sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ffc5a92e1fa2014e8d5f45a2267eee03f11b3f0cd50c66118aaccc6e1dc9945a | Shell | 1,417 | 54 | #!/usr/bin/env bash
# A simple SLURM script to run AlphaDIA end2end tests on a SLURM cluster.
# Prerequisites:
# - conda environment with working AlphaDIA installation
# - input parameters (see below) set to desired values
# - (optional) SBATCH directives adapted to current use case
#SBATCH --job-name=alphadia
#SBATCH ... |
1034347cdbe492a8bad3748ce196fece2651635908869162484e57061e0e1abf | Shell | 1,423 | 33 | #!/bin/bash
#SBATCH --job-name=label_split # Job name
#SBATCH --output=/dev/null # Suppress the default SLURM log file
#SBATCH --error=/dev/null # Suppress the default SLURM error file
#SBATCH --time=03:00:00 # Max time for job (4 hours)
#SBATCH --nodes=1 ... |
548df5923bd43ce696a90ed0e81e9665d4c1e12f4f295ade4060e56a17d00e7a | Shell | 1,431 | 39 | #!/usr/bin/env bash
# note: model doesn't include any interactions anymore
set -euo pipefail
3dLMEr -prefix "ln_conn_3dlmer_simpler" \
-mask '/opt/ni_tools/standard/mni_icbm152_nlin_asym_09c/mni_icbm152_gm_tal_nlin_asym_09c_2mm.nii<.2..1>' \
-model "scan_age+sex+hemi+visit+(1|Subj)" \
-qVars "scan_age" \... |
d883b3de57f397c0df2da79f6a965185ae0ae2fb353bb230d858ae839fd70cb9 | Shell | 1,431 | 39 | #!/usr/bin/env bash
# note: model doesn't include any interactions anymore
set -euo pipefail
3dLMEr -prefix "bn_conn_3dlmer_simpler" \
-mask '/opt/ni_tools/standard/mni_icbm152_nlin_asym_09c/mni_icbm152_gm_tal_nlin_asym_09c_2mm.nii<.2..1>' \
-model "scan_age+sex+hemi+visit+(1|Subj)" \
-qVars "scan_age" \... |
521341b0b072f9c68773af65c36eb1fa7ab7ffba2c50e0f2c2ca24b91777c06c | Shell | 1,432 | 52 | #!bin/bash
# This script removes the first 4 volumes from timeseries.
#
# Please remember that 3dTcat counts from 0.
# It is possible to specify a TR (-tr option)
# Input: ts in nifti. BIDS like dataset structure is expected
# -----------------------------------------------------------
# Script written by Ludovico... |
ee91ce458c531e8d60739731f20dadf471ed4df4ecb5bc9f66d66e1dfe8e2327 | Shell | 1,432 | 41 | #!/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... |
05664de538160deebd2823e554765d52a18d0a2b214edd8e2333b542b30cf0f6 | Shell | 1,433 | 39 | #!/usr/bin/env bash
# note: model doesn't include any interactions anymore
set -euo pipefail
3dLMEr -prefix "cat_conn_3dlmer_simpler" \
-mask '/opt/ni_tools/standard/mni_icbm152_nlin_asym_09c/mni_icbm152_gm_tal_nlin_asym_09c_2mm.nii<.2..1>' \
-model "scan_age+sex+hemi+visit+(1|Subj)" \
-qVars "scan_age" ... |
16fdcfbcb1e5bada61775c9c60e9934d1e4b7239f8ad4362ea6e9c84663b054e | Shell | 1,433 | 53 | #! /bin/bash
# 07 May 2021 Siwei
## use conda aligners environment
## Set these environment vars to point to
## your local installation
gatk37_path="/home/zhangs3/Data/Tools/GATK37"
gatk36_path="/home/zhangs3/Data/Tools/gatk_36/opt/gatk-3.6"
gatk4_path="/home/zhangs3/Data/Tools/gatk-4.1.8.1"
jre_8="/home/zhangs3/D... |
5ff10655194c91d8490408a08d6b376fb13e32f13f77db7408bbe4a44ed5eb8e | Shell | 1,433 | 68 | #!/bin/bash
source ./env.sh
# Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# enforce using portable C locale
LC_ALL=C
export LC_ALL
# arg1 = file, arg2 = file it depends on
action() {
if (test $mode = 0); then
rm -f ../$1
elif (! cmp -s $1 ../$1); then
if (te... |
650aa37a970dfa814aa3deb967df5f54fbb954154761b9d5dd1a19f2b4da12cb | Shell | 1,433 | 39 | #!/usr/bin/env bash
# note: model doesn't include any interactions anymore
set -euo pipefail
3dLMEr -prefix "abn_conn_3dlmer_simpler" \
-mask '/opt/ni_tools/standard/mni_icbm152_nlin_asym_09c/mni_icbm152_gm_tal_nlin_asym_09c_2mm.nii<.2..1>' \
-model "scan_age+sex+hemi+visit+(1|Subj)" \
-qVars "scan_age" ... |
e32abf1fb5820637d6f932ccfb3392a1b2b9dcd81e32a9727afad98f43e00d8c | Shell | 1,433 | 39 | #!/usr/bin/env bash
# note: model doesn't include any interactions anymore
set -euo pipefail
3dLMEr -prefix "cen_conn_3dlmer_simpler" \
-mask '/opt/ni_tools/standard/mni_icbm152_nlin_asym_09c/mni_icbm152_gm_tal_nlin_asym_09c_2mm.nii<.2..1>' \
-model "scan_age+sex+hemi+visit+(1|Subj)" \
-qVars "scan_age" ... |
6a07f5dc0d85677ca2f29eb4d4af5c71e07c81230618649f6ce6de6b8cbd8f65 | Shell | 1,448 | 45 | set -e
SCRIPT_PATH=$(dirname "$(realpath -s "$0")")
if [ -z "${INSTALL_PREFIX}" ]; then
INSTALL_PREFIX=$(realpath -s "${SCRIPT_PATH}/../../dp")
fi
mkdir -p "${INSTALL_PREFIX}"
echo "Installing DeePMD-kit to ${INSTALL_PREFIX}"
NPROC=$(nproc --all)
#------------------
BUILD_TMP_DIR="${SCRIPT_PATH}/../build"
mkdir -p ... |
3f0ac3983898a495d8b19be0758a6a7dc6d874bb35249de321a086efc0521c28 | Shell | 1,454 | 57 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -S /bin/bash
#$ -cwd
#$ -V
#$ -l h_vmem=1.9G,h_rt=20:00:00,tmem=1.9G
#$ -pe smp 2
# join stdout and stderr output
#$ -j y
#$ -R y
if [[ ( $@ == "--help") || $@ == "-h" ]]; then
echo "Usage: source submit.sh CONFIG_PATH (RUN_NAME)"
echo
echo "... |
1902c5610a2e71f5564b6ff6cecc431faa2581d954fec06acde689b6855e43a9 | Shell | 1,458 | 37 | #!/bin/bash
# copy data into structure that FS asegstats2table understands.
MCRIBS_DIR=$1
DATA_DIR=$2
#-------------------------------------------------------------------
# Step 1: Create subject-session IDs for all subjects
#-------------------------------------------------------------------
while IFS=";" read -r S... |
d94c7ca504d809c8f78bd4150df671ef72c859431a4b6eb4bfb844875ad65d23 | Shell | 1,460 | 42 |
# Define the cell lines array
cell_lines=("A549_corrected_pos_emb" "MCF7_corrected_pos_emb" "MDAMB231_corrected_pos_emb" "BT20_corrected_pos_emb" "PC3_corrected_pos_emb" "VCAP_corrected_pos_emb")
# cell_lines=("PC3_corrected_pos_emb" )
# Iterate over each cell line
for cell_line in "${cell_lines[@]}"
do
# Create a... |
844bb5c08e5a3e3fa5eef22f5f52110cdfe4508399eee04fd60bc41250cbf7f5 | Shell | 1,466 | 53 | #!/bin/bash
#SBATCH --job-name=j_firstlevel
#SBATCH --partition=short
#SBATCH --time=48:00:00
#SBATCH -n 1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=4G
#SBATCH --output=logs/%x.%A-%a.out
#SBATCH --error=logs/%x.%A-%a.err
#############################################
freesurfer_version="X.X.X"
export FREESURFER_... |
3ec2d5b8e96c1b8eebc6e197769a98851f8c3b9e6ce3dcc4d23b3bb725512bfd | Shell | 1,468 | 31 | #!/usr/bin/env bash
# "Automates" calling of the "MASTER shell script" by looping through the "batches & comparisons"
# My 'OBJs'
WD=$(pwd)
SCRIPT="source_step0_MASTER.sh"
DONE="\tDone!\n"
# Declares 'arrays' of batches & comparisons
#declare -a BATCHES=("batch1-2" "batch1" "batch2")
declare -a BATCHES=("batch2")
#d... |
61a9ac55ca7631ca7a318842213f7e15fa89210a8e06f248ed319c9c735b81d9 | Shell | 1,468 | 28 | #!/bin/bash
DIR="/mnt/disks/r8/prs/panel/" #path where to output/work
PANEL_DIR="/mnt/disks/r8/panel/sisuv4_panel_hm3" #path to root of bed file of panel
LABEL="1kg" #output label
BLOCKS="/mnt/disks/r8/prs/panel/blocks.bed" # bed file with regions
cwd=$(pwd)
cd $DIR
rm -rf ldblk && mkdir ldblk && rm -f blk_chr blk_s... |
bd373af4ac5586f1b5065c1bcf9a21cf535f3d5fc467f4cf496cab564d245138 | Shell | 1,474 | 26 | #!/bin/bash
#SBATCH --time=120:00:00
#SBATCH --ntasks=1
#SBATCH --cores 1
#SBATCH --mem-per-cpu 128GB
mkdir Allen_M1_Subsamples_cross_species_cluster_label
mkdir Allen_M1_Subsamples_subclass_label
python process_for_ctp.py mouse cross_species_cluster_label Allen_M1_Subsamples_cross_species_cluster_label
python proces... |
d15e91ba07dfd9cd10caef4f96cde459ee1a85507127d2b261f97d5605d59979 | Shell | 1,488 | 33 | #!/bin/bash
#SBATCH --job-name=batch_tensor_val_new_misc # Job name
#SBATCH --output=/dev/null # Suppress the default SLURM log file
#SBATCH --error=/dev/null # Suppress the default SLURM error file
#SBATCH --time=2-00:00:00 # Max time for job
#SBATCH --nodes=1 ... |
dcaaef0fce7e075d09a108bdea3d0acfa239fd84e5434b15f50e4eb3fe658f06 | Shell | 1,488 | 33 | #!/bin/bash
#SBATCH --job-name=tensor_label_check_new # Job name
#SBATCH --output=/dev/null # Suppress the default SLURM log file
#SBATCH --error=/dev/null # Suppress the default SLURM error file
#SBATCH --time=2-00:00:00 # Max time for job
#SBATCH --nodes=1 ... |
48206b5a6dc96290955aa3c1463cc2ddb719d1e2491642bfe1dd8ae138de01eb | Shell | 1,489 | 19 | #!/bin/zsh
stringtie -p 14 -L control_pooled_sort.bam -G dm6_flybase_bdgp.gtf -o control_pooled_Nanopore_stg.GTF -A control_pooled_Nanopore.counts.txt
stringtie -p 14 -L tau_pooled_sort.bam -G dm6_flybase_bdgp.gtf -o tau_pooled_Nanopore_stg.GTF -A tau_pooled_Nanopore.counts.txt
# short read illumina reads
stringtie -p... |
561a0ce78a0d1dd7801f677a53778f1942f3cba9145b84458457599a1069e4ab | Shell | 1,489 | 33 | #!/bin/bash
#SBATCH --job-name=consolidation_all_tensors_test # Job name
#SBATCH --output=/dev/null # Suppress the default SLURM log file
#SBATCH --error=/dev/null # Suppress the default SLURM error file
#SBATCH --time=2-00:00:00 # Max time for job
#SBATCH --nodes... |
0e658e56dde88c3f179a1279bf639e401e7ee5c51eeea9ae0369b07059c8f51f | Shell | 1,491 | 33 | #!/bin/bash
#SBATCH --job-name=batch_tensor_test_new_misc # Job name
#SBATCH --output=/dev/null # Suppress the default SLURM log file
#SBATCH --error=/dev/null # Suppress the default SLURM error file
#SBATCH --time=2-00:00:00 # Max time for job
#SBATCH --nodes=1 ... |
3f8cbfe6eb9118b87a6af749d540c46c3f00828932363231bbfb40ae7551c4ac | Shell | 1,494 | 33 | #!/bin/bash
#SBATCH --job-name=batch_tensor_train_new_misc # Job name
#SBATCH --output=/dev/null # Suppress the default SLURM log file
#SBATCH --error=/dev/null # Suppress the default SLURM error file
#SBATCH --time=2-00:00:00 # Max time for job
#SBATCH --nodes=1 ... |
d5e27b9fabbcd9a0c2cda3a2c03d995c0f808c3988026288259d847a347f3fca | Shell | 1,495 | 32 | #!/bin/bash -l
set -e
export OPENBLAS_NUM_THREADS=1
export OMP_NUM_THREADS=1
export NUMEXPR_MAX_THREADS=1
export DASK_DISTRIBUTED__LOGGING__DISTRIBUTED="info"
export DASK_DISTRIBUTED__WORKER__USE_FILE_LOCKING=False
export DASK_DISTRIBUTED__WORKER__MEMORY__TARGET=False # don't spill to disk
export DASK_DISTRIBUTED__W... |
376283b289c30b22cfd50c104eae93b7f69096f6b65e111600c09b850e93ac3e | Shell | 1,503 | 24 | #!/bin/bash
# test file to test vga_spotLight -- edit the paths to point to the correct files and test if ibrun is the correct command on your system
# Option A - example
# ibrun -n 1 vga_spotLight --optAdat /work/02076/abacolla/stampede2/rnaSeq_tcga_18/acc/Part2_BasicDataProcessing/ACC__geneExpT.txt --optAgene1 GRB... |
71afff529dea8ff033d3fa52a9e1191ce09b02a1156bf376bf170e69b216d214 | Shell | 1,503 | 46 | #!/bin/bash
# This script performs nuisance regression and bandpass filtering as implemented by AFI's 3dTproject (i.e simultaeous regression and bp).
# Volumes flagged for high motion are interpolated before the regression
# time series are normalized to have sum of squares = 1
# --------------------------------------... |
dda3cba51192a1eb14225d1124cd2c627f558a077b27f384830470b66caef743 | Shell | 1,505 | 49 | # Get Nest installation folder
if [ -z "$NEST_FOLDER" ]; then
SCRIPT_DIR="$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}"; )" &> /dev/null && pwd 2> /dev/null; )";
NEST_FOLDER="$(dirname $SCRIPT_DIR)/.nx/installation/nest";
fi
# Get NEST version
if [ -z "$NEST_VERSION" ]; then NEST_VERSION="3.7"; fi
# Trying to lo... |
5fd4464890e38ed9f053a15c88b62015feb459cb5ec213fa427f334b5b9143e3 | Shell | 1,510 | 32 | #!/usr/bin/env bash
# "Automates" calling of the "PCA R script" by looping through the "comparisons"
# My 'OBJs'
WD=$(pwd)
SCRIPT="make_PCA_COUNTS.R"
DONE="\tDone!\n"
# Declares 'array' of comparisons
declare -a COMPARISONS=("ASC-10_vs_ASC-30" "ASC-10_vs_ASC-CTRL" "ASC-30_vs_ASC-CTRL" \
"C136-... |
1ed8ad19f614263c26e4e7ceb1000d3ee464f1b1109a532def89db9613cab9ab | Shell | 1,511 | 43 | # Runs evaluation on manually selected model checkpoint
# (note: on different architecture layouts might need some extra args, ideally the same as the used training script)
eval_all_disasters () {
for event in floods fires hurricanes landslides
do
rm -rf /data/cache
rm -rf $HOME/cache/
... |
cb6f4dea4b9f6fa5320722543313a90cbb57aa2a7b39d5756379b7d34c1f06dd | Shell | 1,512 | 56 | #!/bin/bash
set -exo pipefail
WORKSPACE=$(pwd)
# Set path
echo "export PATH=$WORKSPACE/anaconda/bin:$PATH" >> $BASH_ENV
source $BASH_ENV
## Passed from .circleci/config.yml (Only 2 or 3 permited)
pythonversion=$1
if (( $pythonversion != 2 && $pythonversion != 3 ))
then
echo -e "\nERROR: Python 2 or 3 designatio... |
5257b9137c4c734c10d36adc73a6b837a95e50e56dc73cff361e3e0116266a99 | Shell | 1,513 | 49 | #!/bin/bash
# This script realigns the mean image of a motion corrected ts to T1 image image of the same subject
# -----------------------------------------------------------
# Script written by Ludovico Coletta
# Nilab, FBK (2022)
# -----------------------------------------------------------
function register_to_str... |
c9f14cac2501925016511f1d3cbf583d7fa94480f0991239a300b4c8364e1227 | Shell | 1,515 | 48 | #!/bin/bash
#
# Copyright 2021 AlQuraishi Laboratory
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law... |
89575f5272341b7d75170d5e1200eab8358a2711e0013b708bce619ebfa4800a | Shell | 1,519 | 42 | #!/bin/bash
path_tck=$PWD/HCP_tck #edit this
echo $path_tck/*/*/*/track.tck | tr " " "\n" > tcklist.txt
path_to_mask=$FSLDIR/data/standard/MNI152_T1_1mm_brain_mask.nii.gz
for path_to_tck_file in $(cat tcklist.txt)
do
dir_name=$(dirname $path_to_tck_file)
for func in ANOMIA SEMANTIC PHONOLOGICAL SPEECH_... |
994a293c8139537d41dbc22bfd7952e5cdba2cd1ac272cb3db9f2b0b5507fa40 | Shell | 1,528 | 44 | #!/bin/bash
# =============================================================================
# Xpra startup script for Aydin Studio (Docker GUI target)
#
# Launches Aydin Studio inside a virtual X11 display and exposes it via
# Xpra's HTML5 client. Users access the GUI at http://localhost:${XPRA_PORT}
#
# Environment va... |
9e96c5fb68cf4999b3247463a31677cb74d0b84157dbbd022d8045dbc186c205 | Shell | 1,533 | 49 | #!/bin/bash
#SBATCH --partition=GPU-a100s
#SBATCH --gres=gpu:a100s:1
#SBATCH --nodes=1
#SBATCH --job-name=test_tsdiff
#SBATCH --array=0-2
cd /home/leonard.galustian/projects/tsdiff-master || exit
mamba activate tsdiff
SPLIT_WEIGHTS=(
"logs/trained_rdb7/train_config_v2_2025_04_11__10_39_53_goflow-train-split-rxn... |
6aee95bd99eeb849b4381e342e5c4b81639a4d06ef75b6bc869ff56b77bb96cd | Shell | 1,545 | 53 | #!/bin/bash
# Script to check policy_perf_test code works with each possible combo of options
echo "Performance test results for parallel_reduce code computing sum of sequence [0,N) with various (nested) policies"
EXECUTABLE=policy_performance
TEAMRANGE=1000
THREADRANGE=4
VECTORRANGE=32
TEAMSIZE=4
VECTORSIZE=1
OREP... |
b6bb68bf39af59c1b69fe16e9a4634e737aa1afb7971fba46b31ff431c7ab84a | Shell | 1,545 | 1 | fsleyes --scene 3d --worldLoc 9.918212890625e-05 -18.000099182128906 17.999900817871094 --displaySpace world --cameraRotation -90.26 -0.84 1.15 --zoom 124.25 --hideLegend --lightPos 181.9999008178711 199.99970245361328 17.999900817871094 --offset 0.0 0.0 --hideCursor --bgColour 0.996078431372549 1.0 1.0 --fgColour 0.0... |
25fa73df5f3b175bf72cee981e3c38a75a7a094d8e18a60b81e18228db0f4179 | Shell | 1,549 | 45 | #!/bin/sh
#Siwei 14 Feb 2018
#Genotype rs1748456 and rs10933 for Hanwen
#Genotype rs78710909, etc.
date > genotyping.txt
echo "All genomic coordinates are based on GRCh38p7." >> genotyping.txt
for EACHFILE in *.bam
do
echo $EACHFILE >> genotyping.txt
echo $EACHFILE
# samtools index -@ 20 $EACHFILE
#printf "rs... |
90fe927a516ab436c776ce80c2697e125a089afce662cc34b81731c5e8a25f9d | Shell | 1,552 | 66 | #!/bin/bash
# LFCNN
# 4 cases
for i in {0..10}
do
./venv/bin/python ./LFCNN_separated.py -cms "B1 B2 B3" "B10 B11 B12" -cmc "LI" "LM" "RI" "RM" --no-params #--tmin 0
done
# left vs right
for i in {0..10}
do
./venv/bin/python ./LFCNN_separated.py -cms "B1 B2 B3" "B10 B11 B12" -cmc "LI LM... |
ae9dedfc4cd356e489291ab9bf20849b3218d68a33775984be4af49a4dc42b3f | Shell | 1,552 | 50 | # Install/unInstall package files in LAMMPS
# mode = 0/1/2 for uninstall/install/update
mode=$1
# enforce using portable C locale
LC_ALL=C
export LC_ALL
# arg1 = file, arg2 = file it depends on
action () {
if (test $mode = 0) then
rm -f ../$1
elif (! cmp -s $1 ../$1) then
if (test -z "$2" || test -e ../... |
22b9476c2ad6a37e2d776208511a5a2c2d698c3a2874720cf39adde259fe2a58 | Shell | 1,553 | 47 | #!/bin/bash
#
# Pack each job in $OUTPATH/000000 into a UUID-named tgz file.
#
# If a variable
#
set -euo pipefail
set -x
if [ -x "${SCRIPTS_DIR:-.}/token_removal.sh" ]; then
echo "Removing sensitive data from $OUTPATH"
"${SCRIPTS_DIR:-.}/token_removal.sh" "$OUTPATH"
echo "cleaning done. – Remember to always check ... |
e005dfeaca7e7dfc672e543142399db396c5775ce808de977fd0bd8c94041530 | Shell | 1,555 | 54 | #!/usr/bin/env bash
ENV_FN=metl-sim_2025-02-13.tar.gz
# exit if any command fails...
set -e
# create output directory for condor logs early
# not sure exactly when/if this needs to be done
mkdir -p output/condor_logs
# echo some HTCondor job information
echo "Date: $(date)"
echo "Host: $(hostname)"
echo "System: $(... |
48a47fefbcd5853a40c16bcccd232ed725d92e960e1de5e3516825a724b96ae6 | Shell | 1,560 | 41 | #!/bin/bash
models=("tcformer" "atcnet" "eegnet" "shallownet" "basenet" "eegtcnet" "eegconformer" "tsseffnet" "ctnet" "mscformer")
datasets=("bcic2a" "bcic2b" "hgd")
seeds=(0 1 2 3 4) # 5 seeds for each model-dataset pair
augs=("interaug" "no_interaug")
gpu_id=1
mkdir -p log
for model in "${models[@]}"; do
for d... |
806431cbc5c1900a9f938b2044747b0daf30d447880681016c93bf97166115a1 | Shell | 1,566 | 49 | #!/usr/bin/env bash
set -e
# Get the directory where the current script is located
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
# Source the common setup file
source "$SCRIPT_DIR/common_setup.sh"
test_module2() {
setup_environment
setup_unique_directory
setup_data_directories
get_deepret... |
debff9902d757db90985b386ad30075ea4bfa7f985243e913a69a3a3f24774bd | Shell | 1,566 | 53 | #!/bin/sh
THIS_SCRIPT_PATH=`readlink -f $0`
THIS_SCRIPT_DIR=`dirname ${THIS_SCRIPT_PATH}`
#OS Ubuntu 14.04
### Common packages for linux/windows
if [ ! -e "pyinstaller" ]; then
git clone https://github.com/pyinstaller/pyinstaller
cd pyinstaller
git checkout v2.1 -b v2.1
cd ${THIS_SCRIPT_DIR}
fi
echo "... |
08d1e6cbae48feda2d15b8ece8f578236b11696632d39e9e909b12c1344a8513 | Shell | 1,567 | 40 | #!/bin/bash
# Download MIMIC-IV from PhysioNet into a directory any of the builds can use.
#
# Usage: ./download_data.sh [destination] [physionet-username]
#
# destination where to put the data (default ./mimic-data)
# physionet-username also read from $PHYSIONET_USER, otherwise prompted for
#
# Requir... |
c56242ccfb34ffcd4dd8649d920de51e3bb738d30d1f7011f97712160a1b2d3d | Shell | 1,567 | 38 | #!/bin/bash
# This script generates the concepts in the BigQuery table mimic_derived.
export TARGET_DATASET=mimic_derived
# generate tables in subfolders
# order is important for a few tables here:
# * firstday should go last
# * sepsis depends on score (sofa.sql in particular)
# * organfailure depends on measurement
... |
88cd0101e004df61a92d9ad72a4d78e17bdb35fae6ac26abf5fe668ed00790bd | Shell | 1,569 | 51 | #!/usr/bin/env bash
#
# This script downloads the hg38 and mm10 reference genomes and chromosome
# size files from UCSC. It will place them in the current directory.
#
# The script checks if the files already exist before downloading,
# so it's safe to run multiple times.
set -euo pipefail
echo "––– Genome Downloader... |
c643b26a79b19aec39ad9481f4c929967b1f282d912c09d883c42c604d51f08a | Shell | 1,575 | 49 | #!/usr/bin/env sh
forceWrite=0
while read roiname maskfile maskidx; do
for f in /Volumes/Hera/Amar/amyg_7T/data/1*_2*/Wbgrndkm_func.nii.gz; do
rsdir=$(dirname $f)
subj=$(echo $rsdir | cut -d "/" -f7)
fname=$(basename $f)
mkdir -p $rsdir/seeds_a... |
2bf07667539570a6f88d02cc35f2b0e78a339423ab12920cbe9be9244e550e50 | Shell | 1,578 | 30 | #!/bin/bash
#SBATCH --time=120:00:00
#SBATCH --ntasks=1
#SBATCH --cores 1
#SBATCH --mem-per-cpu 64GB
mkdir Allen_MTG_Subsamples_cross_species_cluster
mkdir Allen_MTG_Subsamples_subclass
python process_for_ctp.py rhesus cross_species_cluster Allen_MTG_Subsamples_cross_species_cluster
python process_for_ctp.py gorilla ... |
88a989aa4c4e4b21b46cf30ab7dfb791e91aba0ee4b831ca0a8ad734a49575bb | Shell | 1,579 | 59 | #!/bin/bash
set -euf -o pipefail
# default vals
chart_path=""
no_import=""
# help message
print_help() {
echo "Usage: $0 --dir <chart-path> --chart-name <chartname> [--no-import]"
echo
echo "Arguments:"
echo " --dir Path to the chart directory (required)"
#TODO echo " --version ... |
2beea57b23114eec560557cb2f9b9527c535be74bc659467ad7a4d8d8ee549f5 | Shell | 1,581 | 38 | #!/usr/bin/env bash
# Regenerate the metafor reference values PyMARE's alignment tests read.
#
# Run from the repository root:
#
# validation/metafor/regenerate.sh
#
# Rewrites all three files in place:
#
# pymare/tests/data/metafor_reference.json rma.uni
# pymare/tests/data/metafor_escalc_referen... |
3f771bd2717dc1a24e65a8107b4cd7aec61e91a01230d83d7c425e1334087214 | Shell | 1,584 | 21 | #!/bin/bash
./venv/bin/python ./LFCNN_decoder.py -es B9 B10 B11 B12 -cmb "RI" "RM" "LI" "LM" --postfix seq
./venv/bin/python ./LFCNN_decoder.py -es B7 B8 B9 B10 B11 B12 -cmb "RI" "RM" "LI" "LM" --postfix seq
./venv/bin/python ./LFCNN_decoder.py -es B5 B6 B7 B8 B9 B10 B11 B12 -cmb "RI" "RM" "LI" "LM" --postfix seq
./v... |
69a3c2cbd55de7fae4b4532c6927783d44423062ad5f76a87c3365d1b40f1d49 | Shell | 1,594 | 23 | wget https://cqsweb.app.vumc.org/download1/annotateGenome/TIGER/20180312_mirbase22.tar.gz
tar -xzvf 20180312_mirbase22.tar.gz
wget https://cqsweb.app.vumc.org/download1/annotateGenome/TIGER/20161214_GtRNAdb2.tar.gz
tar -xzvf 20161214_GtRNAdb2.tar.gz
wget https://cqsweb.app.vumc.org/download1/annotateGenome/TIGER/201609... |
09ea7c0533ec7f314c5c3256480a0d003a8dd228c9220aa7bb4a61470722cc48 | Shell | 1,596 | 53 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=100G
#SBATCH --job-name=07_deconvolution_CIBERSORTx_FULL
#SBATCH -c 1
#SBATCH -o logs/07_deconvolution_CIBERSORTx_FULL.txt
#SBATCH -e logs/07_deconvolution_CIBERSORTx_FULL.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo ... |
31aa95a88771b2ef3a9cf28318e7982f6ceb7378c11500f3d44ebb476ec2c052 | Shell | 1,597 | 52 | #!/bin/bash
# This script carries out slice timing correction using AFNI's 3dTshift command
# Required inputs: despiked ts ad the json file coming from the dicom to nifti conversion and containing the "SliceTiming" field.
# EDIT the TR (in seconds)
# The tools jq is needed. For Ubuntu: sudo apt... |
250988c590f83415be1d2347e8e9cb55d87caa42c88c105f78a55f0f26d329c6 | Shell | 1,608 | 43 | #!/bin/bash
if [ "$#" -ne 2 ]; then
echo -e "\nUsage: vga_survivalCurve_s.sh <TCGA_TUMOR> <GENE_NAME>\nTCGA_TUMOR and GENE_NAME must be capital\n"
exit 1;
fi
module load intel/18.0.2
module load impi/18.0.2
module load Rstats/3.5.1
module load RstatsPackages/3.5.1
s1=`echo $1 | tr '[:upper:]' '[:lower:]'`... |
a3535cc533779363d50254a5dad9b4dddb75c8eca1614ce2225c1408d191b62b | Shell | 1,610 | 42 | #!/bin/bash
#SBATCH -p XiaoYueHe
#SBATCH --nodes=1
#SBATCH --cpus-per-task=30
#SBATCH --mem=170GB
#Date: 2023-05-25
#Need to modify
# /work/home/sdxgroup01/Workspace/20240124rds/Spleen.rds
# Main
#parameter setting
cpu_num="30"
wpath=~/Workspace/Part2/pyscenic;cd ${wpath}
#input file prepare
tf_data="${wpath}/data/... |
edef276d60e2d56a005f97f5a4de9308f1db6cea163931b848d4775b70c36713 | Shell | 1,616 | 33 | #!/bin/bash -l
# Set SCC project
#$ -P ivc-ml
# Request n CPUs
#$ -pe omp 3
#$ -m ea
# Request 1 GPU
#$ -l gpus=1
#$ -l gpu_memory=48G
#$ -l h_rt=1:00:00
module load miniconda/23.11.0
conda activate py3.11
roi=64
ps=4
augment="none" #"RegionModalMix1.1" #"none" #
fusion_type=null #"concat"
# ckpt="checkpoints/I... |
59381b80f316dd57057653294527b20878d5156db61dc66901d52f4c5bd57651 | Shell | 1,618 | 45 | #!/bin/bash
set -eu -o pipefail
if [ "$EUID" -ne 0 ]; then
echo -e "Please run the script with root privileges!"
exit 1
fi
# Check if FAST_DATA_DIR and SLOW_DATA_DIR are provided
if [ $# -lt 2 ]; then
echo "ERROR: Both FAST_DATA_DIR and SLOW_DATA_DIR must be provided."
echo "Usage: $0 <FAST_DATA_DIR> ... |
59caccfcda2d9ccac0437c9359e984664e3df7487c561e9a551374cf52efef80 | Shell | 1,618 | 61 | #!/bin/sh
#============================================================
# JSONLAB inline documentation to wiki convertor
#
# Author: Qianqian Fang <q.fang at neu.edu>
#============================================================
print_help()
{
awk '/^%/ {dp=1} / this file is part of EasyH5/ {exit} \
/-- ... |
0edcf61bbf0b924302dfbd64d5c0bb0f08819fe2cb4df14e4a2f2d179850a371 | Shell | 1,620 | 51 | #!bin/bash
# Siwei 9 Aug 2021
# Siwei 3 Sept 2018
# Siwei 12 Feb 2021
# make adaptation to genres01 and STAR 2.7.7
rm -r ~/NVME/temp_cache_STAR
date > stat.txt
for EACHFILE_L1 in *_1.fq.gz
do
echo $EACHFILE_L1
echo ${EACHFILE_L1/%_1.fq.gz/_2.fq.gz}
echo $EACHFILE_L1 >> stat.txt
####init
#date
r... |
2d9cff00cb1b358b12df28024dd612bd45f27b9998b05ffe49ced869630349c3 | Shell | 1,627 | 27 | #!/bin/bash
set -euo pipefail
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=${THREADS_PER_COMMAND:-$(nproc)}
movingfile=$1
fixedfile=$2
outputdir=$3
shift 3
fixedmask=$(dirname ${fixedfile})/$(basename ${fixedfile} _t1.nii.gz)_mask.nii.gz
movingmask=$(dirname $movingfile)/$(basename $movingfile _t1.nii.gz)_mask.nii.gz... |
6320b804a85cf4e611cfddd0d7a176f0227d125eca77ed4643c69eb2868098a4 | Shell | 1,629 | 46 | #!/bin/bash
cwd="/user_data/weifanw/familiarity_plot" # project directory
# ====================================================================================================
# set all parameter the same as the those used in the simulation
# different task specify different parameter!
task="assoc"
postfix="mix50%_a... |
a9d56ae51c6cacf5d8e89fa4376df382ace32b26426aeca931598c0982765577 | Shell | 1,630 | 53 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=07_deconvolution_CIBERSORTx_1vALL_top25
#SBATCH -c 1
#SBATCH -o logs/07_deconvolution_CIBERSORTx_1vALL_top25.txt
#SBATCH -e logs/07_deconvolution_CIBERSORTx_1vALL_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JH... |
0c20e7364c8601d9f69aeae0ec8c81979c8ae80b24f6bed750120d7d8dab6dad | Shell | 1,639 | 51 | #!/bin/sh
# Copyright (c) 2021 Thomas Ward <thomas@thomasward.com>
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS... |
160d352d3f1852fe45cdf712bdb23da810cab79c75f747a1bf8ccafe05a98432 | Shell | 1,645 | 53 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=07_deconvolution_CIBERSORTx_MeanRatio_MAD3
#SBATCH -c 1
#SBATCH -o logs/07_deconvolution_CIBERSORTx_MeanRatio_MAD3.txt
#SBATCH -e logs/07_deconvolution_CIBERSORTx_MeanRatio_MAD3.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo... |
19cdd7aa17a5d2f62a2d5a294ba6750325312f65c40c99a7dc5c11cca9c15d3d | Shell | 1,647 | 38 | #!/bin/bash
# script was run interactively - but could ideally be included in the workflow
source activate rnaseq
cd data/external/strains/
#### VCF files ####
# Download VCFs (and their indexes) - SNPs and indels for CAST/EiJ strain
wget ftp://ftp-mouse.sanger.ac.uk/current_snps/strain_specific_vcfs/CAST_EiJ.mgp.v... |
41025b73f61ff0eb95da185b310c303860fcf7d7897cb00154d70207541d97be | Shell | 1,650 | 53 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=07_deconvolution_CIBERSORTx_MeanRatio_over2
#SBATCH -c 1
#SBATCH -o logs/07_deconvolution_CIBERSORTx_MeanRatio_over2.txt
#SBATCH -e logs/07_deconvolution_CIBERSORTx_MeanRatio_over2.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
e... |
d160d2d1244900e27bd04a970351b639a661024ad6ff8b0ecbff498e5517ee0a | Shell | 1,650 | 53 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=07_deconvolution_CIBERSORTx_MeanRatio_top25
#SBATCH -c 1
#SBATCH -o logs/07_deconvolution_CIBERSORTx_MeanRatio_top25.txt
#SBATCH -e logs/07_deconvolution_CIBERSORTx_MeanRatio_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
e... |
0fffcfb0a5dfae3ffa855d21bfb64d0d22b70a86dc31593089646ac1cb861814 | Shell | 1,652 | 49 | #!/bin/bash
#SBATCH --job-name=j_func_preproc
#SBATCH --partition=short
#SBATCH --time=48:00:00
#SBATCH -n 1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=4G
#SBATCH --output=logs/%x.%A-%a.out
#SBATCH --error=logs/%x.%A-%a.err
#############################################
freesurfer_version="X.X.X"
export FREESURFE... |
244f754c0991bdbb2e57351ec10cc765e13bb10446902c16fa4199dd67c417d9 | Shell | 1,658 | 49 | #!/bin/bash
CONDA_INSTALL_URL=${CONDA_INSTALL_URL:-"https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"}
source scripts/vars.sh
# Install Miniconda locally
rm -rf lib/conda
rm -f /tmp/Miniconda3-latest-Linux-x86_64.sh
wget -P /tmp \
"${CONDA_INSTALL_URL}" \
&& bash /tmp/Miniconda3-latest-Li... |
9e00dae1275e8fd316f94fa81be03b53b56a6894c96b8cd07d41385d43e718b7 | Shell | 1,661 | 52 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=07_CIBERSORTx
#SBATCH -c 1
#SBATCH -o logs/07_deconvolution_CIBERSORTx_test.txt
#SBATCH -e logs/07_deconvolution_CIBERSORTx_test.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo... |
7e03caaec4e7e9ee324f64fb88d6ed5a6adc3b6763487659dead32a0ee9c74ec | Shell | 1,663 | 28 | source ./config.sh
source activate proteinnpt_env
export model_config_location=$Embeddings_Tranception_config_location #Path to model config [Embeddings_MSAT_config_location|Embeddings_Tranception_config_location|Embeddings_ESM1v_config_location]
export sequence_embeddings_folder=$Tranception_embeddings_indels_folder ... |
b0f9a0668118176c73814a4c7f303ad7fc840ac9e94c0335c43434d7abd7f5cf | Shell | 1,664 | 37 | #!/bin/bash -l
module load unstable neurodamus-neocortex
export USE_NEURODAMUS=1
#ticket: https://bbpteam.epfl.ch/project/issues/browse/BBPP134-996
#config_file:
#/gpfs/bbp.cscs.ch/project/proj134/scratch/tickets/BBPP134-901-emodel-generalisation-example/zisis/stage/recipe.json
#morphs:
#/gpfs/bbp.cscs.ch/data/sc... |
88a3dd41ec0811e521303ff3e1ae59f873f45259e6998a2265cf40b04057182b | Shell | 1,665 | 38 | #!/bin/bash
# project ccf results from native space to fsaverage space
set -u -x -e
sub=$1
ses=$2
path_anat_data=$3
path_output_dir=$4
path_HCPtemplates_standardmeshatlases=$5
path_fsaverage=$6
path_wbcommand=$7
threshold="00"
for hemi in L R; do
if [ $hemi = "L" ]; then
hemi_down="left"
elif [ $hemi... |
efb208cf6967f890bd73039c94bcd07c3705ecc9b1f9679035b30a4416b96115 | Shell | 1,666 | 39 | #!/bin/bash
# project ccf results from native space to fsaverage space
set -u -x -e
sub=$1
ses=$2
path_anat_data=$3
path_output_dir=$4
path_HCPtemplates_standardmeshatlases=$5
path_fsaverage=$6
path_wbcommand=$7
threshold="00"
for hemi in L R; do
if [ $hemi = "L" ]; then
hemi_down="left"
elif [ $hemi... |
921a2eca40b2a72e9d03d837a088554ddc6f261317e8cf76b85f27bc83277bb2 | Shell | 1,670 | 45 | #!/bin/bash
set -ev
# 01. Set up environment
exec_dir=$( pwd )
cd "${exec_dir}"
sud_dea_dir="${exec_dir}/scripts"
# 02. Set up config files
# 02a. Specify config file path
cfg="${exec_dir}/configs/config_DEA_setup_example_SUD_DEA.yaml"
echo "${cfg}"
# 02b. Add root directory to config file if not specified
if ! $( g... |
50b13779d4ba438fbf22f4938824809b64abd5be3b7e163e5a7eabdb879d5189 | Shell | 1,673 | 51 | #!/usr/bin/env bash
set -e
# Get the directory where the current script is located
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
# Source the common setup file
source "$SCRIPT_DIR/common_setup.sh"
test_module1() {
common_init
cd "$TOOLBOX_PATH"
# Clean existing surfaces for testing
... |
9f611fe63d574c1f355184b8ccbab0b3c51b69bea6201b476ebb206ca7f3b2bc | Shell | 1,673 | 42 | # Higher level script to call Sandrine's code for converting physio files to FSL format and find the correct peaks manually. Paths need to be absolute
# Author: Valeria Oliva
echo -n "where did you mount the Project folder? write path (e.g. for vale it is ${projectpath}/) >"
read projectpath
echo -n "sub? Only inse... |
456e3ec33d287e5f19159bde5fc652a2dc12a09af2ffbf78df59425338061174 | Shell | 1,688 | 19 | #!/bin/bash
#
#SBATCH --job-name=SRRegBaseS
#SBATCH --output=/outpath/reg_%j.txt # output file
#SBATCH -e /outpath/reg_%j.err # File to which STDERR will be written
#SBATCH -p a6000
#SBATCH --gres=gpu:1
#SBATCH --cpus-per-task=8
#SBATCH --ntasks=1
#SBATCH --time=5-23:59 # Runtime in D-HH:MM
#SBATCH --mem-... |
e1cc2fabad3bdfa3380884b6a5838e8391438b22fbba5ed59e323a790c930db4 | Shell | 1,690 | 46 | set -e
## Get subject number
subj=$1
subj=${subj}_V1_MR
echo ${subj}
## Specify directories
projectDir=/projects/f_mc1689_1/ReliableFC
rawDir=${projectDir}/data/downloads/imagingcollection01/${subj}/unprocessed/Diffusion
preproDir=${projectDir}/data/preprocessed
## Set up HCP environment
envScript=${projectDir}/docs... |
b6c382a19b650c815cd3f03b3dee065dee378a684a3dfaaa9805b34f56d3544b | Shell | 1,693 | 52 | #!/bin/bash
#
# Copyright 2021 AlQuraishi Laboratories
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable la... |
08d2bfe783be2a1ea9af69dbc7a798376d12c79b4d30d89023fce98080cec3a9 | Shell | 1,697 | 52 | #!/bin/bash
#
#
# Functionality: Generates qc reports for already existing images and their corresponding segmentations/labels
# Usage:
# sct_run_batch -script qc_generation.sh --path-data PATH_TO_BIDS_DATA --path-output PATH_TO_QC_OUTPUT
# Output: The index.html in the qc folder will have the qc reports fo... |
226ab1a33836142c15ee2883a4b0333f15caac0cca6940007b4d6f2ea24e867f | Shell | 1,701 | 67 | #!/bin/sh
#
# shell script to automatically copy configuration files for ktan.
#
# The script takes 1 argument which is the name of the user
#
# It assumes that the configuration files of the user have the same name as the one
# used by ktan but with the .user extension.
# For example ktan.file.base.julia instead of k... |
39ce972ade040cafaf6a2347f8713cd99f9b21685a690378c466f2619c258cdf | Shell | 1,702 | 54 | #!/bin/bash
# set our directories
dir_out=$(pwd)
log_file="$dir_out/logfiles/log_runFSL-3.txt"
dir_ostt="$dir_out/results_ostt"
if [ ! -d "$dir_ostt" ]; then
mkdir -p "$dir_ostt";
fi
nsim=5000
## Hypothesis about neural adaptation
code="SMP_all_cope4"
echo "$(date) start $code" >> "$log_file"
# negative
fslmaths... |
9a51adbf848368e639d6b8382561f7b5468985f2a83c1684dfedcf79013ee374 | Shell | 1,708 | 71 | #!/bin/bash
help()
{
echo ""
echo "Usage: $0 -i indir -o outdir -a append_string -s"
echo -e "\t-h Show this help message"
echo -e "\t-i Path to a directory containing input time-series files (.txt with one time series value per line). Default: './timeSeries'"
echo -e "\t-o Path to a directory in which ... |
c2d81eaed7056d95a755052442957fd2ed245e20fb2e0ecb9e30be29c5d6d7f1 | Shell | 1,709 | 42 | #!/usr/bin/env bash
# Run the repeatable CPU validation for chemtrain's parallel force matching.
set -euo pipefail
repository_root="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
python_executable="${repository_root}/../../venv/bin/python"
mpi_executable="/opt/openmpi-4.1.8-cuda/bin/mpiexec"
cd "${repository_root... |
dfd6a4914a3e291cd8082bd66d1a0e02b8cc0491b60c6935a7c26bfef12153ba | Shell | 1,712 | 29 | #!/bin/bash
IFS=$'\n'
rds_path="/work/home/sdxgroup01/Workspace/20240124rds"
file_list=$(find ${rds_path} -type f -name "*.rds")
Workspace="/work/home/sdxgroup01/Workspace/Part2/pyscenic/output20240305"
for file in ${file_list[@]}
do
tissue=$(basename "$file" .rds)
echo "#############"
echo "$tissue"
... |
97518f9f564b945d2f7415051750f4822d6c5421969e4cbd369005d6988166e3 | Shell | 1,715 | 39 | ## bash script to get the old retinotopy and ROI data from the NYU retinotopy dataset and overlay it on the new anatomical data
export SUBJID=wlsubj138
export SESS_TA=ses-nyu3t99
export SESS_SO=ses-nyu3t01
export EXP_DIR=/Volumes/server/Projects/attentionpRF/derivatives
export SUBJECTS_DIR=${EXP_DIR}/freesurfer
expor... |
89a751669aca9af5a634d483b5f3a26247a21540622b308d2964007be1fd8e47 | Shell | 1,718 | 45 | #!/bin/bash +e
echo " -o- Preparing kMoL source..."
rm -f docker/kmol.tar.gz
cp environment.yml docker/environment.yml
tar \
--owner=0 --group=0 --no-same-owner \
--exclude='*.egg-info' \
--exclude='__pycache__' \
--exclude='*.so' \
-cf docker/kmol.tar.gz \
LICENSE.txt pyproject.toml setup.cfg ... |
f8b632e961001e75795d20ae07dbbe755717eb30ae406ad9202e4f5d6fcf2986 | Shell | 1,727 | 49 | #!/bin/bash
ENV_NAME="dockbiotic"
CURRENT_DIR=$(dirname "$(readlink -f "$0")")
DATA_DIR=$CURRENT_DIR/../../data
echo 'All datasets will be prepared in debug mode, i.e. using up to 5000 samples. ' \
'To use the whole dataset, remove the --debug flags. ' \
'However, this will make the example experiments muc... |
2d0c2689cc4b5cf92bbe12a53c8d9d50f5fedfe3418bec6faf7556180d8861f1 | Shell | 1,729 | 63 |
#################----------------------connectiong with MeFit
cd /
cd home/federico
cd lsvirtualenv/local/bin
source ./activate
cd casper_v0.8.2
#./mefit -s sample -r1 sample_R1.fastq -r2 sample_R2.fastq -avgq
##Now defining input variables
seqPath="/media/sf_Y_DRIVE/Federico/NDcollect/Compressed"
outDir="/media/s... |
6588feb479cdadff143bc8ea5c23f139bdddb408bdd1dc4c8cffda82165cc267 | Shell | 1,729 | 41 | #!/bin/sh
#
#
data_path=/home/kenweber/Projects/Neuromuscular_Signature_R01_Pilot
scripts_path=${HOME}/Neuromuscular_Signature_R01_Pilot
subjects=(sub-NSPilot006 sub-NSPilot007 sub-NSPilot009 sub-NSPilot010 sub-NSPilot012 sub-NSPilot014 sub-NSPilot015 sub-NSPilot016 sub-NSPilot019 sub-NSPilot021 sub-NSPilot022 sub-N... |
dc9cc834f8acfc4c6500c8f8473bd3d75ed27c3b1a638482d610a08fdf22cf39 | Shell | 1,732 | 52 | #!/bin/sh
# Copyright (c) 2021 Thomas Ward <thomas@thomasward.com>
#
# Permission to use, copy, modify, and distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
#
# THE SOFTWARE IS PROVIDED "AS IS... |
6e559c1c6962b7321bc38638a4fffa22dbb8ca7bb10f865410665a3a58219a3a | Shell | 1,756 | 82 | #!/bin/bash
# ---- Default Settings -----
# Paths
KOKKOS_PATH=${PWD}/kokkos
KOKKOS_KERNELS_PATH=${PWD}/kokkos-kernels
MINIMD_PATH=${PWD}/miniMD/kokkos
MINIFE_PATH=${PWD}/miniFE/kokkos
# Kokkos Configure Options
KOKKOS_DEVICES=OpenMP
KOKKOS_ARCH=SNB
# Compiler Options
CXX=mpicxx
OPT_FLAG="-O3"
while [[ $# > 0 ]]
do... |
7928a84339a0b3c7cc7f072513064be62a064699bd49a61ce892068ff32d4880 | Shell | 1,756 | 44 | #!/bin/bash
#qsub -l 'procs=1,mem=24gb,walltime=12:00:00' -I
#cd /home/traaffneu/margal/code/multirat_se/asset/
# ./fslorient.sh
base_dir='/project/4180000.19/multirat_stim/scratch/to_convert/test_marie/converted/export_sumiyoshi/fslorient/'
# Loop through subdirectories
for sub_dir in "$base_dir"sub-*/ses-*/f... |
99b20b9799b6cfbe7113ec50ebf83669331020c7159d8df5a5af249cb6e17523 | Shell | 1,767 | 74 | #!/bin/bash
# =============================================================================
# PHYSICS PARAMETERS
# =============================================================================
# System size (number of particles/sites)
N=6
# Hopping parameter
t=0.18
# Basis type: "hf" (Hartree-Fock), "chiral", or "ba... |
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