sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
26e88fc11bb2e6ceec1a889538f5d1238a3aa33d43b4c77ac6261c8c0713e910 | Shell | 1,512 | 27 | #! /bin/bash
# Using info from
# https://stackoverflow.com/questions/35350607/ffmpeg-add-text-frames-to-the-start-of-video
# https://stackoverflow.com/questions/22710099/ffmpeg-create-blank-screen-with-text-video
# https://stackoverflow.com/questions/8213865/ffmpeg-drawtext-over-multiple-lines
# FIRST USE ../render_S... |
59287dc6267fa7c71668b0f707ab6a11591b892b016e78d2ac14ecdb7d73be16 | Shell | 1,514 | 56 | #!/bin/bash
# Downloads and extracts the Kitti dataset
# First argument == path to desired dataset destination
echo "Starting to download TartanAir"
[ -z "$1" ] && echo "ERROR: No dataset destination path argument supplied"
if [ -z "$1" ]
then
exit 1
fi
SCRIPT_DIR="$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &>... |
60a168857ad80702515864cb07a0b20bea16903bf549fcd3de7748cc6146294b | Shell | 1,519 | 49 | #!/bin/bash
# ----------------------------------------------------------------------------
# process_cortical_expression_data
# Author: Antoine Beauchamp
#
# Process mouse and human cortical expression data sets.
#Data directory
datadir=data/isocortex/
#Create a mouse voxel-wise expression matrix with only isocortic... |
80108cd2aaab1edb0de7daa3cdac1f52769346e07c6c7b7fb69d3c0587f0c6ce | Shell | 1,523 | 56 | #!/bin/bash
#SBATCH --account=rlmolecule
#SBATCH --job-name=all_decors_reward
#SBATCH --output=/scratch/jlaw/all_decors/slurm-%j.out
#SBATCH --time=04:00:00
#SBATCH --nodes=5
#SBATCH --ntasks=180
##SBATCH --partition=debug
##SBATCH --time=1:00:00
##SBATCH --nodes=2
##SBATCH --ntasks=72
set -e
source $HOME/.bashrc_con... |
776d04abff8bc14df0c98088eaa58e5f0a0827c5d7419345abc4a4e0219d382c | Shell | 1,525 | 42 | #! /bin/bash
#install docker, adapted from here: https://docs.docker.com/engine/install/ubuntu/
#NOTE this assumes you don't have docker installed already. If it's already there, it might get overwritten!
sudo apt-get update -y
sudo apt-get install -y ca-certificates curl gnupg lsb-release unzip bzip2
#install dock... |
428b54c310653cd363de7e516b2cbeb045d957542044dcde6d5b0bcf2b763c80 | Shell | 1,548 | 47 | #!/bin/bash
wget https://bioinf.uni-greifswald.de/bioinf/learnMSA/learnMSA_large_data.tgz
tar xfvz learnMSA_large_data.tgz
chmod -w large/train/*.fasta
chmod -w large/refs/*.ref
#only version of this script below
#Warning:
#Full pfam uniprot is downloaded!
#Allow 2TB of free disk space and quite some time.
#Afterwards... |
4b7e94e0fced0521ac8816b40b12319a36c7743d711b8d19983125007d230451 | Shell | 1,549 | 27 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
while IFS= read -r line
do
SUBJ=$(echo "$line" | awk -F, '{printf "sub-"; printf $1}')
SESS=$(echo "$line" | awk -F, '{... |
3bb110eb3fcfe6f219466334355d4620257acd65d47f3694ddf10a7dd42fab40 | Shell | 1,551 | 41 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
1221a58a978c4417cb862aa53e07015adf910940c540fe7f937882158269252b | Shell | 1,563 | 29 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# SNRCoil (resliced in the individual space) is sampled to give SNR values for new [schaefer40week_537 or schaefer40week_1763] head positions:
# Graham King 08/2022 TCIN
cd /dhcp/fmri_anna_graham/GKgit... |
72d7db4f10847fed3298e14b47d45f28e461877a59c490df1d20310ddef41f20 | Shell | 1,565 | 21 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Edit input csv file below
# Edit ouput file name below
SNR=`cat 416onescan.csv | awk -F, '{printf "sub-"; printf $1; printf "/ses-"; printf $2; printf "/sub-"; printf $1; printf "_ses-"; printf $2; p... |
0d88a77ff356529ea0fdede50e266c66411645ed1808147b75170cabea59ff07 | Shell | 1,569 | 58 | #! /bin/bash
#hypertron v1.0 - Michel Thiebaut de Schotten & Chris Foulon
[ $# -lt 3 ] && { echo "Usage : ""$0"" LesionFile ResultDir Threshold"; exit 1; }
fileName() {
name=$(basename "$1")
name="${name%%.*}"
echo -n "$name"
}
subject=$(fileName "$1")
#Those lines are the handling of the script's trace and err... |
323b536d7a1b94526c74e5410c93af8cfedeb8b6a6e76a7c0d73c8923d464f5b | Shell | 1,575 | 25 | #!/bin/bash
#SBATCH --output=./reg.%A_%a.log
#SBATCH -J reg ... |
7ac8ca587ed1504691f3ea12330025a3ec33806c6b3ded747be40051b4b59028 | Shell | 1,581 | 46 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
9f917bdf737f1752c9ca72ba6cddce90a9d5af1892839ea67e8bec580ff09cf2 | Shell | 1,587 | 25 | #!/bin/bash
#SBATCH --output=./reg.%A_%a.log
#SBATCH -J reg ... |
13cb6989e5812b40be4909828f92de94132b155781c689e8b73ef44ac514530d | Shell | 1,609 | 57 | #!/bin/bash
# Shelli Kesler 6/17/15
#This script copies the ROI folder into the subject directory, applies the transformation
#to each ROI, removes the original ROIs, creates a path text file for the ROIs, computes
#number of tracks and track stats for each pair of ROIs and the extracts the volume for
#each ROI.
ex... |
f9148e1f8de9d0b0147d319fa61a156148409c07788b2a99693d0e695f64faab | Shell | 1,641 | 23 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Edit input csv file below
# Edit ouput file name below
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
SNR=`cat 416onescan.csv | awk -F, '{printf "sub-"; printf $1; printf ... |
20f8c06a7b3b217e6147505235b501f3850e9779e2b9bd5f64ddbccda6ce3d07 | Shell | 1,642 | 57 | #!/bin/sh
# This script installs uv if it's not already installed in the user account.
# It then runs uv inside Galaxy's root directory, potentially updating
# pyproject.toml and uv.lock, and the pinned requirements files.
set -e
this_directory="$(cd "$(dirname "$0")" > /dev/null && pwd)"
usage() {
printf "Usag... |
bb18640ebd65045f04a30e1938c765453fb7f094781fa6bfb260de4e9f27ad0e | Shell | 1,652 | 35 |
# set CUDA variable (defaults to cpu if no argument is provided to the script)
# available options for for pytorch 1.7.1 are cpu, cu92, cu100, cu101
CUDA_VERSION=cu110
# set Your Conda Path
your_conda_path=/home/anaconda3/bin/
# create virtual environment and activate it
conda env create -f environment.yaml
source $... |
044f152d7c5f8485bdb5a4eff510157bcda62cccdf00987dc9462f418ac01508 | Shell | 1,674 | 41 | # 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"); you may not u... |
5e2bab4224061cebdeec20de682c4ccb737483c321eca33f095d2753886520cd | Shell | 1,685 | 76 | #!/bin/bash
dataset=$1;
if [ ! -z "$2" ]
then
savepath=$2
fi
case "$dataset" in
"midair")
if [ -z "$2" ]
then
savepath="pretrained_weights/midair"
fi
db_seq_len=""
data="data/midair/test_data"
;;
"kitti")
if [ -z "$2" ]
then
... |
3c6320ce90957dc0f3b124002a6d142d69dabb0a49393fb0c5bf254dec234493 | Shell | 1,695 | 43 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
8aa58f8be89e07a92f0ab731bea3800201ddeca562c89da606fcb83a4d8bf590 | Shell | 1,695 | 26 | #!/bin/bash
# run_qti_cov_cohort.sh - drive the cohort QTI covariance fit (run_qti_cov_cohort.m) for one subject.
#
# Input: <subject_dir>/dmri/ (linear_corrected + spherical_corrected + bval/bvec)
# Output: <subject_dir>/fit/qti_cov/{cov_mfs.mat, cov_dps.mat} (oriented <D>)
# Usage: bash pipeline/run_qti_cov_cohort.... |
e8418bb0904f28b045f5af00ca5166fc542491aecab691c281c5ee93fa6f83c0 | Shell | 1,695 | 42 | #!/bin/bash
#SBATCH --time=4:00:00
#SBATCH --mem=8GB
#SBATCH --cpus-per-task=8
#SBATCH -J fba_12
########## Warp DTI, DKI, and NODDI metrics to template space fixels, and smooth them across fiber populations ##########
# Stop on error
set -eu
# Get variables from config
config=/PATH/TO/config
source $config
# Get s... |
c8a13a9d53b7c1dd91583cc5d926fb0296a5386946f02f300978a716c49bb3f5 | Shell | 1,699 | 57 | #!/bin/bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); ... |
d02d54fbeb81480160b79ab3a32e3d25bccabe30edd0480b6922972fc63db4b7 | Shell | 1,705 | 54 | #!/bin/sh
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
set -e
GENERATOR_VERSION="v6.0.1"
VERSION="2.82.1"
LIB_NAME="cvat_sdk"
LAYER1_LIB_NAME="${LIB_NAME}/api_client"
DST_DIR="$(cd "$(dirname -- "$0")/.." && pwd)"
DOCS_DIR="$DST_DIR/docs"
GEN_DIR="${DST_DIR}/gen"
POST_PROCESS_SCRIPT="${GEN_D... |
708299027203cfc6443a828a89943310c5efd40f331faf084261b2e4833a0880 | Shell | 1,720 | 33 | #!/bin/bash
if ! [ -x "S(command -v conda)" ]; then
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/Downloads/miniconda3.sh && \
sudo chmod 777 ~/Downloads/miniconda3.sh && \
bash ~/Downloads/miniconda3.sh -bp ~/conda && \
echo ". $HOME/conda/etc/profile.d/conda.sh" >> ~... |
78c2142cf4e828cb43370dfbf451a48e382972c1918dcd91cf2e60c9a807cd52 | Shell | 1,724 | 35 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Edit input file below
# Use adult T1 to define space for reslicing
REF=/usr/local/fsl/data/standard/MNI152lin_T1_1mm.nii.gz
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
... |
2ea9448ada0ac39a299de9711e2ede7776364c107e439e26fc839d1208bbe13f | Shell | 1,731 | 53 | #!/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"); ... |
7a0c33f982bbf32d2143cb0b2c276fab5bb49572a7b600e610cf7dc9022ecef4 | Shell | 1,736 | 91 | #!/bin/bash
# Various utility functions used through CI.
# Finds Cargo's `OUT_DIR` directory from the most recent build.
#
# This requires one parameter corresponding to the target directory
# to search for the build output.
cargo_out_dir() {
# This works by finding the most recent stamp file, which is produced b... |
bb3af3ec0ea6a7b9072281f82b76ac79c7b0e15042a8555b4bf6b975fb12c9ff | Shell | 1,753 | 38 | # 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"); you may not u... |
011422926b3da1068aebf64e56e0687d4453bbf854b2774a49673826cc1dc124 | Shell | 1,767 | 42 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
9f04776652cc22f29d8eff279ba15212909fe1f0e3894a0798d3dc71c6f1ef9b | Shell | 1,773 | 21 | # rmf 4.10.2020, last modified 5.12.2020
# NOTE that the fimo_original file is the input, but does not get overwritten!
# motif 13
python ../../scripts/renameMemeMotifs.py allTranscriptsOutput6000/allTranscripts6000_cncERR649813_1.out/fimo_original.gff cnc13_
python ../../scripts/renameMemeMotifs.py allTranscriptsOut... |
5a70fc07b4d7da160f22cb77eb628475d872a033d36fac0f21efc01ccd2f8d91 | Shell | 1,776 | 24 | #!/bin/bash
# rmf 2.2.2020, last modified 11.4.2020
# filter against DE transcripts from cuffdiff output
# ELCs down
for f in ELCs*.txt; do echo python ../scripts/filterDEtranscripts.py $f /nfs0/BB/Hendrix_Lab/Drosophila/CircadianRhythms/RNASeq/RP24Analysis/Hisat2AlignmentTranscripts/transcriptGroups_q0.05/upAndDown... |
442286cf5cb54003ba92176f6592ddc68e571d9a5d85274232dcd2c834b69482 | Shell | 1,782 | 39 | #!/bin/bash
# Get variables from config
config=/PATH/TO/config
source $config
# Stop on error
set -eu
# Identify right file
# Exmaple - $outdir/template/modelarray_outputs/mifs_${metric}_${subtest}${suffix}
metric='fdc' # log_fc, fd, or fdc
subtest='TOWRE' # swe or pde
suffix='_eff' # in case there's additional tex... |
32e8e912aba387ca1110474446d56b37eaf1ae7b90dde3ec079ef7c2a03cfb28 | Shell | 1,788 | 43 | #!/bin/bash
# -----------------------------------------------------------------------------
# resample_DSURQE_CCFv3
#
# Resample imaging files from the DSURQE common coordinate space to the
# Allen Institute CCFv3 space.
module purge
module load minc-toolkit/1.9.18.1-mp7vcse minc-stuffs/0.1.25-4jzbv5d
echo "Resampli... |
cebb3de9cab9632146d60d6e2ab9922fbb46a63c2a0ad60afde116b1d69fe0bf | Shell | 1,795 | 18 | # rmf 1.12.2021, last modified 9.20.2021
# filter clusters on DAVID enrichment score and TFs on expression
# usage: python scripts/filterMotifSummaryFile.py <motif summary file> <expression file> <secondary FBID file> <JASPAR secondary ID file> <FPKM threshold> <N number of transcripts in group> [enrichment score tabl... |
9a8cc7a15793053e9a582bbc9b4ba84e4ae39caa3171dd3383eedad6869ddf4e | Shell | 1,806 | 54 | #!/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"); ... |
c9fa9680d49399b65c9693283de56c5bf5f6e515d3dde82ed51068d86372d156 | Shell | 1,812 | 71 | modelname="t5-large"
savename="t5-large"
evalset="test"
batchsize=8
task="NLU"
echo "Model '"$modelname"' training on task '"$task"'"
python finetune_trainer_sp.py \
--model_name_or_path $modelname \
--data_dir $task/ \
--task summarization \
--max_source_length 512 \
--max_target_length 128 \
... |
f7f625b829ce48e3ab86286505a825527e2cbde351000d2e5e9bf7ece5d02b4d | Shell | 1,826 | 43 | #!/bin/bash
HOMFAM="../../data/homfam/refs/*.ref"
BALIFAM100="../../data/balifam100/refs/*.ref"
BALIFAM10000="../../data/balifam10000/refs/*.ref"
BALIFAMFRAG="../../data/balifrag/refs/*.ref"
LARGE="../../data/large/refs/*.ref"
cd $1
#rm *.out
export MAX_N_PID_4_TCOFFEE=434668
eval () {
for f in ${1}
do
... |
a041c7aaf873c7a9a76419fedfb1d9f86cbbb8c0e0d1b1c0827f2f5353e7107e | Shell | 1,831 | 64 | #!/bin/bash
# behavior depends on scripts directory's presence
if [ -d "$PWD/scripts" ]
then
# check for update flag
update=0
while test $# -gt 0
do
case "$1" in
-u|--update)
update=1
shift
;;
*)
echo "$1 is not an accepted option..."
shift
;;
... |
41ee53751a6b191016035ae3601f0eabf4ae3084a75e753154ceb0188ac58833 | Shell | 1,832 | 58 | #!/bin/bash
# The IPython image starts as privileged user.
# The parent Galaxy server is mounting data into /import with the same
# permissions as the Galaxy server is running on.
# In case of 1450 as UID and GID we are fine, because our preconfigured ipython
# user owns this UID/GID.
# (1450 is the user id the Gala... |
9ae8372f3a92d9a5d2079b4862706c5ebc93dd031005f18e97d13755b69741a3 | Shell | 1,833 | 46 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Edit input file below
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
while IFS= read -r line
do
SUBJ=$(echo "$line" | awk -F, '{printf "sub-"; printf $1}')
SESS=$(... |
407d9b5141e6965aec340080bd1f652515c9baae7dcd8a5befce8e00bca33325 | Shell | 1,834 | 56 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
b03b8dad7b7b153796aab2850588fd74c3981e6f1d6c1322c7fcad41acf9404e | Shell | 1,853 | 41 | #!/bin/bash
# Once mean SNR has been calculated across all subjects, this reslices back to indivudal space and then samples in ROIs
# Rhodri Cusack TCIN 04/2021, cusackrh@tcd.ie
FILES=`ls -1 /dhcp/dhcp_fmri_pipeline/*/*/func/*brainmask.nii.gz` # All sessions
# FILES=`ls -1 /dhcp/dhcp_fmri_pipeline/*/*/func/*brainmas... |
580843f1db36ef8353b36e02379d6ce15bf15ec398d735a69ad5087d4be8dc64 | Shell | 1,877 | 47 | DATASET=TR2000
TASK=memory
res=3.5mm
for sdx in 01 02 03 04 05 06 07 08 09 10 11 12
do
# Create output folder
OUTPATH=${DATASET}/derivatives/fsl_feat/sub-${sdx}
mkdir -p $OUTPATH/anat
cp ${DATASET}/sub-${sdx}/anat/sub-${sdx}_T1w.nii.gz $OUTPATH/anat/.
mkdir -p $OUTPATH/func
cp ${DATASET}/sub-$... |
0d1663909b7fcd1edc772c264355521f775916f621eeb2f375e444f6e010c036 | Shell | 1,888 | 47 | DATASET=TR600
TASK=hrf
res=3.0mm
for sdx in 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17
do
# Create output folder
OUTPATH=${DATASET}/derivatives/fsl_feat/sub-${sdx}
mkdir -p $OUTPATH/anat
cp ${DATASET}/sub-${sdx}/anat/sub-${sdx}_T1w.nii.gz $OUTPATH/anat/.
mkdir -p $OUTPATH/func
cp ${DAT... |
3f740cf6f35337ab0e13bdf044d213e0577a6787845abb644c544534f5b545d7 | Shell | 1,907 | 51 | #!/bin/bash
#Shelli Kesler 5/7/14
#change path below to location of Diffusion Toolkit
export PATH=$PATH.:/Applications/Diffusion\ Toolkit.app/Contents/MacOS
#This script performs DTI tensor reconstruction and tractography and transforms ROIs
#into DTI native space
# Check the dti.trk file and define ROIs before mo... |
3e1e7949778ccec77be994cc27178621b9befdbd4da8ed8d5d20f4d0cfe39fda | Shell | 1,918 | 47 | DATASET=TR1000
TASK=MGT
res=2.0mm
for sdx in 001 002 003 004 005 006 008 009 010 011 013 014 015 016 017 018 019 020 021 022
do
# Create output folder
OUTPATH=${DATASET}/derivatives/fsl_feat/sub-${sdx}
mkdir -p $OUTPATH/anat
cp ${DATASET}/sub-${sdx}/anat/sub-${sdx}_T1w.nii.gz $OUTPATH/anat/.
mkdir... |
015ded6f01ebb81a65acb63c72487d73ee9e611f171f1bbce4d22942f278f850 | Shell | 1,927 | 58 | #!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -l h_rt=100:0:0
#$ -l h_vmem=18G
#S -l mem_free=18G
#$ -pe smp 1
#SBATCH -o job.%j.out
#SBATCH -J image_human_view
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 1
#SBATCH --mem 24G
#SBATCH --time=99:99:99
set -oe pipefail
echo "Job started on `hostname` at `date`"
#export PATH=$HO... |
718ff8e609e98ac0f2fd79db8e59e7ee4adb7442949275dcbc35f25098b5003c | Shell | 1,937 | 48 | #!/bin/bash
#=============================================================================
#SBATCH --account=bd1179
#SBATCH --partition=prepost # Specify partition name
#SBATCH --ntasks=12 # Specify max. number of tasks to be invoked
#SBATCH --cpus-per-task=2 # Specify number of CPUs per task
#SBATC... |
cb24c548f51384bb47e35104db6256fd999c3de34ba8d099893efe9938b97b7f | Shell | 1,942 | 44 | #!/bin/bash
#SBATCH --output=./reg_eval.%A_%a.log
#SBATCH -J reg_eval ... |
7fc929fb97f4e90612762e43daa8690aca8bd4167bed35773f0c1122dd35653c | Shell | 1,949 | 17 | # rmf 4.9.2020, last modified 5.19.2020
# fimo text files
mv allTranscriptsOutput6000/allTranscripts6000_cncERR649813_1.out/fimo.txt allTranscriptsOutput6000/allTranscripts6000_cncERR649813_1.out/fimo_original.txt
mv allTranscriptsOutput6000/allTranscripts6000_cncERR649813_2.out/fimo.txt allTranscriptsOutput6000/allTr... |
5641ac04d0bd872d46ff7cb1d4a1d17b85e98d0cffb54eb190a849a6e9d84cad | Shell | 1,954 | 44 | #!/bin/bash
#SBATCH --output=./mafft_eval.%A_%a.log
#SBATCH -J mafft_eval ... |
ee3c4fdfa25d98b19fc3c8532d5ac6c6860ee2cc60b9c4d2879a524d83c62176 | Shell | 1,959 | 61 | #!/bin/bash
#SBATCH --time=12:00:00
#SBATCH --mem=16GB
#SBATCH --cpus-per-task=8
#SBATCH -J fba_3
########## Compute fiber orientation distribution functions (FODs) ##########
# Get variables from config
config=/PATH/TO/config
source $config
# Stop on error
set -eu
# Get subject name from job array
args=($@)
subjs=... |
ff2c1053a0a5ba86217bdc40642f19023c14cb6529552cafc077fda602942397 | Shell | 1,966 | 44 | #!/bin/bash
#SBATCH --output=./learnMSA_eval.%A_%a.log
#SBATCH -J learnMSA_eval ... |
411daa68ac5f04374676dbce34564dcbd1814605826cc8ac5ea022b934a05245 | Shell | 1,969 | 48 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
f4ae7e1c1df06e99ca8dbd9457262639929621de4f36ffa6dc34a8c22a36ef2a | Shell | 1,971 | 86 | # Deployment script
# UNC-specific but can be adapted for other clusters with a module system
# Run like this, where x.y.z is the version:
# source deploy_clpipe.sh x.y.z
DEV_PYTHON_PATH="venv/bin/activate"
PYTHON_VERSION="3.7.14"
DEPLOY_ROOT="/proj/hng/software"
MODULE_ROOT="${DEPLOY_ROOT}/modules/clpipe"
VENVS="${... |
bb51e1f5c27781d2ec7e074f94cfafb0a694ff1d56a2974e0387c875ebae922b | Shell | 1,978 | 44 | #!/bin/bash
#SBATCH --output=./reg_eval.%A_%a.log
#SBATCH -J reg_eval ... |
eb7051f9069e8ea0239c24dfc3361e0fd4d4f69ec9eb3e9834a2e068ceb37738 | Shell | 1,998 | 44 | #!/bin/bash
#SBATCH --output=./mafft_eval.%A_%a.log
#SBATCH -J mafft_eval ... |
1d24d1adb46b81eebfed28f9e675c56056741661ae11c0bad4b50a91992eae7b | Shell | 2,004 | 61 | #!/usr/bin/env bash
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Licen... |
3ba6b2bc878aa98ae940658670b15d10e7732757b6f5fda1dfa07ebf5d3b54a8 | Shell | 2,006 | 51 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
ec6f85c0308118841e4b76837d94874b878f900b583becd616cb7cf29f3e5839 | Shell | 2,036 | 39 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Edit input file below
# Use adult T1 to define space for reslicing
REF=/usr/local/fsl/data/standard/MNI152lin_T1_1mm.nii.gz
while IFS= read -r line
do
SUBJ=$(echo "$line" | awk -F, '{printf "sub... |
07e930dc9e7ea5c7868a18e217a57bf682e14cacadad4d2aafc92feb0245cd71 | Shell | 2,086 | 53 | #!/bin/bash
#script de test, limpia archivos, comparadolos con una lista negra
#Uso
#
#bash limpiador_VVD17RA03.sh
#_reg_borrado="/home/cafetero/logs/registro_limpieza_VVD17RABIOBANCO03_$(date +"%m_%d_%Y__%H-%M").log"
#PATH_RECOLECTOR="/home/cafetero/ceibanon/data_ra600/VVD17RABIOBANCO03"
function test_cleaner() {
... |
bec55a9b50cb1e92f2c102a94981bbf328602ca6f44b7219ce82a918304b4552 | Shell | 2,098 | 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
# "Lic... |
d334193277fbc4a6e7eacab1b521739595cee3f5ba84c89c0b34907978cea5dd | Shell | 2,130 | 43 | list_of_datasets=(HCR Narr-KDML-2012 STS-gold SemEval13 SemEval15-Task11 SemEval16 SemEval17-test SemEval18 SentiStrength
Target-dependent VADER archeage debate08 hobbit iphone irony movie ntua person sanders sarcasm sentiment140)
Models=(RoBERTa BERT BERTweet)
seeds=(12 34 56)
OriginalModels=(roberta-base bert-base-... |
fa91892a496c1feb3f466fea10a61ea978ba673bcfb0b52d0afdcea4e753416c | Shell | 2,131 | 54 | #!/bin/bash
#SBATCH --time=12:00:00
#SBATCH --mem=12GB
#SBATCH --cpus-per-task=8
#SBATCH -J fba_1
########## Reorient subject data and fit their fiber response functions (FRFs) ##########
# Get variables from config
config=/PATH/TO/config
source $config
#Stop on error
set -eu
# Get subject name from job array
args=... |
a354885332539267ea61ab5aea3283ada8e09ae47638873bd49b54ccebd766c1 | Shell | 2,148 | 63 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
479d954eae473f48968876befcafcbb13e6635f2fdc2e35133ad2041463cfbd1 | Shell | 2,165 | 51 | #!/bin/sh
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); yo... |
1e8ad2fee707012f9df5b217fb17fc08bbe65677d249d167d065c7d83c215e43 | Shell | 2,168 | 70 | #!/bin/bash
# Copyright 2019 The Go Authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
set -e
shopt -s nullglob
winerror="$(printf '%s\n' "/mnt/c/Program Files (x86)/Windows Kits/"/*/Include/*/shared/winerror.h | sort -Vr | head -n 1)"
... |
9bbab6d1b42cbed80039c92e1a563036e3150552821774fb9736ca8dd69d5352 | Shell | 2,169 | 42 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Edit input file below
# Use adult T1 to define space for reslicing
REF=/usr/local/fsl/data/standard/MNI152lin_T1_1mm.nii.gz
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
... |
c33d487a18fa36eade2cee6ad7f10a1c7e5c1fa3206db1c36ab17c26947dadbd | Shell | 2,178 | 54 | #!/bin/bash
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
#pip3 install -r $DIR/../test_requirements.txt
pip3 install -r $DIR/test_requirements.txt --use-feature=2020-resolver
cd $DIR
mkdir -p temp
cd temp
if [ ! -f "hg19.2bit" ] ; then
echo "Downloading hg19.2bit"
wget -q http://h... |
84e0ef61cb65a100c827431aa52717a7181d8c2aebb59163f711986ac350865b | Shell | 2,213 | 43 | seeds=(12 34 56)
edin=(25 50 250 500 1500 6600)
Models=(RoBERTa BERT BERTweet)
OriginalModels=(roberta-base bert-base-uncased BERTweet_base_transformers)
evaltype="normal"
for seed in "${seeds[@]}"; do
i=0
for models in "${Models[@]}"; do
for edin_data in "${edin[@]}"; do
echo "Model: $models"
echo ... |
e2739da7ef654fe5f745a19a20b57ac3a6b61b6996e87a38e33fa029a5d8808a | Shell | 2,215 | 79 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
4462e5d3d78e1e7b04ed1636ee42b987a237bfe79086cc4d823fde83e78cb92d | Shell | 2,219 | 47 | equil_time=900000
stride=25000
whole_state_file="out.STATE"
total_time=$(cat out.STATE | tail -n 5 | head -n 1 | awk '{print $1}')
blocks=$( echo "1+($total_time - $equil_time) / $stride " | bc -l )
blocks=$(printf "%.0f\n" $blocks)
echo $blocks
#last_FIELDS_line=$(cat $whole_state_file | grep -n FIELDS | cut -f1... |
ef92fa10ebb941482b7b16515f8b2ffcb7e1cd3e565b931620f0da5a92316ef0 | Shell | 2,222 | 44 | list_of_datasets=(HCR Narr-KDML-2012 STS-gold SemEval13 SemEval15-Task11 SemEval16 SemEval17-test SemEval18 SentiStrength
Target-dependent VADER archeage debate08 hobbit iphone irony movie ntua person sanders sarcasm sentiment140)
Models=(RoBERTa BERT BERTweet)
seeds=(12 34 56)
OriginalModels=(roberta-base bert-base-... |
096ede793376e7de3ab964020facbae72de9da50f7ef153b61d5d0eacc51fd5a | Shell | 2,238 | 49 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
f073520e80e6dc341b957e74fb86a5013f3c5b4084f5e92d9d208c78043de349 | Shell | 2,252 | 70 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
83676c78cddc58b633fc241442fe9cdf48554dc8ed908e5bd04e1977b2380ce8 | Shell | 2,254 | 52 | #!/bin/bash
module load bedtools/2.30.0
module load anaconda3
source activate maxATAC_IS59
mkdir -p /scratch/war9qi/data/aronow/Balaji_Iyer/Projects/Maxatac_IS59/Maxatac_Predictions/20211015_DCNN_ATAC_DELTA/ARNT1
cd /scratch/war9qi/data/aronow/Balaji_Iyer/Projects/Maxatac_IS59/Maxatac_Predictions/20211015_DCNN_ATAC... |
6e98e8a3d0b0a51e43672598104df8d4ebb9cbf8c567c193f37b0d6bf57a4383 | Shell | 2,269 | 76 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
c810948b17826c2a964053e895b60aff0ec24f8e2293412fe597e88ee3bec40f | Shell | 2,282 | 17 | #!/bin/bash
# rmf 5.4.2021
# ELCs not significant, then significant
for f in transcripts_*ELC*.txt; do if test -f "$f"; then base=${f##*/}; outbase=${base%%.txt}; echo python ../../../../../scripts/plotExpressionProfilesGeneList_3D.py --exp1 ../transcriptExprYoung.txt --exp2 ../transcriptExprOld.txt --gl $f --ggy ..... |
610be747919c304ff029d9d28d4a5532440c644648bb610b5d4e6577539c7943 | Shell | 2,290 | 55 | #!/bin/bash
# Build tsne-cuda Python wheels for the supported CUDA toolkits and collect them
# into ./wheelhouse. Each wheel is py3-none-any and tagged +cuXXX (the CUDA
# runtime it needs); a single wheel serves every Python 3.x for that CUDA build.
#
# tsne-cuda 4.0.0 targets modern datacenter GPUs (A100/H100/H200/B20... |
f70adad5a5a804f54f1b27ea904cc8ababb046680b975835ad6bb3617237b1e7 | Shell | 2,312 | 42 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
#Chops out 6 motion parameters from specific volume
#Uses par_to_affine.py to translate these to FLIRT format transformation matrix (FLIRT (FMRIB's Linear Image Registration Tool))
#Reorients the Schaef... |
afa315cc2e8cbbb0a65d9067ce57d504c638ef8d6bf12487b254978eca94683d | Shell | 2,329 | 65 | # Set up environments for
# 1. fsl (tested with 6.0.1)
# 2. freesurfer (tested with 5.3.0)
# 3. matlab (tested with R2018a)
source /cluster/software/fsl/6.0.1/setup.source
module load freesurfer/5.3.0
export FSLOUTPUTTYPE="NIFTI_GZ"
module load matlab/R2018a
# Declare
# 1. the name of the subject to analyse: s
# 2. t... |
f22759a5206a6e55b6beb6561bd870cc09ff06f266280f5a7bf2f64e0fa2f4cf | Shell | 2,356 | 51 | #!/bin/bash
#SBATCH --time=12:00:00
#SBATCH --mem=12GB
#SBATCH --cpus-per-task=4
#SBATCH -J fba_7
########## Compute Fiber Density (FD), Cross-Section (FC) and their product (FDC) ##########
# Get variables from config
config=/PATH/TO/config
source $config
# Stop on error
set -eu
# Get subject name from job array
a... |
3354e141bf51dac3d64de7d3584d2ad7dde70784b5adc7ac89c98f078bc6fb0d | Shell | 2,373 | 82 | #!/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"); ... |
97e733b67b1104ffbc0a98de4b16f573ce5d312313f5759bc3fe1c38eb6fbccc | Shell | 2,401 | 49 | list_of_datasets=(HCR Narr-KDML-2012 STS-gold SemEval13 SemEval15-Task11 SemEval16 SemEval17-test SemEval18 SentiStrength
Target-dependent VADER archeage debate08 hobbit iphone irony movie ntua person sanders sarcasm sentiment140)
Models=(RoBERTa BERT BERTweet)
seeds=(12 34 56)
OriginalModels=(roberta-base bert-base-... |
312aed21aba8d1a894b6c8680cf7d26b6069923279a45fcebbe8dfb8b20b800e | Shell | 2,417 | 95 | #!/bin/bash
# Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# Exit if any error occurs
set -e
usage() {
echo "Usage: $0 [-b] [-o] [-r] [-t]"
echo ""
echo "Build Ax documentation. Mu... |
df573203ac868e512f055249b120cdc7cddbae673a9c6b056099f9e86dbbd7a7 | Shell | 2,433 | 52 | #!/bin/bash
#SBATCH --time=1:00:00
#SBATCH --mem=2GB
#SBATCH --cpus-per-task=2
#SBATCH -J fba_9
########## Calculate globally-averaged and tract-averaged fixel-stats ##########
# Get variables from config
config=/PATH/TO/config
source $config
# Stop on error
set -eu
# Get subject name from job array
args=($@)
subjs... |
c40118801b1580e3312d4a1fd43df58f0daeb16602d26168419b627454c21e6f | Shell | 2,436 | 68 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
4cdbd46b09f165176dca248b9becc78df2e8fd485f1bad89e2a7caf57bb7a568 | Shell | 2,468 | 94 | #!/bin/bash --login
#SBATCH --account=rlmolecule
#SBATCH --job-name=qed
#SBATCH --time=4:00:00
##HEAD RAY NODE
#SBATCH --tasks-per-node=1
#SBATCH --nodes=1
##ROLLOUT NODES
#SBATCH hetjob
#SBATCH --tasks-per-node=1
#SBATCH --nodes=2
##TRAINING NODE (GPU)
#SBATCH hetjob
#SBATCH --tasks-per-node=1
#SBATCH --nodes=1
#S... |
1a876baa873423d2fbe56c7a386faf028926f53973b1a5a1fcc6012fc62a7cca | Shell | 2,489 | 63 | # 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"); you may not u... |
a7245fbc59169b694cbeda79027d466dcbd3b01d46a19bf9c3e07eb79ac502c7 | Shell | 2,515 | 99 | #!/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"); ... |
194ddad805563098247e98d5bbb7faf9c17e409e1768fb5a6e7a308a311f896f | Shell | 2,587 | 77 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "Lic... |
6bc6180109e3e7932813487132716cb61cf5fda572f26264c598762f8536daea | Shell | 2,616 | 95 | #! /bin/bash
#tractotron v1.0 - Michel Thiebaut de Schotten & Chris Foulon
[ $# -lt 3 ] && { echo "Usage : $0 LesionFolder TractsFolder ResultDir"; exit 1; }
#Those lines are the handling of the script's trace and errors
#Traces and errors will be stored in $3/logTractotron.txt
export PS4='+(${LINENO})'
echo -n "" > $... |
61c43d6d8fa01e13fd550ebfb515600510f95f10c1280e76045d52c5c83c9d8a | Shell | 2,642 | 82 | #! /bin/bash
#hypertron v1.0 - Michel Thiebaut de Schotten & Chris Foulon
[ $# -lt 3 ] && { echo "Usage : $0 LesionFolder ResultDir Threshold"; exit 1; }
#Those lines are the handling of the script's trace and errors
#Traces and errors will be stored in $2/logDisconnectome.txt
export PS4='+(${LINENO})'
echo -n "" > $2... |
d9cbc025297f67810e6355397ffefee3e56bb8caf72bc9884bac608b71586fba | Shell | 2,698 | 90 | #!/bin/bash -l
# ----------------------------------------------------------------------------
# generate_latent_spaces.sh
# Author: Antoine Beauchamp
#
# This script generates 500 gene expression latent spaces by repeatedly
# training the multi-layer perceptron neural network and using the network
# architecture to t... |
550389406bce9cce7b90847469eea3329b49d8b067be6c307a92cd8043d7e71e | Shell | 2,750 | 38 | #!/bin/bash
# Authored-by: James Trimble <james.trimble@yahoo.co.uk>
# expanded beyond /algorithms/ by Dan Schult <dschult@colgate.edu>
echo ALGORITHMS
find networkx/algorithms -name "*.py" | xargs cat | tr -d ' \n' | grep -o '__all__=\[["a-z0-9_,]*\]' | grep -o '"[a-z0-9_]*"' | tr -d '"' | sort | uniq > tmp_funcs.txt... |
791e3c357f69c06bdbe4fbbb768a6c2389e3d56742981117c83292a65873bb6e | Shell | 2,788 | 50 | # Pipeline configuration template.
#
# cp config/config.example.sh config/config.sh then edit for your paths.
#
# config/config.sh is gitignored - keep machine paths and subject IDs out of
# version control. Both the bash scripts (source this file) and the Python
# scripts (via pipeline/_config.py) read these value... |
c950cbc754e71c6b416bd6d58609e57807fbcfd4331c6c4ea8ded55b1b3d485c | Shell | 2,823 | 94 | #!/bin/bash
function helpscript {
echo ""
echo "SumstatsQC folder that is completed would be archived to google cloud"
echo "bucket"
}
while [ "$1" != "" ];do
PARAM=`echo $1 | awk -F= '{print $1}'`
VALUE=`echo $1 | awk -F= '{print $2}'`
case $PAR... |
4ae4e6e59b869cf101d770e000f13837025c24290cc634a31429721b62d0d7c4 | Shell | 2,848 | 51 | #!/bin/bash
#### All original code is copyright of Graham King, Trinity College Institute of Neuroscience, 12/2021.
# Edit input file below
# Use adult T1 to define space for reslicing
REF=/usr/local/fsl/data/standard/MNI152lin_T1_1mm.nii.gz
cd /dhcp/fmri_anna_graham/GKgit/head_position/HEADCOIL/participant_files/
... |
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