sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ad5215e12c506099618a69b8276347abeba827b0e78f82797c05d4d84560fea7 | Shell | 1,770 | 46 | #!/bin/bash
a=$1
bed_file="/notebooks/snp/liftover/ukb_c1-22_GRCh38_full_analysis_set_plus_decoy_hla_merged.bed"
bim_file="/notebooks/snp/liftover/ukb_c1-22_GRCh38_full_analysis_set_plus_decoy_hla_merged.bim"
fam_file="/notebooks/snp/liftover/ukb_c1-22_GRCh38_full_analysis_set_plus_decoy_hla_merged.fam"
snplist="/not... |
9b34a53f95c348969eaf3273e93db1e958786b6e55068f41607319ebe02e28bc | Shell | 1,772 | 77 | #!/bin/bash
# Siwei 3 Apr 2018
# Siwei 13 Sept 2018
# Siwei 12 Dec 2019
# Siwei 04 May 2021
jre_8="/home/zhangs3/Data/Tools/jre1.8.0_291/bin/java"
ref_genome="/home/zhangs3/Data/Databases/Genomes/CellRanger_10x/refdata-cellranger-arc-GRCh38-2020-A/fasta/genome.fa"
mkdir -p pre_bams
for EACHFILE_1P in *_1.fastq
d... |
7cbaa1c5ef053859c530dd9d715830a76222b457fbe4d4b98ce8e8a7faff21bf | Shell | 1,785 | 81 | #!/bin/bash
# Siwei 3 Apr 2018
# Siwei 13 Sept 2018
# Siwei 12 Dec 2019
# Siwei 04 May 2021
jre_8="/home/zhangs3/Data/Tools/jre1.8.0_291/bin/java"
mkdir -p pre_bams
for EACHFILE_1P in *_1.fq.gz
do
####init
date
rm *.bam
rm *.list
rm *.table
rm *.bai
####variables
echo $EACHFILE_1P
echo ${EACHFILE_... |
db5122cefd142ca0a56d40aa31efd1609505d494bfc7dc51c29468c9cee53f9e | Shell | 1,785 | 42 | #!/usr/bin/env bash
sampleId="${1}";
bam="${2}";
if [ ${#@} -ne 2 ] ; then
printf 'Usage: mapping_summary.sh sampleId bam_file\n' >&2;
exit 1;
fi
# Get mapping statistics from BAM file:
# - Read BAM file and write uncompressed BAM.
# - Uncompressed BAM file is written to each samtools command with tee (... |
30a2eca2245fe5caf324343b14c7305fa96f3ff941edc00c824607616bfa8a81 | Shell | 1,797 | 52 | #!/bin/bash
################################ Begin license #################################
# Copyright (C) Laboratory of Imaging technologies,
# Faculty of Electrical Engineering,
# University of Ljubljana.
#
# This file is part of PyXOpto.
#
# PyXOpto is free software: you can redistribut... |
b24fdca3224835f34e9a8d76dc5773c06fdb869c2f4f3a68009dc5ece36c57fb | Shell | 1,797 | 51 | #!/bin/bash
#SBATCH --partition=prod
#SBATCH --nodes=16
#SBATCH -C cpu
##SBATCH --ntasks-per-node=36
#SBATCH --time=24:00:00
#SBATCH --account=proj85
#SBATCH --no-requeue
#SBATCH --exclusive
#SBATCH --mem=0
# SPDX-License-Identifier: Apache-2.0
source ../../environments/atlasEnv/bin/activate # Needs to be set by the ... |
1d8e690de5c07c6caf86ba574c13462d099cdba0ff7189bd86d20390901be5f1 | Shell | 1,802 | 55 | function register_to_mni {
ts=$1
study_folder=$2
subject_epi=$(basename $ts _mcf_mean_reg.nii.gz)
sub_folder_epi=$(dirname $ts)
reg_t1_mni_matrix=$(echo ${sub_folder_epi}/../anat/*to_MNI.mat)
subject_t1=$(basename $reg_t1_mni_matrix _to_MNI.mat)
sub_folder_t1=$(dirname $reg_t1_mni... |
e7f31f1896b287ed3e30ac7ebeb545e3129246376430073380794501343e8f4e | Shell | 1,805 | 19 | #!/bin/bash
#
#SBATCH --job-name=SRReg0s
#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-per... |
47b352991f05e5d1d495c1e21c4ebf17eafa57442a1dec9b317e83209016f560 | Shell | 1,811 | 64 | #!/bin/bash
# Siwei 3 Apr 2018
# Siwei 13 Sept 2018
# Siwei 12 Dec 2019
# Siwei 04 May 2021
jre_8="/home/zhangs3/Data/Tools/jre1.8.0_291/bin/java"
# check if output directory exists
if [ ! -d "pre_bams" ]; then
mkdir pre_bams
fi
for EACHFILE_1P in *_R1_001.fastq.gz
do
####init
date
rm *.bam
rm *.list
... |
2af860b18e6a5cf6e00bdace3201b2fc102105a2def9bb507ca087b144db38ab | Shell | 1,813 | 17 | #!/usr/bin/env bash
echo 'iCLIP coverage for bleedthrough exon starts, SH-SY5Y expressed background'
Rscript scripts/cl_iclip_coverage.R -r processed/iclip_regions/2023-12-14_papa_cryptic_bleedthrough_uniq.background_shsy5y.le_start.bed -i data/iCLIP/tardbp-shsy5y.concat.sort.chr.bed -c data/GRCh38.primary_assembly.g... |
3308e682a677a25bec3a8f36d5ad8ee7235186df93957532d6dd948c1bfd04ec | Shell | 1,813 | 19 | #!/bin/bash
#
#SBATCH --job-name=SRReg1S
#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-per... |
7bca8f3f2020802044b103c3cd3ed99bca76077cd0a45d7e2b08d06a7b90e968 | Shell | 1,818 | 17 | #!/usr/bin/env bash
echo 'iCLIP coverage for 3pUTR proximal PAS, SH-SY5Y expressed background'
Rscript scripts/cl_iclip_coverage.R -r processed/iclip_regions/2023-12-15_papa_cryptic_d3utr.background_shsy5y.pas.proximal.bed -i data/iCLIP/tardbp-shsy5y.concat.sort.chr.bed -c data/GRCh38.primary_assembly.genome.chromsiz... |
ef7e555272774ed44aea810718b9d2f46bcc4ec5173c50f5370eceda83f7064c | Shell | 1,818 | 19 | #!/bin/bash
#
#SBATCH --job-name=SRReg05S
#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-pe... |
e2301bae00a01e6b597a6d66fc640c7280db3392d416daa082edbd2dbcdc7f4b | Shell | 1,827 | 19 | #!/bin/bash
#
#SBATCH --job-name=SRReg025S
#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-p... |
f3a52ee58e02ed97390eb5be5c191ff2493b7c9a8cd1f19e1bd953bdc1a50e33 | Shell | 1,832 | 48 | #!/bin/bash -l
#$ -P vkolagrp
#$ -t 1-4
#$ -pe omp 16
#$ -l gpus=1
#$ -l gpu_c=6
#$ -l gpu_memory=32G
#$ -N ppmi_fastsurfer_patch
#$ -j y
#$ -m bes
#$ -l h_rt=12:00:00
module load miniconda
conda activate mri_radiology
export PYTHONPATH="/usr4/ugrad/spuduch/RadiologistRatings/:$PYTHONPATH"
# Calculate the starting an... |
88c18e3f897be62713b8e30f5ebc0881a871b66ae8a7398c587225fb09aaec40 | Shell | 1,835 | 51 | #!/bin/sh
# ============================================================
# 04_subsample_and_merge_pulvinar_tractograms.sh
# ============================================================
# Description:
# This script processes structural connectivity data from the HCP dataset.
# For each subject, it subsamples 1000 st... |
ca8cc8060c40be8cee5c3a0683d54919e33d4292fd873f69a0820a57a516c14f | Shell | 1,835 | 34 | #!/bin/bash -l
set -e
# stops Dask workers from spilling to disk
# see https://docs.dask.org/en/latest/setup/hpc.html#local-storage
export DASK_DISTRIBUTED__WORKER__MEMORY__TARGET=False # don't spill to disk
export DASK_DISTRIBUTED__WORKER__MEMORY__SPILL=False # don't spill to disk
export DASK_DISTRIBUTED__WORKER__M... |
798d91f88f62dae35058a8cdfa10a8d3fda0fbbea8ad17a994aab05d16f77065 | Shell | 1,836 | 19 | #!/bin/bash
#
#SBATCH --job-name=SRReg0125S
#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-... |
708c2ce5aa0be6955f3f49233a663b2a49965cf659550d31898c6097b7abaa6b | Shell | 1,843 | 33 | #!/bin/bash
#
# Usage: datalad_get_sample.sh {path for data}
# Requires Datalad installation:
# For local install (with sudo ability for git-annex installer):
# pip install datalad-installer && datalad-installer git-annex -m datalad/packages && pip install datalad
# -or-
# Using d... |
9a2c862fe9354b4304298dd89d8897795abec4f2883d29a18f70a051d82c7a30 | Shell | 1,844 | 41 | #!/bin/sh
exome_file_dir=""
#set this to the exome data field
data_file_dir=""
#set this to data directory
burden_file_dir="/Data/burden"
#set this to output directory
for pheno in {...}; do #Adjust to phenotype naming scheme
for i in {1..22}; do
run_regenie_cmd="regenie \
--step 2 \
... |
3cfb902e7a1d5760cfaa79f5cb5a5af6b8a7947ba93f02f40efc57e36f28d042 | Shell | 1,845 | 65 | #!/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") || $@ == "-h" ]]; then
echo "Usage: source submit.sh CONFIG_PATH (BIND_PATH) (RUN_NAME)"
ech... |
f2b9a6c7139fe3cd86fa7ddfb214e59f2a991f0f2620cbdbe63566e1b3149d95 | Shell | 1,846 | 77 | #!/bin/bash
cores=24
mem=100
new_sample_dir=
transcriptome_rna_cr_ref=
atac_cr_ref=
# non treated scRNA seq
sname="105_2g_DMSO"
cellranger count --id=${sname} \
--transcriptome=${transcriptome_rna_cr_ref} \
--fastqs=${new_sample_dir} \
--sample=${sname} \
--localcores=$cores \
--localmem=$mem \
... |
e2ca36740b8ad192e793390d0e7a1f4abc3357889e4f682ac1ccf77a39185391 | Shell | 1,856 | 88 | #!/bin/bash
##
## exome/targeted sequencing somatic copy number variant calling
##
# specify maximum runtime for sbatch job
# SBATCHTIME=24:00:00
# script filename
script_path="${BASH_SOURCE[0]}"
script_name=$(basename "$script_path")
route_name=${script_name/%.sh/}
echo -e "\n ========== ROUTE: $route_name ======... |
f82fb5fa9e742474a3ceebeca942a4b5e0c97233b81d8c1e11e13dab56775184 | Shell | 1,861 | 53 | #!/bin/bash
# This script runs a bash function on a large number of subjects (executing the HCP Preprocessing Pipelines) using the supercomputer queuing system
# Directory containing scripts to run
scriptsDir="/projects/f_mc1689_1/ReliableFC/docs/scripts/diffusion"
# Where batch scripts for each subject are written
... |
328ce416e6ad1e5998de38fd9d7b1d45145a05f92dea61108646ed7b92732471 | Shell | 1,864 | 75 | #! /bin/bash
set -xe
if [[ -z "${TMPDIR}" ]]; then
TMPDIR=/tmp
fi
set -u
if [ "$#" -lt "1" ] ; then
echo "Please provide an installation path such as /opt/ICGC"
exit 1
fi
# get path to this script
SCRIPT_PATH=`dirname $0`;
SCRIPT_PATH=`(cd $SCRIPT_PATH && pwd)`
# get the location to install to
INST_PATH=$1
... |
31c3cb8270577290d36d5366d7512bb6942a3af8f27909287f80656cb3835f49 | Shell | 1,867 | 51 | #!/bin/sh
#Siwei 14 Feb 2018
date > 23Jun2020_genotyping.txt
echo "All genomic coordinates are based on GRCh38p7." >> 23Jun2020_genotyping.txt
for EACHFILE in *WASPed.bam
do
#samtools index -@ 24 $EACHFILE
#samtools index -@ 24 $EACHFILE
echo $EACHFILE
#samtools index -@ 24 $EACHFILE
echo -n $EACHFILE >> 23... |
dfe711acf5a2b69a80ae944b5db427ee75b7dd68bd3e4ed59cccdb852ac427c2 | Shell | 1,869 | 55 | #!/bin/bash
# This script performs nuisance regression and bandpass filtering as implemented by AFI's 3dTproject (i.e simultaneous regression and bp).
# Volumes flagged for high motion are interpolated before the regression
# time series are normalized to have sum of squares = 1
# -------------------------------------... |
286558968c11ea749f202481404d8bff31f0c9d8283e6702656899cd69a1bc46 | Shell | 1,884 | 56 | #!/bin/bash -ef
set -eo pipefail
WANT_PYTHON_VERSION="$1"
if [[ "$WANT_PYTHON_VERSION" == *'t' ]]; then
WANT_FREETHREADED=true
else
WANT_FREETHREADED=false
fi
WANT_PYTHON_VERSION=$(echo "$WANT_PYTHON_VERSION" | sed 's/t$//g')
if [[ -z "$WANT_PYTHON_VERSION" ]]; then
echo "::error::Missing required argument: want P... |
ab1262e9cf5f5a42a19786ed51afd0c2b8c26a954215d5375f52300110a97b7c | Shell | 1,884 | 63 | #!/bin/bash
set -e -u
# Build the install package for Linux.
# This script must be run from the root of the repository after running build_installer_linux.sh
PACKAGE_NAME=alphadia
# BUILD_NAME is taken from environment variables, e.g. 'alphadia-1.2.1-linux-x64'
rm -rf ${BUILD_NAME}.deb
BIN_PATH=dist_pyinstaller/${B... |
9526cf18c35af0432d46c92380414801dffb596c2e6fb3d4643e52c107e848e7 | Shell | 1,889 | 55 | ## Author : Gabriel Gattaux
#!/bin/bash
# This will cause bash to stop executing the script if there's an error
set -e
# Define the parameters
irl_path="../data/raw/images_offline/images_100523_AVM_line_mapping/Expl4"
it_path="../data/raw/images_offline/images_100523_AVM_line_mapping/all"
param_values="10000,4,5,0.01... |
f8ab8176ef031d938b97c340810bcfe3243af9dd24cc87516c5aa0b7f52f1e73 | Shell | 1,890 | 72 | #!/bin/bash
##activate conda if required
#source /home/arh49/miniconda3/etc/profile.d/conda.sh
#source /usr/bin/Rscript
##usage: ./run_wf_alignment.sh arg1 arg2
##args as listed below
##need to implememtn check to get enofgh args. NBt do that later.
##the thrid arg is in case things have been run in 2 batches. So f... |
c10d8f91c4bdb73e73026975b8a5c28099e188884380dadf8bc765c622823806 | Shell | 1,895 | 93 | #!/bin/bash
##
## get or set (if not set) specified setting for a specified setting
##
# script filename
script_name=$(basename "${BASH_SOURCE[0]}")
# check for correct number of arguments
if [ $# -lt 2 ] ; then
echo -e "\n $script_name ERROR: WRONG NUMBER OF ARGUMENTS SUPPLIED \n" >&2
echo -e "\n USAGE: $script... |
c21b301d1ae2502e4d7dc4b0546c11ff6bc8399f5157c97e58d39f71d69b2ca6 | Shell | 1,915 | 17 | 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 ... |
252618ac7daed2d8aefe14a9e69a4db73dccbd581cc035bdcbe177f4b3e43192 | Shell | 1,923 | 59 | #!/bin/bash
module load plink2
GCTA="./gcta_nr_robust"
PLINK="plink --allow-no-sex"
GEMMA="./gemma"
FUSION="./FUSION/"
PRE="Adipose_Subcutaneous"
PRE="Prostate"
PRE="Whole_Blood"
NR=10
PRE=$1
NR=${SLURM_ARRAY_TASK_ID}
### Input files needed:
# "$PRE.v7.normalized_expression.bed.gz.HEADER" is generated by `cat [bed.... |
a9a13198b4bb9f51b2a5f880e2da3fba66ee65a097c8e037a2ecb9c28e92cdaf | Shell | 1,927 | 48 | #!/usr/bin/env bash
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License... |
a60a6f951ab649d25dc4a21421451d53cea1185728a5dc51ccc87977799e4f3f | Shell | 1,930 | 55 | #!/usr/bin/env bash
set -e
# Get the directory where the current script is located
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
# Source the common setup file
source "$SCRIPT_DIR/common_setup.sh"
test_module3() {
common_init
local model="model"
echo "Model: $model"
# Setup resa... |
13319dbd9dd366c060fc33da3b1ccd789c67356b1f0c0c1eca7c3f11ab62b39d | Shell | 1,935 | 85 | #!/bin/bash
##
## RNA-seq using RSEM aligner
##
# script filename
script_name=$(basename "${BASH_SOURCE[0]}")
route_name=${script_name/%.sh/}
echo -e "\n ========== ROUTE: $route_name ========== \n" >&2
# check for correct number of arguments
if [ ! $# == 2 ] ; then
echo -e "\n $script_name ERROR: WRONG NUMBER OF... |
e72acb200e14b9db37ab26f1b5696ba1dc3b78cdc2389fa3e6b65b90b0414c3f | Shell | 1,935 | 69 | #!/bin/bash
#SBATCH -p shared
#SBATCH --mem=50G
#SBATCH --job-name=07_deconvolution_CIBERSORTx_HVG
#SBATCH -c 1
#SBATCH -t 1-00:00:00
#SBATCH -o /dev/null
#SBATCH -e /dev/null
#SBATCH --mail-type=ALL
#SBATCH --array=1,4-9%10
## Define loops and appropriately subset each variable for the array task ID
all_HVG=(10 20 30... |
63d2639edbb6b5a4075eabac200bcd1265146c3ba6a2b1a3fa370ad98e5e6cc9 | Shell | 1,937 | 60 | #!/bin/bash
# Siwei 23 Mar 2021
# convert STAR ReadsPerGene.out to table format
# use inter_df.txt to store the intermediate df
# use current_col.txt to store the current column
# note paste use \t as the default delimiter
# use file_names.txt to store all file names, remove the ReadsPerGene.out.tab part
# init
rm ou... |
a30915eb7e980e215fffa82e4ceeaab59db1dae5118719eab9d8fd580ab22788 | Shell | 1,937 | 56 | #!/usr/bin/env bash
echo "Set git email and name"
git config --global user.email "bot@statsmodels.org"
git config --global user.name "Statsmodels Doc Bot"
echo "Git pull for any commits since docbuild started"
pushd statsmodels.github.io
git remote -v
git pull origin master
popd
echo "Remove devel"
rm -rf statsmodels... |
c9f18ca82abe1382a981da5bce373f2f02663887b4e84af0d2851e652226805c | Shell | 1,939 | 45 | #!/bin/bash
projectFolder=
sourceFolder=${projectFolder}/02.Renamed
outputFolder=${projectFolder}/03.LanesMerged
for sampleName in $(ls ${sourceFolder}); do
if [ ! -d ${sourceFolder}/${sampleName} ]; then
continue
fi
if [ ! -d ${outputFolder}/${sampleName} ]; then
mkdir -p ${outputFolder}... |
55aa86801ea605e90d3c98fbf6a6bd248c5b0994706c3da547f0710fe62fe765 | Shell | 1,940 | 62 | #!/usr/bin/env bash
if [[ ${USE_CONDA} == "true" ]]; then
conda config --add channels defaults
conda tos accept
conda config --set always_yes true
conda update --all --quiet
conda tos accept
conda create -n statsmodels-test python=${PYTHON_VERSION} -y
conda init
echo ${PATH}
source activate statsmode... |
923c38e762e187bc59f5e547a0bf6276cc65a207f9e4e5fd6373b32cbcc3a259 | Shell | 1,941 | 64 | #!/bin/bash
# Validates the derived concepts built in a BigQuery dataset by checking:
# 1. every concept SQL file has a corresponding table in the dataset
# 2. no concept table is empty
#
# Usage: validate_concepts.sh [dataset]
# dataset defaults to mimiciv_derived
set -euo pipefail
PROJECT_ID=${PROJECT_ID:-phys... |
9a65938211708493fdf3dcd70d775e76db6a2bee4706464a2f38cf710fcd13a6 | Shell | 1,942 | 90 | #!/bin/bash
seed=0
dseed=1
N=10000
# Ensure directory for priors exists
if [ ! -d ./ABC_prior_samples/ ]
then
mkdir ./ABC_prior_samples
fi
# First, sample parameters from the prior distribution
paramFile='./ABC_prior_samples/prior_'"$seed"'.dat'
PRIOR_GENERATOR_SCRIPT=$PWD'/ABC_generate_prior_samples.py'
if [ ... |
f2b8e25274137af3f7ad8591d4d470dde410c0d57b06b5fefb073a2093e11aa5 | Shell | 1,942 | 40 | #!/bin/bash
set -euo pipefail
tmpdir=$(mktemp -d)
#for file in /data/chamal/projects/steele/working/AllenBrain_coords/*_LPS_x-z-y.csv; do
#H0351.2003 H372.0006 don't have data!
#XYZ must be in LPS coordinates
for subject in H0351.1009 H0351.1012 H0351.1015 H0351.2001 H0351.2002; do
file=AllenBrain_coords/${sub... |
17d1a36e76949c8b821c16c39f42501c8c671c98bfb3e59b3812329e50724ff3 | Shell | 1,951 | 64 | #!/usr/bin/env bash
# conda needs to be installed for us to proceed
if ! command -v conda &> /dev/null;
then
echo "Conda not found. Install miniconda to continue."
exit 1
fi
conda config --set always_yes yes
# make sure we are in the base environment
if [ "$CONDA_DEFAULT_ENV" != "base" ];
then
conda deactivate... |
bba91e8a71cef1c9c576acaf3617ec2a0a07daee4fa05a127183cb31abe9be39 | Shell | 1,954 | 22 | source config.sh # To get the paths to $proteinnpt_data_path and $proteinnpt_repo_path
# Environment setup - Conda
conda env create -f $proteinnpt_repo_path/proteinnpt_env.yml
conda activate proteinnpt_env
# Environment setup - Python venv (Optional: if you prefer python venv over conda)
# python -m venv $proteinnpt... |
952c7e4b8c19f3ce202a5be45c242f4265e1665467fd90eff7b2527a3d02529d | Shell | 1,955 | 39 | set -e
SCRIPT_PATH=$(dirname "$(realpath -s "$0")")
MANYLINUX_CUDA_IMAGE=${MANYLINUX_CUDA_IMAGE:-quay.io/manylinux_cuda/manylinux_2_28_x86_64_cuda12_9:latest}
PYTHON_BIN=${PYTHON_BIN:-/opt/python/cp311-cp311/bin/python}
PYTORCH_DEPENDENCY_GROUP=${PYTORCH_DEPENDENCY_GROUP:-pin_pytorch_cpu}
PYTORCH_TORCH_BACKEND=${PYTOR... |
65441bb23a1af2a14119f715733d1af4ad4c0cec6912b7a6df1f829200e015b3 | Shell | 1,958 | 55 | #!/bin/bash
################################ Begin license #################################
# Copyright (C) Laboratory of Imaging technologies,
# Faculty of Electrical Engineering,
# University of Ljubljana.
#
# This file is part of PyXOpto.
#
# PyXOpto is free software: you can redistribut... |
98695c0cce22ee20c4b85814cddef9d5b42728ad9d09ba34f6a03a99c6c5b415 | Shell | 1,958 | 49 | #!/bin/bash
for pretrained in True False
do
for model in r2plus1d_18 r3d_18 mc3_18
do
for frames in 96 64 32 16 8 4 1
do
batch=$((256 / frames))
batch=$(( batch > 16 ? 16 : batch ))
cmd="import echonet; echonet.utils.video.run(modelname=\"${model}\", frames=... |
34fa641a09b8f8d1bdf8fcb792942f57f1d08431df8f2077d2d58c81b6598cb3 | Shell | 1,967 | 33 | #!/bin/bash
# registration has been done in fMRIPrep > following Mumford's workaround:
# https://mumfordbrainstats.tumblr.com/post/166054797696/feat-registration-workaround
subs=( "" )
dir_out="/home/emba/Documents/EMBA/VMM_analysis/01_FSL"
for sub in "${subs[@]}"
do
:
rm "$dir_out/sub-$sub/sub-${sub}_HG... |
78ac966865438db0bd4088c426fb23380d5fc07ba8885253928407da7571bf4e | Shell | 1,972 | 66 | #!/bin/bash
# parse command-line arguments
if [ $# -ne 3 ]; then
echo Usage: $(basename "$0") fusions.tsv annotation.gtf output.tsv
echo
echo "Description: For each breakpoint, this script annotates the exon numbers in reference to the transcripts given in the columns 'transcript_id1' and 'transcript_id2'. It appen... |
443733f54a91276d6a9fa016786c22145c4b3bd6da307871835656d656d5e7c9 | Shell | 1,975 | 60 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=4G,h_vmem=4G,h_fsize=100G
#$ -N compute_weights_full_NAc_genes
#$ -o logs/NAc_genes/compute_weights_indv_full_NAc_genes.$TASK_ID.txt
#$ -e logs/NAc_genes/compute_weights_indv_full_NAc_genes.$TASK_ID.txt
#$ -t 1-56888
#$ -tc 40
#$ -m a
## Notes on the -t parameter
# > load("NA... |
d2685fbadbb0e3e508851b8fd44278f08141a6d981b3e5f098f4e52672708b3b | Shell | 1,977 | 61 | #!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=2G,h_vmem=2G,h_fsize=400G
#$ -N update_permissions_human_dlpfc_deconvolution
#$ -o logs/update_permissions.txt
#$ -e logs/update_permissions.txt
#$ -m e
#$ -hold_jid move_bulk_round1
echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job ... |
f406ebecfedf8e956fa3a55f5c342bb8dfa0bca45813e9fb9fca6bd67bbddd73 | Shell | 1,979 | 32 | #!/bin/bash
# 10x cellranger count - align sequences to transcriptome and generates a .cloupe file for visualization
# Author: Kate Castellano
# ----------------------------
##align all samples to genome (ref made with gene_name attribute added and filtered gtf)
#data for each FBS condition separately
/data/app/cellr... |
34b1b92814906d8e02a28ab905b1ad32e4f5c1b0becf11a59d38aa7ae8be5e1f | Shell | 1,984 | 43 | #!/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 [ $hem... |
7f78f8af5fdd183300fa7a8abfd60ee65f14b1ca12671a18192665fd515538a2 | Shell | 1,984 | 43 | #!/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 [ $hemi... |
1b043aad686c96524909741300f1a684d23d04256ae162f2fcf9527ee5b3baf8 | Shell | 1,988 | 67 | #!/bin/bash
# install.sh - ALineMol Installation Script
# Usage: ./install.sh [cpu|cu118|cu121|cu124]
set -e
# Default to CPU
DEVICE="${1:-cpu}"
PYTHON_VERSION="${PYTHON_VERSION:-3.11}"
# PyTorch wheel URLs
case "$DEVICE" in
cpu)
PYTORCH_INDEX="https://download.pytorch.org/whl/cpu"
echo "Installi... |
59b252de8aa5cb8574dcab1dcf91deebac577a24f83972de4d67e339ab26930a | Shell | 1,989 | 39 | source ./config.sh
source activate proteinnpt_env
#########################################################################
###############################Tranception###############################
#########################################################################
export checkpoint=$Tranception_location
export... |
ccf4b0d0f03f613aa2dbdae96c354ced6ce8ce475fffde416ed2393f4aefcb89 | Shell | 1,989 | 43 | #!/usr/bin/env bash
# Helper to run a command, capture its output, and build a context-rich log.
set -euo pipefail
if [ "$#" -lt 4 ]; then
echo "Usage: run_with_context.sh <log-path> <step-label> <script-path> <command...>" >&2
exit 2
fi
LOG_PATH="$1"
shift
STEP_LABEL="$1"
shift
SCRIPT_PATH="$1"
shift
WORKFLOW_P... |
e38714f7251bc35d0e59b5b66bb8a27661580e5eda182c69594a73cae95fcc52 | Shell | 1,995 | 89 | #!/bin/bash
# run second level for each subject
# first, load in the subIDs that should be processed from a space separated file
subs=()
while IFS=$' ' read -r -a line
do
subs+=("${line}")
done < "all_use-new"
nos="${#subs[@]}"
# set our directories
dir_out="/home/emba/Documents/EMBA/VMM_analysis/01_FSL"
log_f... |
895436fcaeb23959cedaa3769cc528a23eebca07550541a9642f0c902bfdfb6d | Shell | 2,000 | 70 |
cd ~/Projects/Neuromuscular_Signature_R01_Pilot/data/BIDS/derivatives/trialwise_analysis/
for scan in FingerTap ForceAbs ForcePercent; do
for sub in {06..48} ; do
if [ -d sub-NSPilot0${sub}_brain_${scan} ] ;
then
echo "working on subject sub-NSPilot0"${sub} ${scan}
for ses in 01 02; do
if [ -d sub-NSPilot0${... |
790c6d5d4ed0b11cca2033e8971e90289f54e98e0c1ceb213d90865e3fcb7721 | Shell | 2,003 | 52 | #!/bin/bash
cwd="/user_data/weifanw/familiarity_plot" # project directory
# =====================================================================================================
# set all parameter the same as the those used in the simulation
postfix="mix50%_all"
tau_train=150
gamma=30
tau_test_1=1000
si_1=50
tau_tes... |
0c3ae3908bc582419110fd9eaca70c1c74c70623b340048169394e21285c83be | Shell | 2,004 | 65 | #!/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... |
c2ffd1494f6a72d0a4c35c8ea1deb0e4ecddb537993f9e0359efc5b1dceabdbc | Shell | 2,008 | 78 | # BBBP
python train.py \
--data_path ./data/bbbp.csv \
--exp_id bbbp \
--dataset_type classification \
--epochs 10 \
--num_runs 3 \
--gpu 5 \
--batch_size 16 \
--seed 2024 \
--init_lr 1e-5 \
--final_lr 5e-6 \
--wd 5e-5 \
--warmup_epochs 0.0 \
--split_type 'scaffold_... |
c728a3d7053647e3eeeeb4249816142e69cbae3c5a6f30f014618992fc1a36d7 | Shell | 2,010 | 68 | #!/bin/bash
if [ -z ${MIMIC_PASSWORD+x} ]; then
echo "MIMIC_PASSWORD is unset";
exit 1
else
echo "MIMIC_PASSWORD is set";
fi
if [ -z ${MIMIC_DB+x} ]; then
MIMIC_DB=mimic
echo "MIMIC_DB is unset, using default '$MIMIC_DB'";
else
echo "MIMIC_DB is set to '$MIMIC_DB'";
fi
if [ -z ${MIMIC_USER+x} ]; then
MI... |
112101efd38b72f971c93d2600e5757b1d42f821a7a7166df75e4b7c0abf5afd | Shell | 2,021 | 70 | #!/bin/bash
# Siwei 3 Dec 2019
for EACHFILE in *.narrowPeak
do
echo $EACHFILE
out=output/${EACHFILE/%_all_peaks.narrowPeak/_max.bed}
tmpd=/tmp/tmp$$
mkdir -p $tmpd
cat $EACHFILE | cut -f 1-6 > $tmpd/tmp.bed
## The master list is constructed iteratively. For each pass through
## the loop, elements not yet ... |
362025e135c6110b8b4ceb5c029f0f9b481dd0cde6663851559ec036dc1166af | Shell | 2,021 | 55 | #!/bin/bash
#-----------------------------------------------
# Filter: read merging
#-----------------------------------------------
# Filter out variants that are not verified in unmerged bam (pile up of unmerged bam at variant candidate sites)
# Uncomment the line below for cluster computing, otherwise make sure yo... |
2c09ce42bd0dd642555d6e62960471ca3ff97e0b0f114cfb4e21ceb30d5e2166 | Shell | 2,027 | 57 | # Download GRNs and other data to reproduce analysis as shown in paper
mkdir -p data/
mkdir -p tables/ # for outputs
mkdir -p data/GNN_labels
mkdir -p data/gtrddb
# links to drugbank files are not provided here.
# Please acquire a licence by writing to them.
# Two files required in the data/ to reproduce the analysis... |
552cfd4ca01af20b92329fa4261d9ec07e0484ad75057b01d0a4447a41905c86 | Shell | 2,049 | 78 | #!/bin/bash
##########LICENCE##########
# Copyright (c) 2014-2020 Genome Research Ltd.
#
# Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
#
# This file is part of alleleCount.
#
# alleleCount is free software: you can redistribute it and/or modify it under
# the terms of the GNU Affero General Public License as publish... |
ebaedd622a30c0b55c9a783435251e96831f4f3882082c5f499a2b142ff3a3f0 | Shell | 2,081 | 71 | #!/bin/bash
set -e -u
# Build the install package for MacOS.
# This script must be run from the root of the repository after running build_installer_macos.sh and build_gui_macos.sh
# Set up package name and version
PACKAGE_NAME="alphadia"
APP_NAME="alphadia"
PACKAGE_VERSION="2.1.5-dev0"
PKG_FOLDER="dist/$APP_NAME.app... |
0ad56c490b02c6eee9feaac4234706a5b444acf2a39315275a7ca0831e97023e | Shell | 2,085 | 52 | # Parameters
INPUT_DIR="${HOME}/illumina_quick_demo"
OUTPUT_DIR="${INPUT_DIR}/output"
mkdir -p ${INPUT_DIR}
mkdir -p ${OUTPUT_DIR}
# Download quick demo data
# GRCh38 reference
wget -P ${INPUT_DIR} -nc http://www.bio8.cs.hku.hk/clairs/quick_demo/ilmn/GRCh38_chr17.fa
wget -P ${INPUT_DIR} -nc http://www.bio8.cs.hku.hk/... |
3f0b516f7e5f1aec2dac4b3c5dcc4baf16e950809052225f40884ef921a18319 | Shell | 2,089 | 79 | #!/bin/bash
# Siwei 3 Jan 2019
beds=(CN_max.bed
DN_max.bed
GA_max.bed
ips_max.bed
NSC_max.bed)
out=Xin_original_peaks.bed
tmpd=/tmp/tmp$$
mkdir -p $tmpd
## First, union all the peaks together into a single file.
bedlist=""
for bed in ${beds[*]}
do
bedlist="$bedlist $bed"
done
bedops -u $bedlist > $tm... |
cc76f60dca69e9a6310e2ba97fc4403598ab66741f6d577e754096cbcb3d4d7b | Shell | 2,090 | 49 | ##Reference:
#https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorials
#Expression matrix (Cellranger)
path1 = "~/Bos_taurus_ARS_UCD1.2.gtf" #change to your genome annotation file
path2 = "~/Bos_taurus_ARS_UCD1.2.filtered.gtf" #change to your corresponding name
path3 = ... |
88e113a119c6a01923d828a5c83933ee61e3231fe42875f5285bd99ee2317909 | Shell | 2,091 | 55 | #!/bin/bash
# For more information about this demo workflow, visit: https://arriba.readthedocs.io/en/latest/workflow/
if [ $# -lt 8 -o $# -gt 9 ]; then
echo "Usage: $(basename $0) STAR_genomeDir/ annotation.gtf assembly.fa blacklist.tsv known_fusions.tsv protein_domains.gff3 threads read1.fastq.gz [read2.fastq.gz]" ... |
f116e3b254f37f1ec8ecb01ddcbea287e4d2966112eb561cafceec7a9d96342d | Shell | 2,096 | 67 | #!/bin/bash
echo " - Setting up conda"
eval "$(conda 'shell.bash' 'hook' 2> /dev/null)"
conda activate base
# Workaround cuda path prepended to conda on gcp instances
unset LD_LIBRARY_PATH
export PATH="$(dirname $(which python)):${PATH}"
ENV_NAME=$(grep "name:" environment.yml | cut -d: -f2)
LOCATION=${1:-""}
if (c... |
5d91a1ac4ec26aa2d3940de9c3fd4a511a3cb2f0ba125555ebe5aac13b980155 | Shell | 2,102 | 50 | #!/bin/bash
## ORIGINAL RESULTS
# set our directories
cd ..
dir_ostt="results_ostt"
dir_out="results_sig"
if [ ! -d "$dir_out" ]; then
mkdir -p "$dir_out";
fi
codes=( "hgf_all_eps_c_ROI" "hgf_all_mu_c_ROI" "hgf_all_mu_e_ROI" "hgf_ctr_eps_c_ROI" "hgf_ctr_mu_c_ROI" "hgf_ctr_mu_e_ROI" )
con="fstat1"
for code in "${c... |
c4f156a02349cd5a0254d664c7053f0cd0e886ec5a7152350f31828893babf7e | Shell | 2,105 | 51 | # Parameters
INPUT_DIR="${HOME}/ont_quick_demo"
OUTPUT_DIR="${INPUT_DIR}/output"
mkdir -p ${INPUT_DIR}
mkdir -p ${OUTPUT_DIR}
# Download quick demo data
# GRCh38_no_alt reference
wget -P ${INPUT_DIR} -nc http://www.bio8.cs.hku.hk/clairs/quick_demo/ont/GRCh38_no_alt_chr17.fa
wget -P ${INPUT_DIR} -nc http://www.bio8.cs... |
8f6ff8b6a0181d8d5fac6f26f1709ee366a1f06dc8dce51b8987c8a66439f6f8 | Shell | 2,107 | 55 | #!/bin/bash
# RNA-seq processing pipeline (multi-sample, robust, reproducible)
# -------- USER CONFIG --------
HISAT2_INDEX="/path/to/hisat2_index/genome"
ANNOTATION_GTF="/path/to/annotation.gtf"
THREADS=8
RAW_DIR="raw_fastq"
OUT_DIR="analysis_output"
TRIM_DIR="${OUT_DIR}/trimmed"
ALIGN_DIR="${OUT_DIR}/aligned"
STRIN... |
e584c9413581bfb2d13de84d02dbd51e505dbd1104e2be34a040d1a8858fb517 | Shell | 2,111 | 75 | #!/bin/bash
set -e
cp /staging/bcjohnson7/eve.tar.gz ./
ENVNAME=eve
# if you need the environment directory to be named something other than the environment name, change this line
ENVDIR=$ENVNAME
# these lines handle setting up the environment; you shouldn't have to modify them
export PATH
mkdir $ENVDIR
echo "un ta... |
ba77e701d37f13a4ef9942b8646be93e957880d89c2b568d3097896d2b10c9c9 | Shell | 2,112 | 78 | #!/usr/bin/env bash
# bf.sh: the script that actually launches a command line tool
BF_DIR=`dirname "$0"`
# Include the master configuration file.
source "$BF_DIR/config.sh"
# Check that a command to run was specified.
if [ -z "$BF_PROG" ]
then
echo The command to launch must be set in the BF_PROG environment vari... |
3dd300484dda6ea11057ebad753bd007345fbf0ade5a0bd7d0e54a23d67838a9 | Shell | 2,119 | 72 | #!/bin/bash
input="Dockerfile"
if test -f "$input"; then
echo "$input exist"
else
echo "$input not found..."
exit 1
fi
bsdocker_registry=""
image=""
version=""
project=""
default_registry="" # eg 'registry.hzdr.de/kaapana'
default_project="" # eg '/kaapana'
while IFS= read -r line;
do
if [[ $line == *"L... |
346a33b41768b50d58318efc34dfbc78754f4d4c584f582bbe9f1de90180db50 | Shell | 2,124 | 64 | #!/bin/bash
#SBATCH --job-name=j_anat_preproc
#SBATCH --partition=short
#SBATCH --time=48:00:00
#SBATCH -n 1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=4G
#SBATCH --output=logs/%x.%A-%a.out
#SBATCH --error=logs/%x.%A-%a.err
#############################################
freesurfer_version="X.X.X"
export FREESURFE... |
dadf71d7db81635b43a6ea45f04861bff3e4e6a0b28d97b7ee3c325fce5caf85 | Shell | 2,124 | 51 | #!/bin/bash
set -ev
# 01. Set up environment
exec_dir=$( pwd )
cd "${exec_dir}"
prpr_dir="${exec_dir}/scripts"
# 02. Set up config files
# 02a. Specify config file path
cfg="${exec_dir}/configs/config_data_build.yaml"
echo "${cfg}"
# 02b. Add root directory to config
# file if it does not exist in there
# yet (meani... |
310be79f84350810369666e940d5a429635f6b727756a707fdfd0587000ccfb9 | Shell | 2,129 | 71 | #!/bin/bash
# cd <Autodock-Vina_directory>
# DOCKER_IMAGE=quay.io/pypa/manylinux2014_x86_64
# PLAT="manylinux_2_17_x86_64"
# sudo docker run --rm -it -e PLAT=$PLAT -v "$(pwd)":/io "$DOCKER_IMAGE" /io/build/python/build-linux-wheels.sh
set -e -u -x
function repair_wheel {
wheel="$1"
if ! auditwheel show "$whe... |
e732e92d00c3809a2707f57bb92e05e14159b55970d0880ee7bb032e558f76e6 | Shell | 2,135 | 75 | #!/bin/sh -e
# Run this from the 'packages' directory, just under rootdir
# We can only build rpm packages, if the rpm build tools are installed
if [ \! -x /usr/bin/rpmbuild ]
then
echo "Cannot find /usr/bin/rpmbuild. Not building an rpm." 1>&2
exit 0
fi
# Check the commandline flags
PACKAGE="$1"
VERSION="$2"
fu... |
da8008e7839fa3b44fbeabd8dac50ca32c11cbcb5d0bd7fca187918102f2f109 | Shell | 2,137 | 47 | #!/bin/bash
set -euo pipefail
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=${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 $movingfile _t1.nii.gz)_mask.nii.gz... |
b2b9b79e1b4a01853f17a614889c64fbe4308ffb0f172423861487bae015eb17 | Shell | 2,150 | 92 | #!/bin/bash
# run first level for both runs of each subject
# first, load in the subIDs that should be processed from a space separated file
subs=()
while IFS=$' ' read -r -a line
do
subs+=("${line}")
done < "all_use-new"
nos="${#subs[@]}"
# set our directories
dir_out="/home/emba/Documents/EMBA/VMM_analysis/0... |
11fcd39b9581a88391fa3402e5911ce811de657153f057f92e0087d3bc28b8ee | Shell | 2,152 | 76 | #!/bin/bash
#$ -S /bin/bash
#$ -cwd
#$ -o /data1/projects/MicroFunc/Jurjen/programs/packages/fmriprep
#$ -j Y
#$ -q long.q
#$ -V
#$ -pe smp 10
#Template provided by Daniel Levitas of Indiana University
#Edits by Andrew Jahn, University of Michigan, 07.22.2020
subj=${1}
nthreads=15
mem=20 #gb
container=singularity #doc... |
c995f9ba00a157c9ffd036cd4dba3224809fcfc1ec782ae4a11864a873c668aa | Shell | 2,157 | 51 | # Parameters
INPUT_DIR="${HOME}/pacbio_hifi_quick_demo"
OUTPUT_DIR="${INPUT_DIR}/output"
mkdir -p ${INPUT_DIR}
mkdir -p ${OUTPUT_DIR}
# Download quick demo data
# GRCh38_no_alt reference
wget -P ${INPUT_DIR} -nc http://www.bio8.cs.hku.hk/clairs/quick_demo/pacbio_hifi/GRCh38_no_alt_chr17.fa
wget -P ${INPUT_DIR} -nc ht... |
2f43653cd22b4f0f04ff85a51a9bbe683e84161b25dc9b87fef84c5c3d96c306 | Shell | 2,159 | 63 | #!/usr/bin/env bash
set -e
# Get the directory where the current script is located
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
# Source the common setup file
source "$SCRIPT_DIR/common_setup.sh"
test_deepretinotopy_full() {
setup_environment
setup_unique_directory
setup_data_directories
... |
917069ebb84ba7a5538b6525275da104de0301352d2706096ecb4c203b808e22 | Shell | 2,168 | 70 | #!/bin/csh
set nonomatch
if ( $#argv != 0 ) then
echo ""
echo "$0 Usage:"
echo ""
echo "Run this without any arguments. It will go into infinite loop"
echo "without returning until killed. While in this loop, it will "
echo "repeatedly look for files called *.wav and soundserver.go in"
echo... |
d11b0b8be43d7ea3fb49bcf9e3be6c34b386313d6a16bbdfea4c1f0a879e31e7 | Shell | 2,176 | 59 | #!/bin/bash
################################ Begin license #################################
# Copyright (C) Laboratory of Imaging technologies,
# Faculty of Electrical Engineering,
# University of Ljubljana.
#
# This file is part of PyXOpto.
#
# PyXOpto is free software: you can redistribut... |
72f5adc2cab90067a45b9a6d53c79c0395b0ea692bd7186b1583dc747e1428ba | Shell | 2,182 | 47 | #!/bin/bash
if [ -z "$GAZEBO_MODEL_PATH" ]; then
bash -c 'echo "export GAZEBO_MODEL_PATH=$GAZEBO_MODEL_PATH:"`pwd`/../assets/models >> ~/.bashrc'
else
bash -c 'sed "s,GAZEBO_MODEL_PATH=[^;]*,'GAZEBO_MODEL_PATH=`pwd`/../assets/models'," -i ~/.bashrc'
fi
#Load turtlebot variables. Temporal solution
chmod +x catkin_... |
1254135b0d32f67e5c680acea58eef2e3ee4f6f48dbfd01f8b041ccf63d9bf84 | Shell | 2,184 | 47 | #!/bin/bash
if [ -z "$GAZEBO_MODEL_PATH" ]; then
bash -c 'echo "export GAZEBO_MODEL_PATH=$GAZEBO_MODEL_PATH:"`pwd`/../assets/models >> ~/.bashrc'
else
bash -c 'sed "s,GAZEBO_MODEL_PATH=[^;]*,'GAZEBO_MODEL_PATH=`pwd`/../assets/models'," -i ~/.bashrc'
fi
#Load turtlebot variables. Temporal solution
chmod +x catkin_... |
a161e8ed998e731833b2adfa7d105aa3f9a871e3379886cd6cb880f87779e59a | Shell | 2,186 | 32 | # sample scripts for running the distillation code
# use resnet32x4 and resnet8x4 as an example
# kd
python train_student.py --path_t ./save/models/resnet32x4_vanilla/ckpt_epoch_240.pth --distill kd --model_s resnet8x4 -r 0.1 -a 0.9 -b 0 --trial 1
# FitNet
python train_student.py --path_t ./save/models/resnet32x4_vani... |
de8c8670102f26b0cbcf18df2d3ebccfcf556cfd12d172d516fe67145e3b1826 | Shell | 2,210 | 65 | #!/bin/bash
APP_NAME=lammps-gui
DESTDIR=${PWD}/LAMMPS_GUI
SYSROOT="$1"
VERSION="$2"
echo "Delete old files, if they exist"
rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64*.zip
echo "Create staging area for deployment and populate"
DESTDIR=${DESTDIR} cmake --install . --prefix "/"
# no static libs neede... |
138955f14941a2fa1617f50916bdf6a1709891fce4ce0f81053faedac51adc7b | Shell | 2,222 | 67 | #!/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... |
029cead2e9973480c2020c2f386ff91d68e6fa4bbe52bd8b3e17681fcc0751a6 | Shell | 2,223 | 70 | #!/bin/bash
##
## Identify species corresponding to the sequencing reads
##
# specify maximum runtime for sbatch job
# SBATCHTIME=6:00:00
# standard route header (validate args, print settings, prepare environment)
code_dir=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." && pwd)
source "${code_dir}/scripts/route-he... |
3e958e54059a6e8edd00964871f14201ca3a9aa56dc94b506f04761b0d6f1038 | Shell | 2,225 | 55 | #!/bin/bash
################################ Begin license #################################
# Copyright (C) Laboratory of Imaging technologies,
# Faculty of Electrical Engineering,
# University of Ljubljana.
#
# This file is part of PyXOpto.
#
# PyXOpto is free software: you can redistribut... |
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