA/Batch.txt
tian_atlas=/mnt/y/PROJECTS/GMmicrostructure/DATA/Tian_Subcortex_S2_3T_1mm.nii.gz
output=$basedir/ALL_SUBJECTS_NODDI_TIAN.csv
echo "SUBJECT,ROI,NDI_MEAN,ODI_MEAN,FWF_MEAN,NDI... |
cb8d28ca5c22eeb15543bef7a3064834e7b2583e4d582bff5e89d5c565e55ffc | Shell | 2,063 | 55 | #!/usr/bin/env bash
#
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... |
d622c2af1ee5303b23dc67ebecc647394a35e5c5af01f2e1084325d049e36892 | Shell | 2,068 | 77 | #!/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)
cellranger_outs=... |
6e5208c94090f0c1a70364011d23c0f4348868925777704684517d0ea452d60d | Shell | 2,070 | 44 | #!/bin/bash
# Output file for HTCondor submit
submit_file="recon-all_Juelich_FreeSurfer.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 ... |
96c7a25581170a87e6be43640ceaee0039cc3a012684e0b769ef9fc56653aec2 | Shell | 2,070 | 67 | ######################################################################
## This script is used to compile and install openmm
## and openmm-velocityVerlet.
##
## Usage:
## ./install.sh [OPENMM_DIR]
## - [OPENMM_DIR] is optional. If not specified, defaults to:
## /usr/local/openmm
################################... |
61c6bf66c6196d611236fed87fa39bb3aa9271c4c75019dc9ff0b39255d11723 | Shell | 2,071 | 62 | #!/bin/bash -e
# Parse args.
if [ $# -ne 1 ]; then
echo "Usage: $0 build_dir"
exit 1
fi
build_dir=$(realpath "$1")
# Set up the venv.
echo "Setting up venv"
if [ ! -e .coverage_venv ]; then
python3 -m venv .coverage_venv
fi
# shellcheck disable=SC1091 # "Not following: .coverage_venv/bin/activate was not ... |
4677f0c68375f82f20cdc501d8199ddd7278f792db695ff6511822332fdc4b3e | Shell | 2,075 | 51 | #!/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
#... |
fef77b8d674cd32e2650bd4fa65ec3bbab6b0de7fd90bbc577fb07344920d9a1 | Shell | 2,075 | 62 | #######################################
#### Run computation time analysis ####
#######################################
python run_time_by_order_HOI_toolbox.py \
--min_T 1000 \
--min_N 30 \
--min_order 3 --max_order 31 \
--output_path ../results/times/time_by_order_library-hoitoolbox.tsv
python run_t... |
393ecc13cb774e44cbf70520d1a7d6d5388696a4a91aeb3e2e75f4e559c3e477 | Shell | 2,078 | 72 | #!/usr/bin/env bash
set -euo pipefail
#
# EAS-SNN HAPQ FPGA build / simulation wrapper (Vivado batch mode)
#
# Usage:
# fpga/scripts/run_vivado.sh [synth|sim]
# - synth (default): 运行综合，输出 utilization/timing 报告
# - sim: 运行行为仿真
#
# 必须在项目根目录 (EAS-SNN) 下执行，或脚本会自动 cd 到根目录。
#
# Board / Part:
# - Target FPG... |
9c360f5fe4791d404e18012380a205401766a123410122b12a6429c466ecd14f | Shell | 2,078 | 69 | # Must be run from the directory that contains this script (docker-aims)
# This script
####################################
# 1. Downloads brainvisa dev image #
####################################
: ${CASA_BASE_REPOSITORY:=/volatile/bv/casa_distro_repo} # set default value
export CASA_BASE_REPOSITORY
export IMAGE_... |
180c7b2d282446a01b2eae5b33e21fa4ef7255e1c670e0154552741455d050ef | Shell | 2,080 | 60 | #!/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
#... |
60948d74ce9619a1897ec0cb052335ef7ce77d27870dd0ea31ded8ed6ba29698 | Shell | 2,080 | 70 | #!/bin/bash
#SBATCH --nodes=1
#SBATCH --partition=cuttlefish
#SBATCH --time=100:00:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --job-name=soPurge
#SBATCH --error=error_%j.txt
#SBATCH --output=output_%j.txt
echo $SLURM_SUBMIT_DIR
echo "Running on `hostname`"
reportElapsedTime() {
eval "echo elapsed t... |
6b385f6f4f2463a33911f2fa3f3c98f4e6884084e834ea5881e305ab6e77b4d9 | Shell | 2,082 | 71 | #!/bin/bash
CONDA_EV=~/miniconda3
SCRIPT_DIR="$(
cd -- "$(dirname -- "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd
)"
WORK_ROT="$(
cd -- "$SCRIPT_DIR/../.." >/dev/null 2>&1 && pwd
)"
cd ${WORK_ROT} || exit
SRCP_DIR=src
BASE_DIR=${WORK_ROT}/data/references
RESL_DIR=${WORK_ROT}/data/results
SAVE_DIR=${RESL_DIR}/... |
538c676b8f5a96c305ecd9e8c70f068067867500e05ef926bc668cda82b6b592 | Shell | 2,084 | 41 | #!/usr/bin/env bash
# Regular installs
sudo apt update
sudo apt install bzip2 -y
sudo apt install cmake -y
sudo apt install tmux -y
# Cuda 9 for Tensorflow 1.10.1
wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/cuda-repo-ubuntu1604_9.0.176-1_amd64.deb
wget http://developer.download.nvid... |
1b8588e12baf22c2a979d11a30354a26fcaf3fb9a09a75160cabb4b2b59551ca | Shell | 2,087 | 56 | #!/bin/bash
chr=$1
tmpdir=tmp/chr${chr}
mkdir -p $tmpdir
data_in=/path/to/imputed/data
# eg data_in=data/imputed/full/$chr\_merged.vcf.gz
wrk_base=multiallelics/istrs/custom_filter/ # or whatever the working directory is
outdir=${wrk_base}/detailled/prepare
mkdir -p $outdir
# Script that annotates the regions corre... |
e8547f84a6593d90da48c232fd5a127a1b192315156d31ef4c69fc183c5473b8 | Shell | 2,092 | 67 | #!/bin/bash
brain_dir=`pwd`
dimNC=`fslinfo mri/non_cort |grep 'pixdim1'|awk '{print $2}'`
dimgray=`fslinfo seg/seg_pve_1.nii.gz |grep 'pixdim1'|awk '{print $2}'`
if [ `echo "${dimNC} == ${dimgray}"|bc -l` -eq 1 ];then
echo "all good"
$FSLDIR/bin/imcp seg/seg_pve_1.nii.gz mri/gray
else
... |
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