sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
24f891e0d432ac35230d9f8196f42606fc0c9e8429b5a5ce26884e9b09014275 | Shell | 1,250 | 20 | FILE=$1
if [[ $FILE != "ae_photos" && $FILE != "apple2orange" && $FILE != "summer2winter_yosemite" && $FILE != "horse2zebra" && $FILE != "monet2photo" && $FILE != "cezanne2photo" && $FILE != "ukiyoe2photo" && $FILE != "vangogh2photo" && $FILE != "maps" && $FILE != "cityscapes" && $FILE != "facades" && $FILE != "iphon... |
5597124e35071668341d7e8e222d39921e715485a8d44274a62b55c82ce9e63d | Shell | 1,251 | 30 | #!/bin/bash
root_path=$"/apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/"
mkdir ${root_path}/comparison_methods/Result/BRCA_stage/MOGOnet
mkdir ${root_path}/comparison_methods/Result/BRCA_stage/MOGOnet/merge
cd ${root_path}/comparison_methods/MOGONet
python3 ${root_path}/comparison_methods/MOGONet/main.py ... |
a5bcf110b32539cc481e9b88bb0a07657405fb5d8ffe594d9ed9b1ebcdffeac9 | Shell | 1,252 | 15 | #!/bin/bash
# Here, we're running one of the motif-scaffolding benchmark examples
# Specifically, we're scaffolding site 5 from RSV-F protein
# This is equivalent to the example in design_motifscaffolding.sh, except that we're adding the contigmap.inpaint_seq flag
# The logic here is that only some of the amino acids a... |
d149cd76aad69133907741c03c28d8ede21b7d862599614841437cdfe84e9320 | Shell | 1,276 | 49 | #!/bin/sh
if [ "$#" -lt 1 ]; then
echo "Usage: $0 <path_swconfig_json> <debug_mode> <print_swconfig> <sweep_progress>"
echo " path_swconfig_json: [*/swconfig*.json]"
echo " debug_mode: [true|false]"
echo " print_swconfig: [true|false]"
echo " sweep_progress: [0..100]"
ex... |
ca6bb32db4d695b92f261f42b4e34ac9c9f3fa3f43417f0bc3f14601cf8ae84d | Shell | 1,284 | 13 | #!/bin/bash
# Here, we're designing binders to a tau peptide. We want to specify that this peptide should adopt a helical conformation.
# We first provide the output path and input pdb of the target protein (tau_peptide.pdb)
# We then describe the protein we want with the contig input:
# - A 70-100 residue binder to ... |
c5a6482c73d0ba35746312d17edd656c469a0585507c33801f8ce7838db913f4 | Shell | 1,287 | 28 | #!/bin/bash
#SBATCH --job-name=NKI_TEST # TODO: why is this called TEST?
#SBATCH --time=10:00:00
#SBATCH --output=/mnt/Data/neuro-dynamic-covariance/datasets/task/rockland/slurm_logs/custom_fsl_pipeline_preprocessing/CHECKERBOARD645/%A_%a.out
#SBATCH --error=/mnt/Data/neuro-dynamic-covariance/datasets/task/rockland/... |
0794845dfdeae22fd2184ab1791c95ed2aab94a221b3c37b4a814fb52df9f064 | Shell | 1,288 | 28 | #!/bin/bash
#SBATCH --job-name=Rockland_default_fsl_pipeline
#SBATCH --time=10:00:00
#SBATCH --output=/mnt/Data/neuro-dynamic-covariance/datasets/task/rockland/slurm_logs/default_fsl_pipeline_preprocessing/CHECKERBOARD645/%A_%a.out
#SBATCH --error=/mnt/Data/neuro-dynamic-covariance/datasets/task/rockland/slurm_logs/def... |
7f8c8fb5aefa6080ac342aa8c1ed66adfee58417135aff406a9c283dd0d66ee2 | Shell | 1,290 | 43 | #!/usr/bin/env bash
usage()
{
echo "Usage: run_all.sh [-h | --help][ -b | --nburn <int>] [ -s | --nsamp <int>]"
}
help_output()
{
usage
echo "-b or --nburn allows the input of the number of Gibbs samples to use for burn-in."
echo "-s or --nsamp allows the input of the number of Gibbs samples to then retain fo... |
d59dfdf43d07238b07e227e1523713185a9196edb9b956e810dcea0c6329611b | Shell | 1,291 | 38 | #!/bin/bash
i=$(tail -n+2 data/cayo_brain_bulk_metadata_animals.tsv | cut -f 1 | sed -n $((($SLURM_ARRAY_TASK_ID-1)/20 + 1))p)
chr=$(( ($SLURM_ARRAY_TASK_ID-1) % 20 + 1))
genome=genomes/Mmul_10.dna.fa
mkdir -p reports
gatk --java-options '-Xmx64g' MarkDuplicates \
--INPUT bam/${i}.chr${chr}.bam \
--OUTPUT bam/${i... |
b9e3ebda6b142c8a2052062a004e4e7803d2940f6897cb27757cb4afdc70558b | Shell | 1,298 | 58 | #!/bin/bash
# This script 1)select data from a SUBJECTS_dir,
# 2) Creates stats directory
# 3) Saves tabulated data for subcortical volume and intenstity; cortical GWC, volume, area, cth
###### set dirs #####
# ..................#
#basefolder=/cluster/projects/p23/projects/Other_projects/VirtualHistology/AIBL
#subs... |
94c7805d55f231cbf2443907d661507b8ec526d69eca06b23f4ab9ede95773b8 | Shell | 1,300 | 48 | #!/bin/bash
#SBATCH --job-name=BrainAgeCV
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=16G
#SBATCH --time=04:00:00
#SBATCH --account=p274
#SBATCH --output scripts/BrainAge/logs_BrainAgeCV/slurm-%j.txt
##SBATCH --partition=hugemem
######################
# setting environment
######################
echo "SETTING ... |
dae6390a3f630c3d3d062f073e8919365f487b936867b35d7b0d09f064068c92 | Shell | 1,305 | 48 | #!/bin/bash
#SBATCH --job-name=BrainAgeCV
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=16G
#SBATCH --time=02:00:00
#SBATCH --account=p274
#SBATCH --output scripts/LifeBrain/logs_BrainAgeCV/slurm-%j.txt
##SBATCH --partition=hugemem
######################
# setting environment
######################
echo "SETTING... |
cfc8415de41a3cb01d0aca2c9ca69eb84ad80930c85d7e2f76c57caaca5a754e | Shell | 1,308 | 8 | CUDA_VISIBLE_DEVICES=0 python train_fully_supervised_2D.py --root_path ../data/ACDC --exp ACDC/Fully_Supervised --num_classes 4 --labeled_num 7 && \
CUDA_VISIBLE_DEVICES=0 python train_entropy_minimization_2D.py --root_path ../data/ACDC --exp ACDC/Entropy_Minimization --num_classes 4 --labeled_num 7 && \
CUDA_VISIBLE_D... |
915f24ed2de9cce14f493f004efd64fa17c86992383149adcb997944c5aa088b | Shell | 1,311 | 18 | export nnUNet_results="nnUNet_training/nnUNet_results"
export nnUNet_raw="nnUNet_training/nnUNet_raw"
export nnUNet_preprocessed="nnUNet_training/nnUNet_preprocessed"
export nnUNet_predictions="nnUNet_training/nnUNet_predictions"
export nnUNet_eval="nnUNet_training/nnUNet_eval"
GPU_ID=0 # Put the GPU IDs here
DATASET=... |
a88ab371aeedcb51e762c6f7ff0c9fef44ad2c380ab99847a124af342b2803fd | Shell | 1,311 | 66 | run=false
# Parse command line arguments
while [[ $# -gt 0 ]]; do
case "$1" in
--nsamples)
nsamples=$2
shift 2
;;
--batch_size)
batch_size=$2
shift 2
;;
--run)
run=true
shift
;;
... |
a631121b7c83277617b2570672f67badf97850a3c5ef1ebbb241be64a40b3edb | Shell | 1,312 | 49 | #!/bin/bash
#SBATCH --job-name=BrainAgeFull
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=16G
#SBATCH --time=04:00:00
#SBATCH --account=p274
#SBATCH --output scripts/BrainAge/logs_BrainAgeFull/slurm-%j.txt
##SBATCH --partition=hugemem
######################
# setting environment
######################
echo "SETT... |
7534f48e5a6faa4a2bdb623a2ccbbd9ec0e18379021d9a19c9f6ad52d4804c27 | Shell | 1,313 | 52 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
DATASET=cifar10
MODELDIR=/tmp/starspace/models
DATADIR=/tmp/starspace/data
mkdir -p "${MODELDIR}"
mkdir -p "${DATADIR}... |
0b34f2f46eacbbadfdfa58b393f827746690f3fb84614b8f22728398f49bc8b9 | Shell | 1,316 | 18 | export nnUNet_results="nnUNet_training/nnUNet_results"
export nnUNet_raw="nnUNet_training/nnUNet_raw"
export nnUNet_preprocessed="nnUNet_training/nnUNet_preprocessed"
export nnUNet_predictions="nnUNet_training/nnUNet_predictions"
export nnUNet_eval="nnUNet_training/nnUNet_eval"
GPU_ID=0 # Put the GPU IDs here
DATASET=... |
7f576a97e519ea2538aa07da7241e94c1ba29d012a59cc0b0255a96782c6bb20 | Shell | 1,316 | 49 | #!/bin/bash
#SBATCH --job-name=BrainAgeFull
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=16G
#SBATCH --time=02:00:00
#SBATCH --account=p274
#SBATCH --output scripts/LifeBrain/logs_BrainAgeFull/slurm-%j.txt
##SBATCH --partition=hugemem
######################
# setting environment
######################
echo "SET... |
6521e19d772b970345cfb1189abe6b00fc2e81cecec2bc421e8800cf236814d2 | Shell | 1,318 | 49 | #!/usr/bin/env bash
IMAGE_PATH=$1
IMAGE_NAME=$(basename $IMAGE_PATH)
DOCKER_IMAGE_NAME=$2
WORK_PATH="/tmp/coinstacImages"
#${IMAGE_PATH#/}"
mkdir -p $WORK_PATH
code=$?
if [ $code != 0 ]; then
>&2 echo "After making dir "
>&2 echo "WORK_PATH = ${WORK_PATH}"
>&2 echo "DOCKER_IMAGE_NAME = ${DOCKER_IMAGE_NAME}"
ex... |
b80d23437183677a5c38e78a9e2a4b3cdf59cace6025d03cd2d38daaa2fa09ec | Shell | 1,321 | 68 | #!/usr/bin/env bash
# The expected output is a new conda env file merging all conda packages for production pipelines
# Global variables
SCRIPT_NAME="$0"
SCRIPT_OPTS="$@"
SCRIPT_FOLDER=$(dirname $0)
REPO_FOLDER=$(dirname ${SCRIPT_FOLDER})
## auxiliary functions
# function to report issues and exit
report_problem(... |
d73866982da100dc054bb2202fc79a6ad59bdcc1b98836ebe1b307672b7d48f8 | Shell | 1,323 | 26 | #!/bin/sh
## Conservation score from the following studies
## 1. Kuderna et al., Nature (2023)
## 2. Siepel et al., Genome Research (2005)
# BigWig → Wig (https://www.biostars.org/p/71692/)
cd lib
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigWigToWig
# Executable
chmod +x bigWigToWig
# bigWigToWig.p... |
a70004eb1b27f82f973eab36d77e4ca13a0d5a5b3c623b92b5da3fa046e52ef8 | Shell | 1,325 | 49 | #!/bin/sh
# get_sum_stat.sh
gene_exp_trait=$1
geno_dir=$2
Score_dir=$3
BGW_dir=$4
LDdir=$5
filehead=$6
block=$7
GTfield=$8
# Score statistics directory
LDwindow=1000000
cd ${Score_dir}
line=$(head -n $block $filehead | tail -n1)
echo Generate sumamry stat for block ${line}
if [ -s ${LDdir}/${line}.LDcorr.txt.gz ... |
91c2d6f8d7d9fb2283c0675a55f111dc8d926b3292433bd2ce4e486e9fae73ed | Shell | 1,331 | 42 | set -e
#This script is best to run interactively to find where the problem is.
#Please note that SampleSheet.csv needs to have the adpater setting removed
#as we are going to use cutadapt to remove the adapter anyway.
bclfolder=$1
samplesheet=$2
outdir=$3
cd $outdir
mkdir -p bcl2fastq
cd bcl2fastq
# the following... |
dd616464c4b0d00f2a9b21aa3a2758b03e3e4426fe93b0b62789d2ccc9f294f5 | Shell | 1,333 | 41 | #!/bin/bash
# Pathways:
# BIDSderiv = folder where the data is
#number of subjects = folder names in BIDS
subjList="sub-01 sub-03 sub-04 sub-05 sub-06 sub-07"
targetList="ontarget offtarget"
#conditions = sub-folders in BIDS
timeList="Pre_stim Post_stim_5min Post_stim_2h"
runList="1 2"
for id in ${subjLi... |
593d265b8283b2366661cffa3702b099da5b8dd857edf1c8e4bd8c3c46132194 | Shell | 1,349 | 41 | #!/bin/bash
# Pathways:
# BIDSderiv = folder where the data is
#number of subjects = folder names in BIDS
subjList="sub-01 sub-03 sub-04 sub-05 sub-06 sub-07"
targetList="ontarget offtarget"
#conditions = sub-folders in BIDS
timeList="Pre_stim Post_stim_5min Post_stim_2h"
runList="1 2"
for id in ${subjLi... |
0395dd6acefaa84f067ae5e0a9bf4cc6faa96274c2cd90df81d1a1dc6d53d187 | Shell | 1,352 | 75 | #!/usr/bin/env bash
# The expected output is a new conda env file merging all conda packages for production pipelines
# Global variables
SCRIPT_NAME="$0"
SCRIPT_OPTS="$@"
SCRIPT_FOLDER=$(dirname $0)
REPO_FOLDER=$(dirname ${SCRIPT_FOLDER})
## auxiliary functions
# function to report issues and exit
report_problem(... |
de1a4101a7dc0f4dcea8e24848ac8a8c28f4bf1bae701446ccc5b20f8311c9d9 | Shell | 1,353 | 33 | #!/bin/bash
# This script calculates the Shapley value
python
import pandas as pd
import numpy as np
from utils import Preprocessing
from anna16 import CopyNumberPredictor
import shap
da0 = pd.read_csv("data/cv/datasets/full_length_reads.csv")
da1 = pd.read_csv("data/test/datasets/full_length_testdata.csv")
da = pd.c... |
100fedeabb7341028e668a52145c8d686a01e14e6287bfa42c9d2542d42ec8cd | Shell | 1,356 | 49 | #!/bin/bash
#
# Pathways:
# BIDSderiv = folder where the processed fieldmaps need to be sent to
#number of subjects = folder names in BIDS
subjList="sub-01 sub-02 sub-03 sub-04 sub-05 sub-06 sub-07"
#conditions = sub-folders in BIDS
timeList="Pre_stim Post_stim_5min Post_stim_2h"
targetList="ontarget off... |
c4f211cedf9da1b4ee9e2e228b7640baea723be39341da8d571bcaceff80aec5 | Shell | 1,359 | 23 | #!/usr/bin/env bash
# PreProcess:
# Usage:
# ./PreProcess.sh <DIR> <CELL> <TotalEpiMarks> <ChIPBINsize>
# $1 = folder path
# $2 = cell code name as listed in rnaseq.csv
# $3 = How many EpiMarks are bein gintegrated? 1, 2, ...,
# $4 = Window size (paper used 10000)
# $5 = Regression flag (1=regression, 0=classi... |
19d800d32db578e0a2c78bd89c2f981dfeb1a3dd5296c4da7daadec875e5f84b | Shell | 1,361 | 59 | #!/bin/bash
set -e
####################### define executables
deseq="./src/rnastability/rembrandts/DESeq.R"
rembrandts="./src/rnastability/rembrandts/REMBRANDTS.R"
####################### identify the input arguments
jobid=$$
metadata=$1
refdir=$2
stringency=$3
fitmode=$4
outdir=$5
if [ "$jobid" = "" ]; then
echo -... |
96d44c8088330cb67a8e35c26a25b9838d83143c2198cfd15ddbce6f609fc48d | Shell | 1,370 | 33 | #! /bin/bash
# Copyright (c) MONAI Consortium
# 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 or agreed to ... |
b16c9e7a585e07de4901770de3390805fe9eb9b3ee1c70c3d393f77b617eec20 | Shell | 1,373 | 27 | #!/bin/bash
# path=/media/hanlin/Liuyang_10T_backup/jiaaoZ/data_converted/mda_files/DataFromBenPurple003/converted_data.mda
# outpath=/media/hanlin/Liuyang_10T_backup/jiaaoZ/msort_results/DataFromBenPurple003
# geom_file=channelmapBEN_notfinal.csv
path=/media/hanlin/Liuyang_10T_backup/jiaaoZ/data_converted/mda_files/Mu... |
e2d7148fe9308c018411615cc635158a97d3da7667ca595e820074f0f4262292 | Shell | 1,373 | 45 | if [[ $1 -eq 0 ]] || [[ $2 = "" ]] || [[ $3 = "" ]]; then
echo "Incorrect arguments"
echo ""
echo "First argument for this script should be your MFA"
echo " device's current valid rotating token"
echo ""
echo "Second argument is the config env [prod, dev, local]"
echo ""
echo "Third is ... |
8fb9b87049a21684518b274a8178d2b83b521c1f124053c6b90488c70f1b6018 | Shell | 1,375 | 14 | #!/bin/bash
# Here, we're generating peptide binders, inspired by the work in Vazquez-Torres et al
# We want to make a binder to a specific peptide sequence, which we know can adopt a roughly helical geometry
# We therefore model the peptide as an ideal helix, docked into a grooved scaffold
# We then noise the whole st... |
3842b1585478a0edd43eadfce14a5e9b2ae4e0c0f7828a028ff425336a598939 | Shell | 1,383 | 39 | #!/bin/bash
#######################################################################################
# Running scripts for AN rates extraction while switching between conda environments. #
#######################################################################################
# Description: This script controls a work... |
9115073b9533efa450030c9c58e49b499f810dc5cb78c4ad4391bc10e5d597e0 | Shell | 1,384 | 47 | #!/bin/bash
# Nicole Gay, modified by Archana Raja
# 31 March 2020
# pull replicate names from ATAC pipeline stucture
#Usage : bash src/extract_rep_names_from_encode.sh <gcp-path-to-atac-run-with-trailing-slash> <gcp-path-to-output-results-bucket-with-trailing-slash>
RUN_DIR=$1
OUT_GCP_PATH=$2
random_string=$(openssl... |
eb1967fe40e6cc11a4a2403d8e1a013a5c2e64c5a21eca72974dc5eab052c69e | Shell | 1,384 | 16 | #!/bin/bash
# In this example, we scaffold an active site from a retroaldolase, and implicitly model the substrate with an external potential
# We specify the output path and the input pdb (a native retroaldolase)
# We provide a contig describing the protein we want to build:
# - 10-100 residues (randomly sampled), t... |
9c976d7e87608ea3244ab5e5fb6c9f36cd1835a60f69b914877f196fe368e112 | Shell | 1,391 | 10 | #!/bin/bash
# Here, we're making a binder, and we're specifying the course-grained topology of the binder, from a set of processed inputs
# We specify the path to the target protein, in this case the insulin receptor, along with an output path
# We tell RFdiffusion that we want to do "scaffoldguided" diffusion (i.e. we... |
ad0160b3b535077904b155be74a87720bff1259d1f7e8b846b273b4cf969c5ca | Shell | 1,394 | 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... |
24f1e94186f64a050f171b70cf6b69b93373bf6665568e8d30f92e1fb98a3923 | Shell | 1,416 | 51 | #!/bin/bash
#SBATCH --job-name=HyperParameterSearch
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=16G
#SBATCH --time=06:00:00
#SBATCH --account=p274
#SBATCH --output scripts/BrainAge/logs_RandomHyperParameterSearchCV/slurm-%j.txt
##SBATCH --partition=hugemem
######################
# setting environment
#########... |
ce8ae8721d7d4b5dc8a8af3932e4722be0e17c6808583de4470783b0a35f8caa | Shell | 1,416 | 41 | #!/usr/bin/env bash
# Copyright (c) MONAI Consortium
# 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 or agr... |
846111668995516a937dbc6ec8840dc4273fc0c2f1bd2052777f285a47802eea | Shell | 1,418 | 39 | #!/bin/bash
DIRECTORY_PROJECT=/scratch/gvignoud/results_dual
NAME_PROJECT=$1
if [ $HOSTNAME == 'cleps.CLEPS.eth.cluster' ]
then
SCRIPT_DIR='/home/gvignoud'
elif [ $HOSTNAME == 'rioc' ]
then
SCRIPT_DIR='/home/rioc/gvignoud'
fi
RUN_TIME_PROJECT=$(date '+%d/%m/%Y %H:%M:%S')
mkdir -p $DIRECTORY_PROJECT/$NAME_PR... |
ce1159d77b95f8b6d11736d98dce0ca56d5bde729dd15549b7dfbf9eb6b486ef | Shell | 1,419 | 35 | #!/usr/bin/env bash
# Submit TRAIN_SEED=42 and 123 for main-text ablation rows.
set -euo pipefail
ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd)"
cd "${ROOT}"
mkdir -p ablation/runs/logs
SPECS=(
"ablation/scripts/train_curriculum_full.slurm|ablation/runs/curriculum_full|abl_cur"
"ablation/scripts/train_... |
9e8ad29f0a13a82a0bb1db5dc6a9db4e730f77b9f9a5573c71efa36ca45e4ff4 | Shell | 1,420 | 51 | #!/bin/bash
#SBATCH --job-name=HyperParameterSearch
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=16G
#SBATCH --time=02:00:00
#SBATCH --account=p274
#SBATCH --output scripts/LifeBrain/logs_RandomHyperParameterSearchCV/slurm-%j.txt
##SBATCH --partition=hugemem
######################
# setting environment
########... |
7d6f970a4ff10da3de4d848fa1efd268e54884d39b194cd19729c923c7ea2193 | Shell | 1,425 | 34 | #!/bin/bash
#Purpose: Create label files in fs6 space - from individual parcellation files
#Inputs: parc2annot annotation files
#Outputs: .label.gii parcellation files
#Written by M. Peterson, Nielsen Brain and Behavior Lab under MIT License 2022
#SET PATHS
HOME=/fslgroup/fslg_spec_networks/compute
HOME_D=/fslgroup/g... |
c0d143a774311989d5fd96742100137ab70f39c394cbbe17fdbb4558490f235d | Shell | 1,432 | 39 | #!/bin/bash
DIRECTORY_PROJECT=/scratch/gvignoud/results_single
NAME_PROJECT=$1
if [ $HOSTNAME == 'cleps.CLEPS.eth.cluster' ]
then
SCRIPT_DIR='/home/gvignoud'
elif [ $HOSTNAME == 'rioc' ]
then
SCRIPT_DIR='/home/rioc/gvignoud'
fi
RUN_TIME_PROJECT=$(date '+%d/%m/%Y %H:%M:%S')
mkdir -p $DIRECTORY_PROJECT/$NAME_... |
8c5730a0856c8be923b6019681d4b82349f2dcaccec2e4fb0bf5409d271e5ddc | Shell | 1,437 | 30 | # Copyright (c) MONAI Consortium
# 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 or agreed to in writing, so... |
a6adbf1bcc8b1521a48da2dfeeb041d288a41218ab64c0514fcc35bf7b5c4660 | Shell | 1,440 | 56 | set -ueo pipefail
if [[ $# -eq 0 ]] ; then
echo 'Please choose genome directory as first input and desired chromosome as second input'
exit 0
fi
genomeDir=$1
chromosome=$2
label="chr_${chromosome}"
echo "Entering genomes directory"
cd /Users/akre96/Documents/github/rrbs_bismark/genome_dir
echo "Activating c... |
778b68d0048fb316564aee683de64d07bd8fe29666d0de20db996aa7504fa5ef | Shell | 1,456 | 27 | # This file contains on the 4th column the most variable genes.
# Use it to go into the metadata of the CleanSamples model and get where these genes are locatet at from Train/Test/Dev datasets
variable_genes_file=/mnt/BioAdHoc/Groups/RaoLab/Edahi/Projects/09.TimeCourse5hmC/ForFerhatGit/FCDNN/results/cpg_composition_d... |
59d343b32e5ca3d4ae40818f89153a10d67bd92fbaffd083a8a9d6fc25192327 | Shell | 1,460 | 39 | #!/bin/bash
DIRECTORY_PROJECT=/scratch/gvignoud/results_succession
NAME_PROJECT=$1
if [ $HOSTNAME == 'cleps.CLEPS.eth.cluster' ]
then
SCRIPT_DIR='/home/gvignoud'
elif [ $HOSTNAME == 'rioc' ]
then
SCRIPT_DIR='/home/rioc/gvignoud'
fi
RUN_TIME_PROJECT=$(date '+%d/%m/%Y %H:%M:%S')
mkdir -p $DIRECTORY_PROJECT/$N... |
d618753197ebfdb90f47232d6ffa3f057eaf0b512af3c4040098dc075b2bab03 | Shell | 1,467 | 34 | #!/bin/sh
# === read phenotype to append in job IDs ===
if [ "$#" -ne 1 ]; then
echo -e "[Error]: No input argument was defined.\nPlease define Job_ID string for current submission (e.g. CKD, IPF, etc.)\n"
exit
fi
pheno=$1
echo "Job ID: ${pheno}"
# ===========================================
#classifiers=(ExtraTree... |
70828dac49b510ad09e1e82f7656813fca4ec95c6b40de8ea80c87ea32a1222c | Shell | 1,470 | 40 | #!/bin/sh
#BSUB -J Aging_AD_transformation
#BSUB -oo Aging_AD_transformation.o
#BSUB -eo Aging_AD_transformation.e
#BSUB -B
#BSUB -N
#BSUB -M 10000
#BSUB -u Shuo.Zhang@Pennmedicine.upenn.edu
#BSUB -W 80:00
module add python/3.6.3
module add R/4.0.2
### set the working directory
workDir="/project/eheller_itmat_lab/shu... |
a7d00d580ac74b3f1c8bb836ec7a2e4e960c480dcd29396e8e2d9df40067d10b | Shell | 1,472 | 41 | #!/bin/bash
i=$(tail -n+2 data/cayo_brain_bulk_metadata_animals.tsv | cut -f 1 | sed -n ${SLURM_ARRAY_TASK_ID}p)
mkdir -p bam_lists
# Make list of bams of this genotype
tail -n+2 data/cayo_brain_bulk_metadata_technical.tsv | \
awk '$2 == "'$i'"' | cut -f 1 | \
sed 's/\(.*\)/star\/\1.bam/g' > \
bam_lists/${i}.bam... |
dbb257323d43bcb25bd9eae63facab391b87815e659ed9f3e67363d99176aa6f | Shell | 1,478 | 56 | #!/bin/bash
if [ $# -lt 3 ]; then
echo
echo "Usage: ./run_croo.sh [WF_ID_MAP] [METADATA_DIR] [CROO_OUT_DIR]"
echo
echo "Example: ./run_croo.sh wfids.json /mnt/test_output/atac gs://my-bucket/croo_output"
echo "[WF_ID_MAP]: JSON file with array of {label, workflow_id} objects (output of submit.sh)"
echo "[M... |
e910d61fdf45dfe918e4582a6119bc89970a713f037f944e7af3087dbb46080d | Shell | 1,478 | 34 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
source $1
CONFIG=""
CONFIG="-x$VIEW_XDIM -y$VIEW_YDIM -l$VIEW_WINLOW -u$VIEW_WINHIGH"
if [[ 1 -eq $VIEW_ABSOLUTE_WINDOWING ]] ; then CONFIG+=" -A" ; fi
if [[ "NLINEAR" == "$VIEW_INTERPOLATION" ]] ; then CONFIG+=" -IL"... |
20a11840725f314b3d077ea98892498db2e9b8841a5b111874353e5141e04529 | Shell | 1,480 | 50 | #!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=32g
#SBATCH --gres=gpu:rtx2080:1
#SBATCH -c 3
#SBATCH --output=example_3.out
# source activate mlfold
# path_to_PDB="./train_pdbs/generated_20.pdb"
gpu=( 1 1 2 3 )
root="/mnt/data/shared/congfu/protein-generation/E3_Protein/code/"
# path="20221129_1101protein_autoencoder_AFPD... |
b4c20022d405e44fbe8146c4f404b2b92d7ed91af153c203fc9eac6c620ab656 | Shell | 1,481 | 53 | #!/bin/bash
#This script uses subject-level beta coefficient maps to create a group-level general linear model using FSl randomise.
#Check if the inputs are correct
if [ $# -ne 8 ]
then
echo "Insufficient inputs"
echo "Input 1 should be the input folder for the beta coef maps in MNI space"
echo "Input 2 should b... |
a8137ab8e105b57c55e82a64eae2b949638a6e44868fa429a5db9f92d8b9674d | Shell | 1,486 | 26 | #!/bin/bash
root_path=$"/apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/"
Rscript ${root_path}/comparison_methods/mixOmics/model_PLSDA.R \
${root_path}/data_TCGA/4.data_feature_filter_of_comparison_methods/2.data_feature_stage/1000/data_count.txt \
${root_path}/data_TCGA/4.data_feature_filter_of_compariso... |
cb9291d238c84a00bb026de5e9af74329ef510e5ada42916ecf03122c70e4ac3 | Shell | 1,486 | 47 | #!/usr/bin/env bash
# Add UCSC-style 'chr' prefix to Ensembl chromosome names in FASTA and GTF files.
#
# The pipeline expects chr-prefixed chromosome names (chr1, chrX, chrM, etc.)
# but Ensembl uses bare names (1, X, MT). This script converts Ensembl naming
# to UCSC/chr convention to match the format used for rn6 an... |
442d347048b253d305c948d42c66166a9c36b6a02585e2e75eb3d202be16528e | Shell | 1,492 | 26 | #!/bin/bash
root_path=$"/apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/"
Rscript ${root_path}/comparison_methods/mixOmics/model_sPLSD.R \
${root_path}/data_TCGA/4.data_feature_filter_of_comparison_methods/2.data_feature_stage/1000/data_count.txt \
${root_path}/data_TCGA/4.data_feature_filter_of_compariso... |
0f22e23f5b6d50400d9dd104875a6c2d6ca604a363153342a8eec87c4712f673 | Shell | 1,503 | 46 | #!/bin/bash
#Purpose: Project tSNR maps to fsaverage6 surface.
#Inputs: tSNR maps from Step1, freesurfer native output
#Outputs: .shape.gii (HCP WB compatible) surface SNR maps
#Written by M. Peterson, Nielsen Brain and Behavior Lab under MIT License 2022
#SET PATHS
CODE_DIR=/fslgroup/fslg_spec_networks/compute/code/... |
5710a145d1c06de1a43c0a5acc39581a9e1667884a50726c83b091c965d3e464 | Shell | 1,511 | 34 | #!/bin/sh
# === read phenotype to append in job IDs ===
if [ "$#" -ne 1 ]; then
echo -e "[Error]: No input argument was defined.\nPlease define Job_ID string for current submission (e.g. CKD, IPF, etc.)\n"
exit
fi
pheno=$1
echo "Job ID: ${pheno}"
# ===========================================
#classifiers=(ExtraTree... |
b9a43322e552f48847e3d9fe29a0f6a444496ca0251140b75fe53ee7e24b293c | Shell | 1,517 | 47 | #!/bin/bash
#SBATCH --time=25:00:00 # walltime
#SBATCH --ntasks=1 # number of processor cores (i.e. tasks)
#SBATCH --nodes=1 # number of nodes
#SBATCH --mem-per-cpu=51250M # memory per CPU core
#SBATCH -J "UT_preproc" # job name
# Set the max number of threads to use for programs using OpenMP. Should be <= ... |
492d78638056241c9daff3ce32566a4bd2124e402a44ac5d1ccbe3b84961b80e | Shell | 1,521 | 56 | #!/usr/bin/env bash
set -euo pipefail
python_bin=${PYTHON_BIN:-python}
device_mode=${DEVICE_MODE:-cpu}
gpu_count=${GPU_COUNT:-1}
cpu_threads=${CPU_THREADS:-1}
echo "Launching minimal test: DEVICE_MODE=$device_mode CPU_THREADS=$cpu_threads"
n_trials=1
n_repeats=1
n_epochs=1
early_stop=1
groupkfold=1
dataset=amide
e... |
d832829f3b17bcbcfd7b14ebe79b8023701d1e7ead25cd45c5b0b87b09c9bfd7 | Shell | 1,523 | 30 | #!/bin/bash
#### Segmentation into CSF, GM, WM (FAST+FIRST) ###############################
<<'comment'
# 1. FAST: tissue segmentation in 3 classes (uses affine matrix from FLIRT for initial segmentation - can be implemented to use the warped transform by FNIRT)
# bet
bet $myT1 $myopath/str_brain -m -f 0.1 -B # ... |
e0c4de4a064fe53acd24c4614e8f3468861ea46ca2bc29512dd74759549a144b | Shell | 1,523 | 30 | #!/bin/bash
#### Segmentation into CSF, GM, WM (FAST+FIRST) ###############################
<<'comment'
# 1. FAST: tissue segmentation in 3 classes (uses affine matrix from FLIRT for initial segmentation - can be implemented to use the warped transform by FNIRT)
# bet
bet $myT1 $myopath/str_brain -m -f 0.1 -B # ... |
fb15fcd6ac77b8bcd625999c37fa8a6328d83054c3878b1e12354fd51fb95f8e | Shell | 1,530 | 40 | #!/bin/sh
#BSUB -J run_transformation
#BSUB -oo run_transformation.o
#BSUB -eo run_transformation.e
#BSUB -B
#BSUB -N
#BSUB -M 10000
#BSUB -u Shuo.Zhang@Pennmedicine.upenn.edu
#BSUB -W 80:00
module add python/3.6.3
module add R/4.0.2
### set the working directory
workDir="/project/eheller_itmat_lab/shuo/mousiplier"
c... |
fd7b9313e1c0f1d80274ce549a833a3a0acd454063f4565c3e26d0265b6c3666 | Shell | 1,543 | 63 | #!/bin/sh
gpu=(4 0 2)
PDE='swe'
field_dim=3
scale_factor=2
HR_resolution=128
LR_resolution=$((HR_resolution / scale_factor))
reference_model='SRCNN'
content_loss_weights=0.1
suffix_list=(
"${PDE}_LRinput_supervised_${reference_model}_bicubic_init_s_${LR_resolution}to${HR_resolution}_contentlossweights${content... |
25f8e193d5d975a8650ce9909125d5aa033295796d38aa995de886419af64807 | Shell | 1,547 | 45 | #!/usr/bin/env bash
#SBATCH --array=0
#SBATCH --nodes=1
#SBATCH --cpus-per-task=13
#BSATCH --mem-per-cpu=5
#SBATCH --time=20:00:00
#SBATCH --export=ALL
#SBATCH --job-name="gwas_pz"
#SBATCH --output=/KIMEL/tigrlab/scratch/pzhukovsky/biobank/genetics/CT/lbl_reg_%j.out
#SBATCH --error=/KIMEL/tigrlab/scratch/pzhukovsky/bi... |
e3160245ab6c737faa46b3c3433ffd435bf7770ca647e9a4978f9a49fd7895d7 | Shell | 1,552 | 40 | #!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=32g
#SBATCH --gres=gpu:rtx2080:1
#SBATCH -c 3
#SBATCH --output=example_4_non_fixed.out
source activate mlfold
folder_with_pdbs="../inputs/PDB_complexes/pdbs/"
output_dir="../outputs/example_4_non_fixed_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
path_f... |
b3b677ded37a8ff7ab7efb734b88b01b44d689d2cadd07665485181060e9f64b | Shell | 1,558 | 40 | #!/bin/bash
#SBATCH -p gpu
#SBATCH --mem=32g
#SBATCH --gres=gpu:rtx2080:1
#SBATCH -c 3
#SBATCH --output=example_4.out
source activate mlfold
folder_with_pdbs="../inputs/PDB_complexes/pdbs/"
output_dir="../outputs/example_4_outputs"
if [ ! -d $output_dir ]
then
mkdir -p $output_dir
fi
path_for_parsed_chains=$ou... |
869d466dad9494610742a75e8284fe280ad1c03fcc3794b1a088bc624cbc7bbf | Shell | 1,562 | 36 | #!/bin/sh
# version.sh -- Script to build the htslib version string
#
# Author : James Bonfield <jkb@sanger.ac.uk>
#
# Copyright (C) 2017, 2019 Genome Research Ltd.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Softwa... |
6aae1a12c861ec3db31d2223dc61d876409eb0dba0ea24818883f517049c1f4f | Shell | 1,578 | 79 | #!/bin/bash
# Script to download files from RCSB http file download services.
# Use the -h switch to get help on usage.
if ! command -v curl &> /dev/null
then
echo "'curl' could not be found. You need to install 'curl' for this script to work."
exit 1
fi
PROGNAME=$0
BASE_URL="https://files.rcsb.org/download"... |
3207517e3aa185ebc065e0f86bf154e070b88d1795a84380894dd1f4fdc399bf | Shell | 1,580 | 54 | #!/bin/bash
#This script uses subject-level beta coefficient and tstatistic maps to create a group-level general linear model using AFNI.
#Check if the inputs are correct
if [ $# -ne 8 ]
then
echo "Insufficient inputs"
echo "Input 1 should be the input folder for the beta coef and tstat maps in MNI space"
echo "... |
d9c515215a084627633b53fb0caa05585a992be7fa5ecebc515e2f7d1b625a5d | Shell | 1,587 | 48 | #!/bin/bash
ROOT="./mor-data"
REF_FILE_A="$ROOT/11427_dyn_151.psf"
PDB_FILE_A="$ROOT/11426_dyn_151.pdb"
TRJ_FILE_A="$ROOT/11423_trj_151.xtc $ROOT/11424_trj_151.xtc $ROOT/11425_trj_151.xtc"
SEL_BASE_A="(not name H*) and protein and "
OUT_NAME_A="traj/condition-a"
REF_FILE_B="$ROOT/11580_dyn_169.psf"
PDB_FILE_B="$ROOT... |
a1b2aaeec2f247d1f4f390f2dec8bdb402af523e9df896185b70b63d6ac6e764 | Shell | 1,599 | 60 | #!/bin/bash
seed=2
run_dir="vqvae_low_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
n_embed=64
embed_dim=64
n_alpha_channels=2
n_channels=256
n_res_channels=256
n_res_layers=3
p_dropout=0.1
latent_resolution="low"
vq_decay=0.5
commitment_cost=0... |
816ecc8b6efd70df80db38c82d97402ef73920056abdc4fcb34fdbd9146e09a4 | Shell | 1,600 | 26 | #!/bin/sh
# https://github.com/mikelove/tximeta/blob/master/inst/extdata/hashtable.csv
mkdir -p "database/align-references/hsapiens"
mkdir -p "database/align-references/mmusculus"
export ftp_proxy=${http_proxy}
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_37/GRCh38.p13.genome.fa.gz \
-O dat... |
c2e11dc5203862f4de75769a9c70aafda7e81897579d3e4d69fc2e7d11b4f3b6 | Shell | 1,604 | 59 | #!/bin/bash
if [ $# -lt 4 ]; then
echo
echo "Usage: ./submit.sh [WDL_FILE] [JSON_DIR] [WF_ID_MAP] [NUM_CORES]"
echo
echo "Example: ./submit.sh atac.wdl json/ wfids.json"
echo "[WDL_FILE]: the WDL file to use as the workflow"
echo "[JSON_DIR]: the directory containing JSON files to use as the WDL inputs"
... |
27ee91b0f9c58e1b38cacb4d5f7b3feaf417106ed52eea250f6f2c1935a37c72 | Shell | 1,606 | 64 | #!/bin/bash
# Collect necessary images, surfaces and editing files for one subject to
# pass to a FS editor
#
# USAGE : fs_mkeditpack <FS subject recon dir> <output directory>
#
# AUTHOR : Mike Tyszka
# PLACE : Caltech
# DATES : 2021-01-21 JMT From scratch
if [ $# -lt 2 ]
then
echo "USAGE : fs_mkeditpack <FS sub... |
32630147ae9b196085a95ae58f932157b8eea3bc68f180612ac3a118c93f11f8 | Shell | 1,608 | 42 | #!/bin/sh
## Preprocessing data of Visel et al., Nucleic Acids Research (2007)
# Go to link (https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?page=1;show=1;form=search;action=search;page_size=100;search.form=no;search.result=yes;search.sequence=1)
# Save data to text file
# Filter only human enhancers.
cat VISTA| grep H... |
b4744fae7ef0ee68db5cbb2d77894fe51db4e662f5123bc8928cb4364fce7627 | Shell | 1,609 | 41 | #!/bin/bash
#This script does the preprocessing on the structural scan (T1w.nii.gz), the T2-weighted single-band reference for the task fMRI scan (sbref_task.nii.gz)
#it also processed the fieldmaps from the magnitude image (fmap_mag.nii.gz) and phase difference image (fmap_phdif.nii.gz)
#Folder structure is
#${bids... |
bef11ca76fb6d0c1dd26e5d5872cf2552907f68d5dd9a49c8ca35ed1ef78b6f9 | Shell | 1,612 | 26 | # This file contains on the 4th column the most variable genes.
# Use it to go into the metadata of the CleanSamples model and get where these genes are locatet at from Train/Test/Dev datasets
variable_genes_file=/mnt/BioAdHoc/Groups/RaoLab/Edahi/Projects/09.TimeCourse5hmC/ForFerhatGit/FCDNN/results/cpg_composition_d... |
054efbb540f1ef1c3646b24e096afc8e4e5f03c711ac83b588bd4f217a079028 | Shell | 1,621 | 25 | #!/bin/bash
rm -rf data/library_sequencing_stats.txt;
echo library$'\t'reads$'\t'read_length$'\t'duplicates$'\t'perc_duplicate$'\t'qual_min$'\t'qual_max$'\t'qual_mean$'\t'perc_A$'\t'perc_C$'\t'perc_G$'\t'perc_T$'\t'bam_total$'\t'bam_secondary$'\t'reads_mapped$'\t'perc_mapped$'\t'splices_total$'\t'reads_multimapped >> ... |
adedcff6a57e4356b4fdc6100e6c70418c624a07463a1385dc9689834875bb59 | Shell | 1,628 | 105 | #!/bin/bash
usage()
{
echo "usage: Download.sh options:<e>"
echo "-e Download only experimental data"
}
exp_only=0
no_args="true"
while getopts 'e' option; do
case $option in
e)
exp_only=1;;
*)
usage
exit 1
esac
no_args="false"
done
if [ ! -d... |
2bcaa3f95265cd33a662b749dbebe6f8daa70b291a34c12a8f81753c17f8da0e | Shell | 1,651 | 60 | #!/bin/bash
#Code to collect the QTL colocalization results after they have all been generated.
#set variables for date and time
today=`date +%F`
now=`date +%T`
pwd
#load config file
source qtl_config.sh
source $setup_config_sh
#write header to the summary results file
printf "SNP\tGene\tGeneID-Tissue\tTrait\tPPID\... |
106cf67ec264063525f1995887257385258412ed1e1260d2e5a5342ee474b099 | Shell | 1,652 | 60 | #!/bin/bash
# Load Local Variables
source ./SET_VARIABLES.sh
# Copy nii files to topup directory
echo "Copy nii files to MNI reorient directory"
cp ${NII_RAW_DIR}/*X${CHECK_REORIENT_SCAN}P1.nii.gz ${REORIENT_DIR}/data.nii.gz
# Reshape image matrix to resemble MNI space
echo "Reshape image matrix to resemble MNI spa... |
e6604f34724f244ae7c0963d18b143d2f1500dbbffd24591d8673731017d6d0d | Shell | 1,657 | 34 | #!/bin/bash
#
# This script was used to perform the primary data processing pipelines for the ATAC-seq datasets generated in this study.
# We used the PEPATAC and looper pipeline (http://looper.databio.org/), which requires third-party software and auxiliary resources
# for execution (e.g., genome indices). We recommen... |
79f0e8771418aca8cc0b23d3bcb3938cab55b7f145f43d101e0cf1410b704ce4 | Shell | 1,665 | 43 | #!/bin/bash
#Purpose: Run CBIG2016 preprocessing for multi-echo data. Restarts the Tedana command and remainder of the preproc.
#Written by M. Peterson, Nielsen Brain and Behavior Lab
#PATHS
HOME=/fslgroup/fslg_spec_networks/compute
CODE_DIR=${HOME}/code/Utah_analysis/CBIG2016_preproc_ALL
OUT_DIR=/fslgroup/grp_proc/c... |
c5852e310896a62ad85e0775ef7d1635223245128fc693cd61e105a4c2db22bb | Shell | 1,668 | 61 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
MODELDIR=/tmp/starspace/models
DATADIR=/tmp/starspace/data
DATASET=FB15k
convert_data() {
while read -r line
d... |
f2cffc50b48550904d669246bc1f3c5180cabafc37331bce60e9e7282201ba71 | Shell | 1,681 | 52 | #!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --mem=20G
#SBATCH --partition=rondror
#SBATCH --constraint=GPU_MEM:12GB
#SBATCH --qos=high_p
ROOT="/oak/stanford/groups/rondror/projects/MD_simulations/amber/INCITE_REMD_trajectories"
REF_FILE_A="$ROOT/remd-rhodopsin-arr/system_reference.psf"
PDB_FILE_A="$ROOT/remd-rhodops... |
afbaf9c2af582d615db562e8b2c1f0269aa89a0fac9fc36a0b6a8a8de2dee415 | Shell | 1,690 | 55 | #!/bin/bash
if [ $# -lt 1 ];then
echo ""
echo "Runs MP2RAGE with FatNavs recon on the CUBRIC cluster."
echo ""
echo "Usage: cluster_submitMP2RAGErecon.sh <full_path_to_input_raw_twix_file> <full_path_to_output_root_folder>"
echo ""
echo "If you pass just one input file you will get the outputs in the current wor... |
58ae01ba77e57131243e68b726fb5a3525c4f100e94f10f8735c7ec1aae2eb44 | Shell | 1,693 | 25 | #!/bin/bash
# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to i... |
c749cb4b225d21f7ddb5c2737d58556d2554e1676cc415bb15d31fbbb03dbb6b | Shell | 1,693 | 100 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
export BART_COMPAT_VERSION="v0.9.00"
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
SLICE=-1
CC=10
ITER=6
COS=2
OS=1.5
BR=160
SPOKES=13
RAW=0
ROVIR=""
RSSNORM=""
while getopts "... |
91b29c176398b3cb48bfc98772e449b1da978135b0813e1bf465de37e4aed41d | Shell | 1,695 | 45 | #!/bin/bash
DIRECTORY_PROJECT=~/Documents/numeric_networks/Articles/Sequential_Learning_Striatum/Figures/simu
NAME_PROJECT=$1
RUN_TIME_PROJECT=$(date '+%d/%m/%Y %H:%M:%S')
rm -r $DIRECTORY_PROJECT/$NAME_PROJECT
mkdir -p $DIRECTORY_PROJECT/$NAME_PROJECT
PARAMS_TXT="$DIRECTORY_PROJECT/params_figure_pattern_$NAME_PROJ... |
d1a3be7dd54fac0e3bc8456951e25c598dd0a0b587cad3d6e1b28a2e65efa828 | Shell | 1,701 | 25 | #!/bin/bash
# Copyright (c) MONAI Consortium
# 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 or agreed to i... |
1ba70f8346b7c44654ebf8774eca9cfedd4a224b538a1004411a45801db9d4e5 | Shell | 1,704 | 62 | #!/usr/bin/env bash
#
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
DATASET=(
wikipedia
)
MODELDIR=/tmp/starspace/models
DATADIR=/tmp/starspace/data
mkdir -p "${MODELDIR}"
mkdir -p "${... |
41b1bedfc290d86aee8012b381315422779a456db1828990a2ead439a4d0a3e9 | Shell | 1,708 | 85 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
export BART_COMPAT_VERSION="v0.9.00"
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
helpstr=$(cat <<- EOF
Creation of Subspace Basis and Inversion Times from Repetition Time
-h hel... |
fd97c9cc0f0860393ae746fe7ab3fa646cfa9e38e03cdb2b95ff12ed71c76088 | Shell | 1,714 | 63 | # Run Stereoscope with bulk samples
# do before running bash script instead?
conda activate scanpy_scvi
############################################################
# folders
OUTDIR="../../../data/deconv/brain/results"
INDIR="../../../data/deconv/brain/inputs"
SC_DATA="$INDIR/snRNAseq_subsampled_220609.h5ad"
#SC_LIST... |
e4d84e784dc10537938626bec574dfe220e70fb54d2ac1bda7633e82059b0bc1 | Shell | 1,715 | 56 | #!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --mem=20G
#SBATCH --partition=rondror
#SBATCH --constraint=GPU_MEM:12GB
#SBATCH --qos=high_p
ROOT="./mor-data"
REF_FILE_A="$ROOT/11427_dyn_151.psf"
PDB_FILE_A="$ROOT/11426_dyn_151.pdb"
TRJ_FILE_A="$ROOT/11423_trj_151.xtc $ROOT/11424_trj_151.xtc $ROOT/11425_trj_151.xtc"
SE... |
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