sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
31454cf7471b05f521b11d532c2968d12f12a8f82272cc677eb582bdb2294d52 | Shell | 953 | 31 | # fetch pre-trained teacher models
mkdir -p save/models/
cd save/models
mkdir -p wrn_40_2_vanilla
wget http://shape2prog.csail.mit.edu/repo/wrn_40_2_vanilla/ckpt_epoch_240.pth
mv ckpt_epoch_240.pth wrn_40_2_vanilla/
mkdir -p resnet56_vanilla
wget http://shape2prog.csail.mit.edu/repo/resnet56_vanilla/ckpt_epoch_240.... |
45142ba6547a60d9bdd30e9c61df2867dfbbf5478038561a93c985e708daade0 | Shell | 953 | 38 | #!/bin/bash
# This script despikes the ts.
#
# https://www.sciencedirect.com/science/article/pii/S1053811914001578#f0090
#
# -----------------------------------------------------------
# Script written by Ludovico Coletta @NILAB (FBK)
# (2022)
# -----------------------------------------------------------
function de... |
21c02aeea858919744055ef5c4c4178d59077cfecceb7114b0f2865ec31c5957 | Shell | 954 | 21 | #!/usr/bin/env bash
## Author: Laura E Cook, University of Melbourne
## Purpose: This script loops through all files in a directory
## These commands are then used in a slurm array script to run jobs in parallel
TRA=($(for file in *.maf; do echo $file |cut -d "." -f 1-2;done)) # change this to whatever your file pref... |
273f6586e3918da09ac1fc4b563d2286f4fa5887864e08aeaf90b1c7d6e86412 | Shell | 955 | 8 | cd PCR1
~/.local/bin/bbmap/bbduk.sh -Xmx6g in1=R1.fq.gz in2=R2.fq.gz out=stdout.fq ref=adapters ktrim=r k=23 mink=11 hdist=1 tpe tbo 2> log_filtering.out | ~/.local/bin/bbmap/bbmap.sh -Xmx6g in=stdin.fq ref=design_files.fasta ordered interleaved nodisk outu=unmapped.fq.gz scafstats=scafstats.txt 2> log_mapping.out
cd ... |
e34430021a082fbe1c62478dbfd44e039c876cfb9ac9a850814f679165d46800 | Shell | 957 | 30 | # runVignette05.sh - Forward simulation
# --------------------------------------------------
# This vignette demonstrates forward simulation of
# blood flow through a vascular network.
# The ESL viscosity model is used, hematocrit is
# non-uniform throughout the network (the phase separation
# effect is included), rela... |
ef3e22dd836a22497b0a92e2fcb8c34c0ba02c089355cb5719b73cb7ac0ba447 | Shell | 961 | 35 | #!/bin/bash
if [ $# -ne 1 ]
then
echo "usage: $0 <tag or branch>"
exit 1
fi
# check out desired LAMMPS version
git checkout $1
# make sure we are in the LAMMPS root directory
if [ ! -e README ] || [ ! -e LICENSE ] || [ ! -e SECURITY.md ] || [ ! -e CITATION.cff ]
then
echo "Must be in the LAMMPS root fold... |
34b5ce94c70f1b23ec31b41e8eeaff64be3fe6942e8517cabce2f9fc2e2bb939 | Shell | 968 | 27 | #!/bin/bash
chr_num="X"
dx login --token TOKEN
my_cmd="plink2 --bfile chr${chr_num}_hqc_nopar \
--out chr${chr_num}_hqc_nopar_pruned --output-chr chrMT \
--exclude chr${chr_num}_hqc.prune.out \
--make-bed \
--threads 16"
bed_file="/notebooks/wes/sample_qc/high_quality_variants/chr$... |
7841aba22cb484b43423d175fb4dc180eca76e6147fb3b3ab9fd84c6d91fb29c | Shell | 969 | 23 | #!/bin/bash
#BSUB -J plot_figure_5 # Job name
#BSUB -n 20 # number of processors
#BSUB -q long # Select queue
#BSUB -o /home/gonzag46/git/PDGrapher/figures/figure_5_use_cases/output-figure3-%J.out # Output file
#BSUB -e /home/gonzag46/git/PDGrapher/figures/f... |
9aae277ae1b428e8f5e2847e28ab7b0bbb37c980a2586a52eac1c2d894834c35 | Shell | 970 | 29 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=400
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
... |
9c2808fc65e75337eb62f095a63c49c6e767aba4314270541ff3b640e5522e93 | Shell | 970 | 19 | #!/bin/bash
set -eo pipefail
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
# uv resolves and installs the full Windows dependency set in a fraction of the
# time pip takes; UV_SYSTEM_PYTHON/UV_CACHE_DIR are set in azure-pipelines.yml.
python -m pip install --progress-bar off --upgrade... |
f7b492245e9da71e306837b0a39c88ef622f8ab5d8d0e318dc6f060ee2a34b3d | Shell | 974 | 37 | #!/bin/bash
# Auto skull stripping via Freesurfer's mri_synthstrip command. You need parallel (sudo apt-install parallel) and Freesurfer to be installed on your pc
function auto_sk {
image_original=$1
file_name=$(basename $image_original _N4.nii.gz)
fold_name=$(dirname $image_original)
mri_synt... |
0427f85eee3735911d5f29d36c08cc4c70803d0c9d2d5627cb854608ab8a8af1 | Shell | 977 | 38 | #!/bin/bash
function reg_linear_flirt {
image_original=$1
study_folder=$2
sub_name=$(basename $image_original _masked.nii.gz)
fold_name=$(dirname $image_original)
flirt \
-in $image_original \
-ref $PWD/${study_folder}/templates/MNI152_T1_2mm_masked_freesurfer.nii.gz \
... |
8393c78b8fc4c5946dea8cabf9ea5775bbb28f7ac3dfcdb8c26e9425d553b739 | Shell | 981 | 22 | FILE=$1
if [[ $FILE != "cityscapes" && $FILE != "night2day" && $FILE != "edges2handbags" && $FILE != "edges2shoes" && $FILE != "facades" && $FILE != "maps" ]]; then
echo "Available datasets are cityscapes, night2day, edges2handbags, edges2shoes, facades, maps"
exit 1
fi
if [[ $FILE == "cityscapes" ]]; then
ec... |
2b9cf14e04f6fa36ecc3ebb253c7fbca03fb092b5396e1729c159adb06a3963d | Shell | 983 | 17 | #!/bin/sh
### Minimum requirements to run script: ImageMagick (6.8) and Perl (5) installation
# Input: Color image files (jpg format), located in the same directory as the count.sh and process.pl scripts; this script can handle single-channel images and merged channel images as inputs
echo "" >> data.csv
date >> data.... |
9d478b1903451c36409cfc2e4f7b09282394aa89da15d9ac04b983c865b4474c | Shell | 983 | 27 | #!/bin/bash
# ------------------------------------------------------------------
# [Aiden Doherty] Create dir structure to process acc files
# ------------------------------------------------------------------
rootDir=$1
# Structure will be created as follows
# <studyName>/
# files.csv #listing all files in... |
27eb35984ca678683b562a6bb57860aad598be1953530b1cf5b1ff6ee9680c5e | Shell | 987 | 31 | # runVignette02.sh - Forward simulation
# --------------------------------------------------
# This vignette demonstrates forward simulation of
# blood flow through a vascular network.
# The ESL viscosity model is used, hematocrit is
# uniform throughout the network, and prescribed pressure
# boundary conditions are us... |
62bf2a1f0a03f45cc96905893304a19d991a4f2320d924348b876ed494ef00c6 | Shell | 989 | 60 | #!/bin/bash
pattern="*tfce_corrp_*.nii.gz"
# go into the directory
cd ../results_tstt-cov
for file in $pattern
do
:
name="${file%.*}"
name="${name%.*}"
echo $name
# create the cluster text files
cluster -i $file -t 0 > "${name}_cluster-summary.txt"
done
# go into the directory
cd ../result... |
ae60d900828b31d47819f511eb8c661334cdd8c495d7e392562f823469c460e8 | Shell | 996 | 38 | #!/bin/bash
#SBATCH --ntasks=12
#SBATCH --mem-per-cpu=4G
# usage
# run_CUTnTAG_mm10_noSpike.sh <full path to file>.NO.EXTENSION
# example:
# ./run_CUTnTAG_mm10_noSpike.sh /media/teamgreenberg/Stagiaire/2021-Line-CUT-TAG/201230_X591_FCHF2YLCCX2_L4_CF1-FLAG
# extension in these cases MUST BE "_R1.fastq.gz"
# load func... |
c62d7ac1e6d535df71c97f0985e1f22078e17b4a9d6669a1f825442d79d5e0d4 | Shell | 999 | 17 | #!/bin/bash
#$ -o /cbica/home/nishiom/qsub_output
#$ -l h_vmem=15G,s_vmem=15G
# based on https://github.com/timhartung/T1T2/blob/main/T1T2_script.sh
project_dir=/mnt/DataDrive3/NishioM/HCPD_structural/fmriresults01
#project_dir=/mnt/DataDrive1/data_preproc/human_mri/HCP_3T
#project_dir=/mnt/DataDrive3/NishioM/HCP-Agin... |
d9f41264976ce9c79a5ad83615970719ffe576c9914555f5407768bddc873c8c | Shell | 999 | 34 | echo -n "Which sub? Only insert number >"
read subject
echo -n "where did you mount the Project folder? write path (e.g. for vale it is /home/valeo/) >"
read projectpath
echo -n "session? 01 or 02 >"
read ses
cd ${projectpath}/Projects/Neuromuscular_Signature_R01/data/BIDS/derivatives/sub-NSPilot${subject}/ses-${se... |
a3f85d45545c706d4caddc2c3d83349eea445db05a9cc7c0e20b220f0e61b70a | Shell | 1,009 | 20 | #!/bin/bash
#SBATCH --partition=prod
#SBATCH --nodes=1
#SBATCH -C cpu
#SBATCH --time=24:00:00
#SBATCH --account=proj85
#SBATCH --mem=0
# SPDX-License-Identifier: Apache-2.0
export moving_nii='../intermediateFiles/sigma_atlas_with_waxholm_labels.nii.gz' # Sigma atlas with waxholm labels, produced by write_waxholm_re... |
412e9e6466e0f7d333331d402883380a0e828a5182c6395df5d428ad776f1b96 | Shell | 1,013 | 24 | #!/bin/bash
echo "Starting MITK Workbench"
/mitk/MitkWorkbench.sh &
PID=$!
# Wait for the main MITK window ('Research - MITK Workbench ...') to map, then make it fullscreen.
# The previous readiness check grepped $HOME/logfile, which is never written (supervisord tees to
# $HOME/mitk-logfile), so it hung here forever ... |
c7fa6b290820d59474939da0c6c55310bbb544cbd2b88f992c930c7cd9ce1237 | Shell | 1,013 | 46 | #!/bin/bash
##
## make csv file more compatible with various tools by removing problematic characters
##
# script filename
script_name=$(basename "${BASH_SOURCE[0]}")
# check for correct number of arguments
if [ ! $# == 1 ] ; then
echo -e "\n $script_name ERROR: WRONG NUMBER OF ARGUMENTS SUPPLIED \n" >&2
echo -e... |
4b12c893c4f5b09371fa734a8453f7915252e35b3f53b3b9c3870b83dca6b242 | Shell | 1,017 | 30 | #! /bin/bash
set -eu -o pipefail
ROOT_FIXED_DIR="/kaapana/app/fixed"
ROOT_MOVING_DIR="/kaapana/app/moving"
ROOT_OUTPUT_DIR="/kaapana/app/registered"
FIXED_IMAGE=$( find ${ROOT_FIXED_DIR} -maxdepth 2 -mindepth 2 -type f -name *.nrrd)
MOVING_IMAGES=$( find ${ROOT_MOVING_DIR} -maxdepth 2 -mindepth 2 -type f -name *.nrrd... |
0bbd9347d886b9ff5c722013f7fffc9cebb19b91718a73a4986b87a7495812ae | Shell | 1,025 | 29 | subj=$1
method=$2
scriptsDir="/projects/f_mc1689_1/ReliableFC/docs/scripts/connectivity"
batchDir=${scriptsDir}/batchScripts
cd ${batchDir}
jobname=${method}_subj-${subj}
batchFilename=${batchDir}/${jobname}.sh
echo "#!/bin/bash" > $batchFilename
echo "#SBATCH --nodes=1" >> $batchFilename
echo "#SBATCH --ntasks=1" ... |
23e0443ce0e3fd512da988f4b90b999bdfbb08239ebb0fc13852608b6a1a4bd6 | Shell | 1,027 | 39 | #!/bin/bash
# PreToolUse Hook - Write Safety Check
# Prevents accidental overwrites of key files
set -e
TOOL_NAME="$1"
FILE_PATH="$2"
# Only run for Write tool
if [[ "$TOOL_NAME" != "Write" ]]; then
exit 0
fi
# Protected files - should never be overwritten without explicit user request
PROTECTED_FILES=(
".e... |
d60821dcc1af8ca6c49f764b29e96dd8b2eb2c0cf518bca51df62cecfe364382 | Shell | 1,029 | 23 | #!/bin/bash
## Increase the h_fsize just in case
# qrsh -l h_fsize=200G
module load bs/1.3.0
## Follow the instructions from
## https://support.illumina.com/bulletins/2017/02/options-for-downloading-run-folders-from-basespace-sequence-hub.html
## and
## https://developer.basespace.illumina.com/docs/content/document... |
57d6ca0fff9b72452c97cde955126e8e2b801d9d513dd8a5002a60d4fe3b2f20 | Shell | 1,030 | 32 | #!/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... |
db0c79cabdec520adf6f31e3e66f93848c340bddfc8c4aa388ae246010101c24 | Shell | 1,035 | 36 | #!/bin/bash
in_volume=$1
in_sphere=$2
vol_template=$3
surf_transform=$4
out_dof=$5
out_sphere=$6
mirtk=$7
wb_command=$8
out_doftxt=$(echo $out_dof | sed 's/\.dof/\.txt/g')
echo newnames $out_dof $out_doftxt $intermediate_sphere
echo mirtk register $vol_template $in_volume -model Rigid -sim NMI -bins 64 -dofout $out... |
63aa60fd813dc31cab522a78e16ebdc69ca417fabd2b089720be96c8e7693b29 | Shell | 1,036 | 38 | #!/bin/bash
#Script to extract spike protein from complete SARS-Cov-2 genome using blast.
#COPYRIGHT 2022
#Created by Mike Mwanga
#mikemwanga6@gmail.com
#motivation from this link
#https://www.biostars.org/p/433926/
module load blast/2.7.1+
#get number of sequences
n=$(grep -c ">" sequences.fasta)
echo create datab... |
c2bec5bce96ea26943438cfd5d68fdb3089880ca3adcf1ddc768ffac818769d6 | Shell | 1,036 | 36 | #!/bin/bash
in_volume=$1
in_sphere=$2
vol_template=$3
surf_transform=$4
out_dof=$5
out_sphere=$6
mirtk=$7
wb_command=$8
out_doftxt=$(echo $out_dof | sed 's/\.dof/\.txt/g')
echo newnames $out_dof $out_doftxt $intermediate_sphere
echo mirtk register $vol_template $in_volume -model Rigid -sim NMI -bins 64 -dofout $out... |
8851d8a550caf5daee7f60e12936f32a95909f39c1f8903f71e3352cc72c4b69 | Shell | 1,037 | 40 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=01_deconvolution_Bisque_1vALL_top25
#SBATCH -c 1
#SBATCH -o logs/01_deconvolution_Bisque_1vALL_top25.txt
#SBATCH -e logs/01_deconvolution_Bisque_1vALL_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JHPCE info ***... |
921e9922080e9a80cade4fd204d04e2425cb914badde58517b2f74a10ae14c3b | Shell | 1,038 | 39 | #!/bin/bash
# Bias field correction of the T1 image using the N4 alg. provided by ANTs
# Input: t1 raw image. BIDS like dataset structure is expected
# -----------------------------------------------------------
# Script written by Ludovico Coletta
# NILAB, FBK (2022)
# ------------------------------------------------... |
d19dffacc6fdc3770aad2bc8a9d28b70f064b36cd1a1849a26043f3fc6b16b1e | Shell | 1,044 | 47 | #!/bin/bash
##
## merge any number of tab or comma-separated files (coreutils join can only do 2 at a time)
## for tab field separator, use $'\t'
## coreutils 8.12+ required (for "-o auto" support)
##
# script filename
script_name=$(basename "${BASH_SOURCE[0]}")
# check for correct number of arguments
if [ $# -lt ... |
5719b3fc7807b238c3a67f9a15da75c94248894d7b8cc52647e547044a30d9aa | Shell | 1,045 | 37 | #!/bin/bash
#SBATCH --job-name=agat_perf
#SBATCH --time=24:00:00
#SBATCH --mem=4G
#SBATCH --cpus-per-task=1
#SBATCH --output=nextflow_%j.out
#SBATCH --error=nextflow_%j.err
# Script pour lancer le pipeline Nextflow sur SLURM
# Ce script soumet le pipeline principal, qui créera ensuite des jobs SLURM individuels
# Cha... |
adf5568db8dcb34ac3aa2903b35c0a5f78c8a7c444ef432c78d55709f9410063 | Shell | 1,048 | 14 | for file in minc/input-classes/final/{1,2,3}/*t1.nii.gz; do
if [[ ! -s registrations/class123/$(basename $file).Warped.nii.gz ]]; then
echo ./mb_register_class123.sh $file templates/templates2/model_extracted_t1.nii.gz registrations/class123
fi
done
for file in minc/input-classes/final/4/*t1.nii.gz; do
if [[ ... |
a483cb2fe033965e4b454cd341b01597196460f80c67400a19e0fcfb7f25880d | Shell | 1,050 | 23 | #!/bin/bash
#run cross every sample size and every data set
#sample size
sample_size=(10k 25k 50k 100k 150k 200k 250k 300k 400k 500k)
data_set=(ds_1 ds_2 ds_3 ds_4 ds_5)
for i in "${sample_size[@]}";
do
for j in "${data_set[@]}";
do
echo "Running for sample size $i and data set $j"
#if the out... |
b9eefa99b388001f4f0d94fb62bb44b7b374720879e63778a8a148680b96e479 | Shell | 1,054 | 45 | #!/bin/bash
### Author: Laura E Cook, University of Melbourne, 22/01/2020
### Last update: 07/02/2020
### Purpose: basic array wrapper script
# Array set up:
#SBATCH --array=1-10
# Partition for the job:
# The project ID which this job should run under:
#SBATCH -A punim0586
# Maximum number of tasks/CPU cores used... |
77a854d253154a714a01987d9daaada3a35315d0afc0f8db2abe794912aee7e1 | Shell | 1,057 | 40 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=01_deconvolution_Bisque_MeanRatio_top25
#SBATCH -c 1
#SBATCH -o logs/01_deconvolution_Bisque_MeanRatio_top25.txt
#SBATCH -e logs/01_deconvolution_Bisque_MeanRatio_top25.txt
#SBATCH --mail-type=ALL
set -e
echo "**** Job starts ****"
date
echo "**** JH... |
04290fc82afe0164681905530515b0fac51d677433fef0e62dae5548aeb069df | Shell | 1,059 | 37 | #!/usr/bin/env bash
# config.sh: master configuration file for the scripts
# Running this command directly has no effect,
# but you can tweak the settings to your liking.
# Set the amount of RAM available to the command line tools.
# Use "m" suffix for megabytes, "g" for gigabytes; e.g., 2g = 2 GB.
#BF_MAX_MEM=1g
#... |
1c32cd2b26f5148ce8235ef8bb4a1b1eda9f62bc4baa99580db4933c08c75077 | Shell | 1,059 | 25 | #!/bin/bash
# Desktop-container launcher for MITK Workbench (target of mitk.desktop).
# MITK restores a saved window geometry that is often pinned to (0,0); at (0,0) openbox draws the
# window's title bar at y=-26 — off the top edge — so the app looks undecorated even though it is
# decorated. Maximize the main window ... |
56cd2751325619c21247761f769a46dec9f43f2a97290d48f4de786f6675d786 | Shell | 1,059 | 42 | # 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
action () {
if (test $mode = 0) then
rm -f ../$1
fi
}
# all package files with no dependencies
for file in *.cpp *.h; do
test -f ${file} && action $file... |
c600a0e8c8fdcc2e201c2ea2608aac4e3bc12cc904db013a5aa5838090750c06 | Shell | 1,066 | 44 | #!/bin/bash
txt_of_int=seedlist_v2.txt
mkdir -p $PWD/HGG_LGG/group_level
for func_map in $(cat $txt_of_int)
do
splits=(${func_map//"seeds_2mm/"/ })
seed_name=${splits[0]}
seed_name_2=$(basename $seed_name .nii.gz)
#echo $seed_name_2
cp subject_maps/*_${seed_name_2}*gz /home/ludovicocoletta/Documen... |
7aac5ea19b2ce387105f3b2256dc0f0d96044d8a3039368309d521ffa5b894c5 | Shell | 1,070 | 37 | torchrun --rdzv-backend=c10d --rdzv-endpoint=localhost:0 repl/scripts/cli.py \
--dataset animals \
--spritevid_max_sprites 8 \
--spritevid_noise_type gaussian \
--spritevid_noise_level 0.1 \
--sprite_noise_on_top \
--seq_len 32 \
--num_sequences 16000 \
--encoder conv2d \
--use_bn \
... |
edaab02fa7883304888c86d859074212a881066bc3056d364a9233dd19c5ddb6 | Shell | 1,071 | 28 | #!/bin/bash
a=$1
my_cmd="plink2 --bfile ukb_c1-22_GRCh38_full_analysis_set_plus_decoy_hla_merged \
--extract final_array_snps_GRCh38_qc_pass_pruned.prune.in \
--keep ${a}_samples.id \
--out final_array_snps_GRCh38_qc_pass_pruned_${a} \
--mac 5 \
--write-snplist \
--threa... |
43747cb82ac78894a62bb80ccc4bad920a729fa76dc9f49430e21041dfe8a59b | Shell | 1,072 | 24 |
numof_category=1000
fillrate=0.2
weight=0.4
imagesize=362
numof_point=100000
numof_ite=200000
howto_draw='patch_gray'
arch=resnet50
# Parameter search
python param_search/ifs_search.py --rate=${fillrate} --category=${numof_category} --numof_point=${numof_point} --save_dir='./data'
# Create FractalDB
python fractal_r... |
0b676ad4477b46e8b7885ffb7fb2bd4cacad9028090741bc6e460b0e5e0859eb | Shell | 1,073 | 41 | # Get all subfolders
mapfile -t folders < <(find . -maxdepth 1 -mindepth 1 -type d ! -name ".*")
# Set NEST_FOLDER variable in case it is not set
if [ -z "$NEST_FOLDER" ]; then
SCRIPT_DIR="$( cd -- "$( dirname -- "${BASH_SOURCE[0]:-$0}"; )" &> /dev/null && pwd 2> /dev/null; )";
export NEST_FOLDER="$(dirname $SCRIP... |
0af5220d4e4cd7868391d8cb6fbf42be63fe5205d2de31330c0039123dc9c1dd | Shell | 1,076 | 15 | #!/bin/zsh
WORK_DIRECTORY=/Volumes/LaCie/
# no tes
python3 sqanti3_qc.py --skipORF /Volumes/LaCie/Drosophila/drosophila_nanopore/DRS_basic/results/stringtie/stringtie_illumina/stringtie_rf/corr_control_pooled_illumina_stg_rf.GTF dmel-all-r6.43.gtf dmel-all-chromosome-r6.43.fa --dir squanti_short --report skip
# to ... |
0d0177194611b9c380cee58fe7a3e2dc14174b213aa7cf7ee0b80da5d96c393a | Shell | 1,076 | 29 | #!/bin/bash
set -e -u
# CPU is default as this is what we need for releasing
CPU_OR_GPU=${1:-CPU}
# Build the installer for Linux.
# This script must be run from the root of the repository.
# Prerequisites: wheel has been build, e.g. using build_wheel.sh
rm -rf dist_pyinstaller build_pyinstaller
WHL_NAME=$(cd dist... |
e4f931ae6f416bd8a352e0e200cec7240305bf0884811d9cd26bf796a373174b | Shell | 1,076 | 47 | #!/bin/bash
# this script is used for renaming the files
subjects_dir=""
while getopts s: flag
do
case "${flag}" in
s) subjects_dir=$(realpath "${OPTARG}");;
?)
echo "script usage: $(basename "$0") [-s path to subs]" >&2
exit 1;;
esac
done
# list of all subjects
file_na... |
baab40ab1f103e56c761db8e3131576e85365154b33a76ad44256bace43ea202 | Shell | 1,084 | 30 | #! /bin/bash
for mode in ood iid; do
for sample in $(cat datasets/scrna-lupuspatients/sample_ids.txt); do
for model in identity random cae scgen; do
echo \
python ./scripts/train.py \
--outdir ./results/oos-lupuspatients/holdout-${sample}/mode-${mode}/model-${model} \
--config ./configs/tas... |
f42380d50ebc146001272ff6af66f2117e061a659252db7587a44ddf5d0ee58e | Shell | 1,084 | 27 | #!/bin/bash
chr_num=$1
dx login --token TOKEN
my_cmd="awk '{ \$6=\"NONE\"; print \$0 }' ukb23158_c${chr_num}_b0_v1.fam > temp.fam && mv temp.fam ukb23158_c${chr_num}_b0_v1.fam && \
plink2 --bfile ukb23158_c${chr_num}_b0_v1 \
--out chr${chr_num}_hqc \
--maf 0.001 --hwe 1e-6 --geno 0.01 \
... |
0847a3f4cdec01403a394f579a4eea0eb30966e013fcfd0405f2b56077a7f2d2 | Shell | 1,086 | 31 | #!/bin/bash -l
#SBATCH --job-name="EEG_2_CoordsV"
#SBATCH --partition=prod
#SBATCH --nodes=80
#SBATCH -C clx
#SBATCH --cpus-per-task=2
#SBATCH --time=24:00:00
##SBATCH --mail-type=ALL
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --output=EEG_2_CoordsV.out
#SBATCH --error=EEG_2_CoordsV.err
#SBATCH --exclusive
#... |
0447c048080a7812cfc53b9f1b9fac71cf722aefb421238d4fc20d78ccbdf360 | Shell | 1,088 | 44 | #!/bin/bash
#Submit to the cluster, give it a unique name
#$ -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") || $@ == "-h" ]]; then
echo "Usage: bash submit.sh CONFIG_FILE RUN_NAME"
echo "CONFIG_FILE -... |
e127582d9123b46f9be557049e338a587896db27923e5537d5ce85c472146feb | Shell | 1,090 | 27 | #!/bin/bash
chr_num="X"
dx login --token TOKEN
my_cmd="awk '{ \$6=\"NONE\"; print \$0 }' ukb23158_c${chr_num}_b0_v1.fam > temp.fam && mv temp.fam ukb23158_c${chr_num}_b0_v1.fam && \
plink2 --bfile ukb23158_c${chr_num}_b0_v1 \
--out chr${chr_num}_hqc \
--hwe 1e-6 --geno 0.01 --split-par hg38... |
ab1659f79e1581d428f69d13e21502f2e98bcb6e8a860060e8fd5fb24ce340c6 | Shell | 1,093 | 36 | #!/usr/bin/env bash
# Input parameters
t1_image=$1
subject_id=$2
output_dir=$3
# FastSurfer docker command
# docker run --gpus device=3 \
# -v "$(dirname "${t1_image}")":/data \
# -v "${output_dir}":/output \
# -v /SeaExp_1-ayan/license.txt:/fs_license \
# --rm --user $(id -u):$(id -g) deepmi/fastsurf... |
0d4f53e5ea23966b22fdece20a676f3684f46f362ef601cfc196d1c1b61f39a7 | Shell | 1,095 | 23 | #!/bin/sh
# $FreeBSD$
#
# This script was taken from FreeBSD.
#
# It uses ImageMagick to generate callout icons.
#
for i in `jot 9 1`
do
convert -size 202x202 xc:green -transparent green -fill black -draw 'circle 100,100 100' -fill white -stroke none -pointsize 160 -gravity center -kerning -5 -font Helvetica-bol... |
426158390f1c5ff65ea42d6838ded7e6353ab282360fe41ef60fa73766568a99 | Shell | 1,097 | 34 | dir=$1
tefunc=$2
outdir="${1}_postprocess_results"
mkdir -p $dir
mkdir -p $outdir
echo $dir
echo $outdir
# Monte Carlo parameters
n_dim=500
n_samples=5000
n_experiments=100
n_x=1
n_trees=100
bootstrap=0
subsample_power=0.88
min_leaf_size=5
max_splits=20
it=0
for tuples in 0,'--R' 1,'' 3,'' 4,'';
do
IFS=',' read m... |
4875be06ec966d045d6ef1200c90ca872a7075b76913f13aacfbe48ca4a7d6d1 | Shell | 1,100 | 28 | #!/bin/bash
path_tracto=$PWD/HCP_tck #edit this
path_to_mask=$FSLDIR/data/standard/MNI152_T1_1mm_brain_mask.nii.gz
for func in SEMANTIC PHONOLOGICAL ANOMIA AMODAL_ANOMIA SPEECH_ARREST VERBAL_APRAXIA MOVEMENT_ARREST
do
echo $path_tracto/*/*/*/wm_hubs_${func}/*gz | tr " " "\n" > ${func}_hubs.txt
fslmerge ... |
f280f35c2b75440cacbcb30b9e10e1c9bb77e2423cce7ea789deab6828e0612c | Shell | 1,100 | 47 | #!/bin/bash
cores=24
mem=100
new_sample_dir=
cellranger_atac_ref=
sname="105_2g_1"
echo $sname
/home/am3019/software/cellranger-atac-2.1.0/cellranger-atac count --id=${sname} \
--reference=${cellranger_atac_ref} \
--fastqs=${new_sample_dir} \
--sample=${sname} \
--localcores=$cores \
--localmem=$m... |
f7840d7088d8c6e86afd9fde4419a583f8b25df011476eccda99c39bdb8b1dbf | Shell | 1,101 | 32 | #!/bin/bash
# Copyright 2021 DeepMind Technologies Limited. All Rights Reserved.
#
# 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 ... |
ec186af5458e0ad88d7b3aefd5a8ab11908d956a2d628d3c6d081ece3c86d6c1 | Shell | 1,108 | 32 | sim=$1
method=$2
sesList=$3
nList=$4
tList=$5
scriptsDir="/projects/f_mc1689_1/ReliableFC/docs/scripts/connectivity"
batchDir=${scriptsDir}/batchScripts
cd ${batchDir}
jobname=${method}_sim-${sim}
batchFilename=${batchDir}/${jobname}.sh
echo "#!/bin/bash" > $batchFilename
echo "#SBATCH --nodes=1" >> $batchFilename
... |
f993cf969334d78eec80fb5a13f990bcd209aa5b3db6f221dc9609ac5e6638fe | Shell | 1,110 | 40 | #!/bin/bash
if [ -z "$ROS_DISTRO" ]; then
echo "ROS not installed. Check the installation steps: https://github.com/erlerobot/gym#installing-the-gazebo-environment"
fi
program="gazebo"
condition=$(which $program 2>/dev/null | grep -v "not found" | wc -l)
if [ $condition -eq 0 ] ; then
echo "Gazebo is not instal... |
f1139dd756299a5ffc9f986da98afe6489cdff2f175f2d6ce0afae022360d878 | Shell | 1,112 | 25 | source ./config.sh
conda activate proteinnpt_env
export assay_index=0 # Replace with index of desired DMS assay in the ProteinGym reference file (`utils/proteingym`)
export batch_size=1
export max_positions=1024
export model_type='MSA_Transformer' # [MSA_Transformer|Tranception|ESM1v]
export model_location=$MSA_Trans... |
4c330a204cf8b5cd93c98094d32735f954242659f11b9b959c8930ed7b8c7424 | Shell | 1,113 | 58 | #!/bin/bash
#
this_work_dir=$1
dtn=$2
#
#
#this_scripts_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
#
echo "start (step_1) this_work_dir = $this_work_dir"
#
work=${this_work_dir}/${dtn}
cd ${this_work_dir}
mkdir -p $work
touch 0
rm 0
ln -s ${dtn} 0
#mkdir -p ${work}/output
cp -R $this_work_dir/src/... |
2b5812fdca50fe9efc6a0bf46fc41b5e6c9e1a12a780a7d83d9abda7d11189aa | Shell | 1,114 | 43 | #!/bin/bash
# Siwei 23 Jun 2023
# Siwei 07 Jun 2022
export OMP_NUM_THREADS=16
export MKL_NUM_THREADS=16
mkdir -p results
shopt -s nullglob
sumstats_list=(/home/zhangs3/Data/Databases/GWAS/MAGMA_ref_new/ldsc_sumstats/*.sumstats.gz)
shopt -u nullglob
weights_chr="/home/zhangs3/NVME/python_projects/ldsc/weights_hm3... |
228ea96cd1de8ea9c1576c4b29c926bf13d26a493893f1dd26f26d4d6032518e | Shell | 1,115 | 33 | # runVignette03.sh - Forward simulation
# --------------------------------------------------
# This vignette demonstrates forward simulation of
# blood flow through a vascular network.
# The ESL viscosity model is used, hematocrit is
# uniform throughout the network, relative pressure boundary
# conditions are prescrib... |
0a2f48490cae5a9ef5ee74f37e006a36ce75fd2374c03b7691c9f5bb076e6284 | Shell | 1,116 | 39 | #!/bin/bash
#
# Runs the various tests.
#
# Set this to your lammps executable
LMP="mpirun -np 2 lmp"
NO_GNUPLOT=$( command -v gnuplot >/dev/null 2>&1 )
NSTEPS=100000000
if [ $# -ge 1 ]; then
NSTEPS=$1
fi
for MANIFOLD in torus sphere cylinder
do
echo "+=== Running example on "$MANIFOLD" ===+"
DATE=$(date | awk '{... |
f20c7a0bca2462fd8515e6e8bb0a4e942ed59473d3fa8c086ff3cbe041cb9321 | Shell | 1,116 | 21 | #!/bin/bash
dataset_category="TDC"
dataset_names="CYP2D6"
#declare -a split_types=("max_dissimilarity")
declare -a split_types=("scaffold" "molecular_weight" "kmeans" "max_dissimilarity" "perimeter")
declare -a filenames=("test_0.csv" "test_1.csv" "test_2.csv" "test_3.csv" "test_4.csv" "test_5.csv" "test_6.csv" "test_... |
844970ddad11bd58bec81203b3053af36a781b93730875a1c6738908f29aa0dc | Shell | 1,120 | 29 | #! /bin/bash
for mode in ood iid; do
for population in $(cat datasets/scrna-statefate/populations.txt); do
for model in identity random scgen cae; do
echo \
python ./scripts/train.py \
--outdir ./results/ood-statefate/holdout-${population}/mode-${mode}/model-${model} \
-... |
2a7aecb4ab7358b93a5754ed5107781208f7680efba3a7b755c13b3d97747e3c | Shell | 1,121 | 29 | #!/bin/bash
#SBATCH --job-name=decoding
#SBATCH --output=logs/slurm/decoding.%A.%a.out
#SBATCH --error=logs/slurm/decoding.%A.%a.err
#SBATCH --partition=shared-cpu
#SBATCH --mem=128G
#SBATCH --ntasks=1 # run one thing per job
#SBATCH --time=12:00:00
out_dir=/mnt/ibl/quarantine/prior/ephys
n_sessions=354 # number of ... |
9f9c58d0660f2223d279bfad6f455a0d8fc437263676f3a52514cf249667daa4 | Shell | 1,125 | 39 | #!/bin/bash
# clean old res
rm res_*.dat
### compute NVT Spin -> Lattice
# test standard Lammps
./../../../../src/lmp_serial -in in.spin.nvt_spin
# test spin/kk with Kokkos Lammps
# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \
# -k on -sf kk -in in.spin.nvt_spin
# extract data from Lammps run
in="$(grep... |
e9fc8bb3c7eaff1065778a5869e7e116ce7cd29f4ebea3fc36823d013108d1c8 | Shell | 1,127 | 54 | #!/bin/sh
# convert ptx assembly output into
# a c-style string constant written
# in portable posix shell script.
# requires: sed, rm, mv
#
# Author: Axel Kohlmeyer, Temple University
num_args=$#
# Check command-line arguments
if [ $num_args -gt 9 ]; then
echo "$0 can only take 9 arguments; not $num_args"
exit ... |
0f44780193f66198c707929ea7d8b3dbaef8dccda8a18da4a609f1a8ebbea059 | Shell | 1,129 | 42 | #!/bin/bash
source_folder=
genomePath="STAR_2710"
outputDir="${source_folder}/05.Star_mapped"
sourceDir="${source_folder}/04.Subsampled"
if [ ! -d $outputDir ]; then
mkdir -p $outputDir
fi
for sample in $(ls $sourceDir); do
if [ ! -d $outputDir/$sample ]; then
mkdir -p $outputDir/$sample
fi
... |
65db2f1d02b8dfac2cb20d5ff31d4e3bd853c3bea21575d2640900bf96e93edf | Shell | 1,134 | 48 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=05_deconvolution_hspe_HVG
#SBATCH -c 1
#SBATCH -t 1-00:00:00
#SBATCH -o /dev/null
#SBATCH -e /dev/null
#SBATCH --mail-type=ALL
#SBATCH --array=1-10%10
## Define loops and appropriately subset each variable for the array task ID
all_HVG=(10 20 30 40 50 ... |
b01216b3c9c5cb193a7dfa9288cfbc80df8908e2d94ed535258b1f9f81c85a12 | Shell | 1,134 | 36 | #!/usr/bin/env bash
# "Source step #1:" runs "TXImport" in order to prepare data for the next step using "R4 - Rscript (4.3.1 / 2023-06-16 / Beagle Scouts)"
# 'CLI' ARGs
COMPARISON=$1 # 'Comparison' to be done
BATCH=$2 # 'Batch' to be used
# My 'OBJs'
WD=$(pwd)
DONE="\tDone!\n"
# My 'PATHs'
# "PS:" Change the INP... |
fc4147a425ca0444a345bb478ce4165c592da8fd9a2b3b0cb8f35ba8f6c2d39d | Shell | 1,134 | 48 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=150G
#SBATCH --job-name=04_deconvolution_DWLS_HVG
#SBATCH -c 1
#SBATCH -t 1-00:00:00
#SBATCH -o /dev/null
#SBATCH -e /dev/null
#SBATCH --mail-type=ALL
#SBATCH --array=7-9%10
## Define loops and appropriately subset each variable for the array task ID
all_HVG=(10 20 30 40 50 ... |
2cf53d962465430c21d56318386c6d0078189529f1f696cd53945ce4a0758302 | Shell | 1,136 | 25 | #!/bin/bash
# 10x cellranger make reference - L variegatus genome, transcriptome and gene annotation file
# Author: Kate Castellano
# ----------------------------
#make v3.0 L variegatus genome into a 10x index
#/data/app/cellranger-6.1.2/cellranger mkref \
#--genome=Lv_genome_10xindx \
#--fasta=GCF_018143015.1_Lvar_3... |
1f59b17926c286b665e11c5e94b50efad602f748eb10295af2aa2545df5b3add | Shell | 1,137 | 48 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=10G
#SBATCH --job-name=02_deconvolution_MuSiC_HVG
#SBATCH -c 1
#SBATCH -t 1-00:00:00
#SBATCH -o /dev/null
#SBATCH -e /dev/null
#SBATCH --mail-type=ALL
#SBATCH --array=1-10%10
## Define loops and appropriately subset each variable for the array task ID
all_HVG=(10 20 30 40 50... |
572c41fb8bb050dba4401b086762b059e3fdfeca30bac27a4f3f67a69fd15f3a | Shell | 1,138 | 5 | mkdir /scratch/cqs/shengq1/references/smallrna/v3/allnonhost
cd /scratch/cqs/shengq1/references/smallrna/v3/allnonhost
cat /scratch/cqs/zhaos/vickers/reference/bacteria/group1/bowtie_index_1.1.2/bacteriaDatabaseGroup1.fa /scratch/cqs/zhaos/vickers/reference/bacteria/group2/bowtie_index_1.1.2/bacteriaDatabaseGroup2.fa /... |
91a97808b58d7c630cb9221b452633f1762a0ee79adf459040fe8868a0316aa7 | Shell | 1,138 | 34 | #!/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... |
3f0b77b30fc7edbaaa238bc26860fddb215bcaa416ec22b58de3fa89b7e93cba | Shell | 1,140 | 48 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=25G
#SBATCH --job-name=01_deconvolution_Bisque_HVG
#SBATCH -c 1
#SBATCH -t 1-00:00:00
#SBATCH -o /dev/null
#SBATCH -e /dev/null
#SBATCH --mail-type=ALL
#SBATCH --array=1-10%10
## Define loops and appropriately subset each variable for the array task ID
all_HVG=(10 20 30 40 5... |
40ddebbb59e54dc47fae18de8d28f0470c7f77bdd78617e8647245a22b94dacf | Shell | 1,142 | 28 | # Author: Somnath Tagore, Ph.D. Title: Running ARACNe using gene expression data
# Script Name: ARACNe_run.sh
# Last Updated: 01/24/2022
#Instructions
#Unzip the ARACNe.zip file and save a copy in the current directory
#Convert the gene expression data (raw counts) to tpm and save it as .rds object
#Run the followin... |
c9ae06ccb230c85d1fbd29c99ed95d69b23fdfacefc498e6861930112a213104 | Shell | 1,147 | 44 | #!/bin/bash
# Define common variables
TRANSCRIPTOME="/ALS_snRNA/refdata-gex-GRCh38-2020-A"
FASTQ_DIR="/ALS_snRNA/fastq/"
EXPECTED_CELLS=6000
# Function to run cellranger count
run_cellranger() {
local sample_id=$1
cellranger count --id="${sample_id}_snRNA" \
--transcriptome="$TRANSCR... |
b3880ef39bb79fbb4d227436bf5dfb55f8d03b70fe937d86162acdbe4eca7466 | Shell | 1,149 | 40 | #!/bin/bash
if [ -z "$ROS_DISTRO" ]; then
echo "ROS not installed. Check the installation steps: https://github.com/erlerobot/gym#installing-the-gazebo-environment"
fi
program="gazebo"
condition=$(which $program 2>/dev/null | grep -v "not found" | wc -l)
if [ $condition -eq 0 ] ; then
echo "Gazebo is not instal... |
4b9809cb945af907b126d96f1e59ede83bd0a761a97859c22c1c70c90d837fae | Shell | 1,157 | 35 | #!/bin/bash
# Auto segmentation via Freesurfer's mri_synthseg command. You need parallel Freesurfer to be installed on your pc
# According to the doc (https://surfer.nmr.mgh.harvard.edu/fswiki/SynthSeg), it is better to input/output txt file
#### Script starts here #####
export FREESURFER_HOME='/home/ludovicocoletta... |
83d50d510c8a1d881386612d5950ea458f8aae315df9e04a7b259d675814390d | Shell | 1,159 | 40 | #!/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... |
8a6ce5eef3b9a84fdab82c2650ae14bb79ed20f0334d8e3a8d8183a01e99aa6b | Shell | 1,159 | 28 | #!/bin/sh
exome_file_dir=""
#set this to the exome data field
data_file_dir=""
#set this to data directory
for i in {...}; do #Adjust to phenotype naming scheme
run_regenie_cmd="regenie \
--step 1 \
--covarFile covars_burden.csv \ #Covariate file with sex, age, age2, height, BMI and the 10 first ... |
76a5ae5ed481a9814491368cef7529e02cada7051c51e53f46129239aec0c8a5 | Shell | 1,160 | 48 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=100G
#SBATCH --job-name=06_deconvolution_BayesPrism_HVG
#SBATCH -c 1
#SBATCH -t 1-00:00:00
#SBATCH -o /dev/null
#SBATCH -e /dev/null
#SBATCH --mail-type=ALL
#SBATCH --array=1-10%10
## Define loops and appropriately subset each variable for the array task ID
all_HVG=(10 20 30... |
ad3fa063deae7755d36dbd9846c7d58f089f33fc0768aa4f5226e34c13b00ec2 | Shell | 1,170 | 33 | dirlist=$1
pwd=$(pwd)
for f in $(less $dirlist); do
cd $f
#double check missingness; require mind 0.05
for r in $(less plink.race.list); do
plink --bfile $r --mind 0.05 --geno 0.05 --out $r.mind005 --make-bed
done
#get match alleles
#remove ambiguous alleles (A/T and G/C)
awk '{if ( ! ( ($5 == "A" ... |
c828aaaa64c7f88cc3edf6fd541b619ca360fc252033f413cc1acd224f29acfc | Shell | 1,171 | 50 | #!/bin/sh
module load python3.9-anaconda
#module load Bioinformatics
#module load kallisto
while getopts ":g:a:s:o:b:x:" j; do
case "${j}" in
g)
genome_path=$OPTARG
;;
a)
gtf_path=$OPTARG
;;
s)
save_path=$OPTARG
;;
o)
output_path=$OPTARG
... |
5553f52cbc97896d0e07113768de17a0e2d2a4d884b4bbad2eca6e712c54c363 | Shell | 1,172 | 36 | #!/bin/bash
#SBATCH -p medium
#SBATCH -t 1-00:00
#SBATCH --mem=200
#SBATCH -c 1
#SBATCH --mail-type=FAIL # Type of email notification- BEGIN,END,FAIL,ALL
#SBATCH --mail-user=EMAIL_ADDRESS
##usage:
# bash run_pipeline.sh [single|pooled] SAMPLE_ID
# sbatch -o LOG_DIR/SAMPLE_ID.%j run_pipeline.sh [sin... |
03a84d0b199ca3d83929026c78fe34398460948aa74c5e176b541315bef3358a | Shell | 1,174 | 27 | source ./config.sh
source activate proteinnpt_env
export assay_index=0 #Replace with index of desired DMS assay in the ProteinGym reference file (`utils/proteingym`)
export batch_size=1
export max_positions=1024
export model_type='MSA_Transformer' # [MSA_Transformer|Tranception|ESM1v]
export model_location=$MSA_Trans... |
d27802c1327166df155ed217277a7a81e9740edc4ec15417d19c5e0e0ecf5b08 | Shell | 1,174 | 33 | set -e
SCRIPT_PATH=$(dirname $(realpath -s $0))
if [ -z "$INSTALL_PREFIX" ]; then
INSTALL_PREFIX=$(realpath -s ${SCRIPT_PATH}/../../dp)
fi
mkdir -p ${INSTALL_PREFIX}
echo "Installing LAMMPS to ${INSTALL_PREFIX}"
NPROC=$(nproc --all)
#------------------
BUILD_TMP_DIR=${SCRIPT_PATH}/../build_lammps
mkdir -p ${BUILD_T... |
8becaf54e3ed2327aa209145ef2003d37a24d05625cc7b7281d855148c040588 | Shell | 1,175 | 47 | #!/bin/bash
JUPYTER_PASSWORD="chemCPA"
# Source conda
source /home/user/conda/etc/profile.d/conda.sh
# Activate conda environment
conda activate chemCPA
# Set LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/home/user/conda/envs/chemCPA/lib:$LD_LIBRARY_PATH
# Create jupyter config directory if it doesn't exist
mkdir -p ~/.j... |
86f9cf81fb4d2920d3eb0102c760c975eb988da8cd2393c3d5910042c83dc83a | Shell | 1,176 | 30 | #!/bin/bash
## Increase the h_fsize just in case
# qrsh -l h_fsize=200G
module load bs/1.3.0
## Follow the instructions from
## https://support.illumina.com/bulletins/2017/02/options-for-downloading-run-folders-from-basespace-sequence-hub.html
## and
## https://developer.basespace.illumina.com/docs/content/document... |
752dd9b451f1c119176083b1d5ab460c0c6ab815a40ac90b38a9a63b1b55559e | Shell | 1,177 | 27 | #!/bin/bash
#SBATCH --job-name=decoding
#SBATCH --output=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/dw_bwmapr_01_1_.%a.out
#SBATCH --error=/scratch/users/bensonb/international-brain-lab/paper-brain-wide-map/brainwidemap/logs/slurm/dw_bwmapr_01_1_.%a.err
#SBATCH --partiti... |
6584211261a603523b26625eada16362202d1ee5717463ea97519da7b3715457 | Shell | 1,182 | 50 | #!/bin/bash
# This script carries out motion correction by using mcflirt.
# Here we use the mean volume as reference
#
# The main outputs of this script are the realligned ts and
# the 6 motion traces (3 rotations + 3 traslations). You will use these
# motion traces to carry out nuisance regression and for the carpe... |
5764c89bb112783c0d4492908479dd5e806148e8320b28f48dc8b0737e3c6dde | Shell | 1,187 | 30 | #!/bin/bash
if [ -z "$GAZEBO_MODEL_PATH" ]; then
bash -c 'echo "export GAZEBO_MODEL_PATH=$GAZEBO_MODEL_PATH:"`pwd`/../assets/models >> ~/.bashrc'
else
bash -c 'sed "s,GAZEBO_MODEL_PATH=[^;]*,'GAZEBO_MODEL_PATH=`pwd`/../assets/models'," -i ~/.bashrc'
fi
if [ -z "$GYM_GAZEBO_WORLD_CIRCLE" ]; then
bash -c 'echo "e... |
b535ec6dac8499eace34a45fb3594a948bd800a26cce401cce5c5387b798338f | Shell | 1,192 | 23 | #!/bin/bash
#SBATCH --partition=scavenge
#SBATCH --requeue
#SBATCH --ntasks=1 --nodes=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=6000
#SBATCH --time=2:00:00
<<COMMENT
This script creates and assigns a job to a node in the cluster with the specifications given above (currently using one node with 4 cpus and 24G... |
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