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source /work/upcorreia/bin/load_masif_environment.sh masif_root=$(git rev-parse --show-toplevel) masif_source=$masif_root/source/ masif_matlab=$masif_root/source/matlab_libs/ export PYTHONPATH=$PYTHONPATH:$masif_source export masif_matlab PDB_ID=$(echo $1| cut -d"_" -f1) CHAIN1=$(echo $1| cut -d"_" -f2) CHAIN2=$(echo $...
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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 ...
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#!/bin/bash # Copyright 2022 Huawei Technologies Co., Ltd # # 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 ...
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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 ...
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#!/usr/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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 ...
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#!/bin/bash # first check that the venv is active if [ -z $VIRTUAL_ENV ]; then echo "Virtual environment is not active, you might want to run:" echo "source external/deface/bin/activate" return fi currenv=$(echo $VIRTUAL_ENV|awk -F "/" '{print $NF}'); if [ $currenv != "deface" ]; then echo "Your act...
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law...
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law...
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#$ -S /bin/bash #$ -cwd #$ -m be #$ -M s.moia@bcbl.eu module load singularity/3.3.0 ########################################################################################################################## ##---START OF SCRIPT-------------------------------------------------------------------------------------------...
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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#$ -S /bin/bash #$ -cwd #$ -m be #$ -M s.moia@bcbl.eu module load singularity/3.3.0 ########################################################################################################################## ##---START OF SCRIPT-------------------------------------------------------------------------------------------...
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#!/bin/bash # login to the latest NSP container # Set default values for parameters # container_name or container_id works the same hear containerName=`docker ps -l -q --filter name=nsp_genesis` # Process command line arguments while [[ $# -gt 0 ]] do key="$1" case $key in -c|--container) conta...
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#!/bin/bash # Copyright 2022 Huawei Technologies Co., Ltd # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law...
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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#!/bin/bash DIR=$(cd "$(dirname "$0")"; pwd) nextflow run $DIR/../main.nf \ -profile awsbatch \ -w s3://janelia-nextflow-demo/multifish/work \ --workers 1 \ --worker_cores 16 \ --wait_for_spark_timeout_seconds 3600 \ --sleep_between_timeout_checks_seconds 2 \ --gb_per_core 4 \ --channe...
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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Shell
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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#!/bin/bash #SBATCH --job-name=get-atlas #SBATCH --time=01:00:00 #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=1 #SBATCH --mem-per-cpu=2gb #SBATCH --account=iacc_nbc #SBATCH --qos=pq_nbc #SBATCH --partition=IB_16C_96G # Outputs ---------------------------------- #SBATCH --output=/home/data/abcd/abcd-hisp...
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Shell
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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Shell
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#!/usr/bin/env bash set -euo pipefail HERE=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd) NUREC_DIR="$HERE/../../nvidia/nurec" SCENE_ID="00040136-e651-4abd-991d-0655ccda9430" DEFAULT_USDZ="$NUREC_DIR/PhysicalAI-Autonomous-Vehicles-NuRec/sample_set/26.04_release/$SCENE_ID/$SCENE_ID.usdz" NUREC_PYTHON="${NUREC_PYTHON:-$...
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#keyword search default glmFile=conf/glm duptime=0.5 case_insensitive=false use_pitch=true # Lexicon and Language Model parameters oovSymbol="<unk>" lexiconFlags="-oov <unk>" boost_sil=1.5 # note from Dan: I expect 1.0 might be better (equivalent to not # having the option)... should test. cer=0 #Declar...
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Shell
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24
#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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 ...
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#!/bin/bash #SBATCH --job-name=MATRIX_PREPARATION_AFR_REPLICATION_EUR #SBATCH --output=/groups/umcg-biogen/tmp01/output/2019-11-06-FreezeTwoDotOne/2020-10-12-deconvolution/deconvolution/matrix_preparation/jobs/MATRIX_PREPARATION_AFR_REPLICATION_EUR.out #SBATCH --error=/groups/umcg-biogen/tmp01/output/2019-11-06-FreezeT...
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#!/bin/bash # Example command for installing dependencies. # JAX installation is environment-specific (CPU, GPU, TPU). Check the official JAX installation guide at https://docs.jax.dev/en/latest/installation.html. # Examples: # CPU: `pip install -U jax` # GPU: `pip install -U "jax[cuda12]"` (Replace `cuda12`; ensure C...
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#!/bin/bash if [ $# -ne 2 ]; then echo "Usage: recipes/sync_from_remote.sh <from_dir> <to_dir>" echo "e.g.: $0 /path/to/remote/project_folder/generated/work ./generated" echo echo "This script synchronizes decoding and segmentation results required in the" echo "realignment process from a remote computing cluster...
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Shell
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#!/usr/bin/env bash # Copyright 2017 Vimal Manohar # This script prepares lang directory with UNK modeled by a phone LM. utils/lang/make_unk_lm.sh data/local/dict exp/unk_lang_model || exit 1 utils/prepare_lang.sh \ --unk-fst exp/unk_lang_model/unk_fst.txt \ data/local/dict "<unk>" data/local/lang data/lang_un...
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#!/bin/bash #SBATCH --workdir=/data/share/htp/TRNP1/MPRA_full_300919/MPRA_data/deML/demult/files #SBATCH --error=MPRA_II_filt2_%J.err #SBATCH --output=MPRA_II_filt2_%J.out #SBATCH --cpus-per-task=8 #SBATCH --mem=32G # Variables # maindir="/data/share/htp/TRNP1/MPRA_full_300919/MPRA_data/" # Matthias Pipeline for barc...
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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...
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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#!/bin/bash # login to the latest NSP container # Set default values for parameters # container_name or container_id works the same hear containerName=`docker ps -l -q --filter name=nsp_genesis` # Process command line arguments while [[ $# -gt 0 ]] do key="$1" case $key in -c|--container) conta...
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cc=1 for Nfeat in 10 100; do for classratio in 1 10; do for flipy in 0.1 0.2; do echo echo ================================================== echo $cc, Nfeat=$Nfeat, classratio=$classratio, flipy=$flipy echo ================================================== ...
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#!/bin/bash #SBATCH -J bstrapCCA ### Job name ### #SBATCH -e /scratch/janine.bijsterbosch/WAPIAW_2/heterogeneity/log/bstrapCCA_tst.err ### Error file ### #SBATCH -o /scratch/janine.bijsterbosch/WAPIAW_2/heterogeneity/log/bstrapCCA_tst.out ### Output file ##...
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#!/bin/bash #SBATCH --time=05:59:00 #SBATCH --mem=100G # Converts SNP <tab> P formatted summary statistics to a binary zscore matrix for use with Depict 2 set -e ml Java # Cluster settings TIME="23:59:00" MEMORY="100G" CORES=1 # DEPICT2 global settings BUNDLE_DIR="/groups/umcg-wijmenga/tmp04/projects/depict2/depict2...
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#!/bin/bash # Copyright 2022 Huawei Technologies Co., Ltd # # 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 ...
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Shell
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#!/bin/bash # do some validation of the input folder infile=$1 # create output folder infolder=$(dirname $infile); filename=$(basename $1) outfolder=$infolder"/mrideface" echo ">> mkdir -p $outfolder" mkdir -p $outfolder # run mrideface outfile=$outfolder"/defaced_"$filename maskfile=$outfolder"/mask.nii.gz" if [ -f...
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#!/bin/bash #SBATCH --job-name=joint_proj_cat #SBATCH --output=/scratch/janine.bijsterbosch/WAPIAW_2/task_residuals/log/job_%j.out #SBATCH --error=/scratch/janine.bijsterbosch/WAPIAW_2/task_residuals/log/job_%j.err #SBATCH --time=23:55:00 #SBATCH --cpus-per-task=16 #SBATCH --mem-per-cpu=500MB sub_list=/scratch/janine...
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#!/bin/bash #SBATCH --job-name=WAPIAW #SBATCH --output=/scratch/janine.bijsterbosch/WAPIAW_2/task_residuals/log/job_%j.out #SBATCH --error=/scratch/janine.bijsterbosch/WAPIAW_2/task_residuals/log/job_%j.err #SBATCH --time=23:55:00 #SBATCH --cpus-per-task=16 #SBATCH --mem-per-cpu=500MB sub_list=/scratch/janine.bijster...
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#! /bin/bash # ============================================================================== # -- Parse arguments ----------------------------------------------------------- # ============================================================================== DOC_STRING="Unpack and copy over CarlaUnreal's Exported Assets...
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#!/usr/bin/env bash check_model () { model=$1 if [ -s $model ]; then echo $model else dir=`dirname $model` latest_model=`ls -lt $dir/{?,??}.mdl 2>/dev/null | head -1 | awk '{print $9}'` echo "*$model is not there, latest is: $latest_model" fi } for model in exp/mono/final.mdl exp/tri{1,2,3}/final...
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#!/usr/bin/env bash check_model () { model=$1 if [ -s $model ]; then echo $model else dir=`dirname $model` latest_model=`ls -lt $dir/{?,??}.mdl 2>/dev/null | head -1 | awk '{print $9}'` echo "*$model is not there, latest is: $latest_model" fi } for model in exp/mono/final.mdl exp/tri{1,2,3}/fina...
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#!/bin/bash #SBATCH --job-name=MATRIX_PREPARATION_AFR_NOCOVCORRECTION_NOENA #SBATCH --output=/groups/umcg-biogen/tmp01/output/2019-11-06-FreezeTwoDotOne/2020-10-12-deconvolution/deconvolution/matrix_preparation/jobs/MATRIX_PREPARATION_AFR_NOCOVCORRECTION_NOENA.out #SBATCH --error=/groups/umcg-biogen/tmp01/output/2019-1...
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#!/bin/bash # script that stop NSP container # Set default values for parameters containerName=`docker ps -l -q --filter name=nsp_genesis ` # Process command line arguments while [[ $# -gt 0 ]] do key="$1" case $key in -c|--container) containerName="$2" shift # past argument shi...
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#!/bin/bash # Copyright 2022 Huawei Technologies Co., Ltd # # 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 ...
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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 ...
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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 ...
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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Shell
905
21
#!/bin/bash echo "this script requires freeesurfer module"; echo "subject dir: $1"; echo "output prefix: $2"; module load freesurfer/5.3.0 export SUBJECTS_DIR=$1 output_prefix=$2 cd $SUBJECTS_DIR # create subject list ls | grep sub- > subject.list echo "Measuring thickess over DKT atlas" aparcstats2table --hemi lh...
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Shell
907
24
#!/bin/bash # Copyright 2020 Huawei Technologies Co., Ltd # # 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 ...
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#!/bin/bash #SBATCH --job-name=rep_FI #SBATCH --output=/scratch/janine.bijsterbosch/WAPIAW_2/task_residuals/log/job_%j.out #SBATCH --error=/scratch/janine.bijsterbosch/WAPIAW_2/task_residuals/log/job_%j.err #SBATCH --time=167:55:00 #SBATCH --cpus-per-task=16 #SBATCH --mem-per-cpu=500MB sub_list=/scratch/janine.bijste...
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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 ...
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Shell
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#!/bin/bash # Copyright 2020 Audio, Speech and Language Processing Group (ASLP@NPU), Northwestern Polytechnical University (Authors: Zhuoyuan Yao, Xiong Wang, Jingyong Hou, Lei Xie) # 2020 AIShell-Foundation (Author: Bengu WU) # 2020 Beijing Shell Shell Tech. Co. Ltd. (Author: Hui BU) # Apache 2....
0cdc6ea1927f760f401105592d631eb69277ba9802cad6739954008cb06b135b
Shell
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module load GATK for CHR in {1..22} do java -Xmx200g -jar ${EBROOTGATK}/GenomeAnalysisTK.jar \ -T SelectVariants \ -R /apps/data/ftp.broadinstitute.org/bundle/2.8/b37/human_g1k_v37.fasta \ -V /groups/umcg-bios/tmp04/projects/genotypes_BIOS_LLDeep_Diagnostics_merged/results/filterGQ20_callRate50/genot...
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#!/bin/sh #author: Mahbub Ul Alam (mahbub@dsv.su.se) #version: 1.0+ #copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se) #license : MIT License #sh run_all_text_experiments.sh -e 1 -b 1 while getopts e:b: flag do case "${flag}" in e) total_experiments=${OPTARG};; b) batch_size=${OPTARG};;...
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913
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#!/bin/bash #SBATCH --time=01:00:00 #SBATCH --mem=4G #SBATCH --output=oargtv_%A_%a.out #SBATCH --array=1-55 # first check that the venv is active source external/deface/bin/activate currenv=$(echo $VIRTUAL_ENV|awk -F "/" '{print $NF}'); if [ $currenv != "deface" ]; then echo "Your active environment is not =defa...
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Shell
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#!/usr/bin/env bash # Copyright 2022 Huawei Technologies Co., Ltd # # 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 applic...
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Shell
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#!/bin/bash #where my PAML outputs are located with 2 folders called NS7 and NS8 workdir=protein/other_protein_alignments/PAML/PAML_out_branch_model rm $workdir/../branch_model_out.txt declare -a arr=("1") declare -a farr=("good_noCuration" "good_curated") for f in "${farr[@]}" do cp $workdir/protein_list_"$f".tx...
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Shell
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#!/usr/bin/env bash # Copyright 2022 Huawei Technologies Co., Ltd # # 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 applic...
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Shell
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --account=rrg-PIID #SBATCH --time=12:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/scratch/authorid/results_brats_rerun/heatmaps/log/%x_%j_%N.out #SBATCH --error=/scratch/authorid/results_brats_rer...
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Shell
920
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#!/bin/bash DATADIR=/Users/frederic/Dropbox_PHC/MR_data/gradertest MYIPADDRESS=`ifconfig en0 | grep 'inet ' | awk '{print $2}'` VERSION=latest # allow network connections in Xquartz Security settings xhost + # Allow your local user access via xhost: xhost +SI:localuser:picachooser and create a similar user with doc...
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Shell
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#!/usr/bin/env bash # Copyright 2020 The TensorFlow Authors. 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...
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Shell
923
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#!/bin/bash # Copyright 2022 Huawei Technologies Co., Ltd # # 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 ...
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Shell
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#!/bin/bash # show list of experiments from s3 # Set default values for parameters container=`docker ps -l -q --filter name=nsp_genesis` n=10 # Process command line arguments while [[ $# -gt 0 ]] do key="$1" case $key in -c|--container) container="$2" shift # past argument shift # pa...
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Shell
929
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --account=rrg-PIID #SBATCH --time=3:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/scratch/authorid/results_brats_rerun/heatmaps/log/%x_%j_%N.out #SBATCH --error=/scratch/authorid/results_brats_reru...
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Shell
929
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --account=rrg-PIID #SBATCH --time=3:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/scratch/authorid/results_brats_rerun/heatmaps/log/%x_%j_%N.out #SBATCH --error=/scratch/authorid/results_brats_reru...
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Shell
929
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --account=rrg-PIID #SBATCH --time=3:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/scratch/authorid/results_brats_rerun/heatmaps/log/%x_%j_%N.out #SBATCH --error=/scratch/authorid/results_brats_reru...
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Shell
929
27
#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --account=rrg-PIID #SBATCH --time=3:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/scratch/authorid/results_brats_rerun/heatmaps/log/%x_%j_%N.out #SBATCH --error=/scratch/authorid/results_brats_reru...
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Shell
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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Shell
930
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#!/bin/bash #SBATCH --time=01:00:00 #SBATCH --mem=4G #SBATCH --output=hecktorResampled_%A_%a.out #SBATCH --array=1-224 # first check that the venv is active source external/deface/bin/activate currenv=$(echo $VIRTUAL_ENV|awk -F "/" '{print $NF}'); if [ $currenv != "deface" ]; then echo "Your active environment i...
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Shell
930
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --account=rrg-PIID #SBATCH --time=12:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/scratch/authorid/results_brats_rerun/heatmaps/log/%x_%j_%N.out #SBATCH --error=/scratch/authorid/results_brats_rer...
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Shell
931
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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Shell
932
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#!/bin/bash #SBATCH --job-name=MATRIX_PREPARATION_EUR_NOCOVCORRECTION_NOENA_NOGVEX #SBATCH --output=/groups/umcg-biogen/tmp01/output/2019-11-06-FreezeTwoDotOne/2020-10-12-deconvolution/deconvolution/matrix_preparation/jobs/MATRIX_PREPARATION_EUR_NOCOVCORRECTION_NOENA_NOGVEX.out #SBATCH --error=/groups/umcg-biogen/tmp01...
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Shell
934
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#MOLGENIS nodes=1 ppn=1 mem=16gb walltime=5:59:00 ### variables to help adding to database (have to use weave) #string sampleName #string project ### #string stage #string checkStage #string samtoolsVersion #string gatkVersion #string markDuplicatesBam #string markDuplicatesBai #string onekgGenomeFasta #string chromos...
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Shell
935
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#!/bin/bash # Copyright 2020 Huawei Technologies Co., Ltd # # 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 ...
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Shell
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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 ...
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Shell
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#====================# # 5.Target data QC # #====================# filepath="" cd $filepath # Load plink module load apps/plink # Step 1: Update sex plink \ --bfile NSHD_QCed \ --update-sex ID_sex.txt \ --make-bed \ --out NSHD.QCsex # Step 2: Keep only unrelated individuals plink \ --bfile NSHD.QCsex \ --keep rel...
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Shell
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#!/usr/bin/env bash # Copyright 2015 University of Sheffield (Author: Ning Ma) # Apache 2.0. # # Kaldi scripts for preparing dictionary for the GRID corpus (or CHiME 1) echo "Preparing dictionary" . ./config.sh # Needed for REC_ROOT and WAV_ROOT # Prepare relevant folders dict="$REC_ROOT/data/local/dict" mkdir -p ...
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Shell
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#!/bin/bash #make a bash script that for each entrance generates a 2bit file and does reciprocal best blat of human protein sequences and back TRNP1=protein mkdir -p $TRNP1/other_protein_alignments/blat_output_full cat data/coevol_species_genomes.txt | while read i j k; do cd $j if [ ! -f $k.2bit ]; then echo ...
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Shell
943
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --account=rrg-PIID #SBATCH --time=5-20:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/scratch/authorid/results_brats_rerun/heatmaps/log/%x_%j_%N.out #SBATCH --error=/scratch/authorid/results_brats_r...
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Shell
943
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --account=rrg-PIID #SBATCH --time=5-20:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/scratch/authorid/results_brats_rerun/heatmaps/log/%x_%j_%N.out #SBATCH --error=/scratch/authorid/results_brats_r...
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Shell
943
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --account=rrg-PIID #SBATCH --time=5-20:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/scratch/authorid/results_brats_rerun/heatmaps/log/%x_%j_%N.out #SBATCH --error=/scratch/authorid/results_brats_r...
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Shell
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --account=rrg-PIID #SBATCH --time=5-20:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/scratch/authorid/results_brats_rerun/heatmaps/log/%x_%j_%N.out #SBATCH --error=/scratch/authorid/results_brats_r...
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Shell
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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 ...
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Shell
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#!/bin/bash # Copyright 2022 Huawei Technologies Co., Ltd # # 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 ...
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Shell
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#!/bin/bash # terminate script die() { echo "install-hts.sh: $1" >&2 exit 1 } LINK=https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 TARBALL=htslib-1.9.tar.bz2 FOLDER=htslib test -e $TARBALL && rm $TARBALL test -d $FOLDER && rm -r $FOLDER wget -O $TARBALL $LINK || curl -o $TARBALL $LINK ...
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Shell
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#!/usr/bin/bash # Copyright 2022 Huawei Technologies Co., Ltd # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable ...
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Shell
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#This script is not really supposed to be run directly #Instead, it should be sourced from the decoding script #It makes many assumption on existence of certain environmental #variables as well as certain directory structure. if [ "${dataset_kind}" == "supervised" ] ; then mandatory_variables="my_ecf_file my_kwlist_...
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Shell
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#!/bin/bash #! Sample PBS submission script for a MATLAB job #! Requesting resource (processors and wall-clock time): #! nodes=1:ppn=1 indicates a single processor. #! nodes=1:ppn=16 would request a whole node for BCp3. #! 02:30:00 indicates 02 hours and 30 minutes #PBS -l nodes=1:ppn=12,walltime=300:00:00 #! Specify ...
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Shell
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#!/bin/bash #! Sample PBS submission script for a MATLAB job #! Requesting resource (processors and wall-clock time): #! nodes=1:ppn=1 indicates a single processor. #! nodes=1:ppn=16 would request a whole node for BCp3. #! 02:30:00 indicates 02 hours and 30 minutes #PBS -l nodes=1:ppn=12,walltime=300:00:00 #! Specify ...
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Shell
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#!/usr/bin/env bash . conf/common_vars.sh . ./lang.conf # This parameter will be used when the training dies at a certain point. train_stage=-100 dir=exp/tri6_nnet . ./utils/parse_options.sh set -e set -o pipefail set -u # Wait till the main run.sh gets to the stage where's it's # finished aligning the tri5 model....
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Shell
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#!/usr/bin/bash path_cur=$(dirname $0) function check_env() { # set ASCEND_VERSION to ascend-toolkit/latest when it was not specified by user if [ ! "${ASCEND_VERSION}" ]; then export ASCEND_VERSION=ascend-toolkit/latest echo "Set ASCEND_VERSION to the default value: ${ASCEND_VERSION}" else...
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Shell
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#!/bin/bash #! Sample PBS submission script for a MATLAB job #! Requesting resource (processors and wall-clock time): #! nodes=1:ppn=1 indicates a single processor. #! nodes=1:ppn=16 would request a whole node for BCp3. #! 02:30:00 indicates 02 hours and 30 minutes #PBS -l nodes=1:ppn=12,walltime=300:00:00 #! Specify ...
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Shell
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#!/usr/bin/bash path_cur=$(dirname $0) function check_env() { # set ASCEND_VERSION to ascend-toolkit/latest when it was not specified by user if [ ! "${ASCEND_VERSION}" ]; then export ASCEND_VERSION=ascend-toolkit/latest echo "Set ASCEND_VERSION to the default value: ${ASCEND_VERSION}" else...
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Shell
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#!/bin/bash #SBATCH --job-name=PCA #SBATCH --output=PCA.out #SBATCH --error=PCA.err #SBATCH --time=23:59:59 #SBATCH --cpus-per-task 22 #SBATCH --mem 100gb #SBATCH --nodes 1 #SBATCH --qos=dev . ~/brain_eQTL/GeneNetwork/PCA_setup_calculon.sh echo "done" cd REPLACEOUT echo "run PCA" /groups/umcg-wijmenga/tmp04/projects/2...
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Shell
952
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#!/bin/bash # Copyright 2020 Huawei Technologies Co., Ltd # # 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 ...
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Shell
952
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#!/bin/bash #! Sample PBS submission script for a MATLAB job #! Requesting resource (processors and wall-clock time): #! nodes=1:ppn=1 indicates a single processor. #! nodes=1:ppn=16 would request a whole node for BCp3. #! 02:30:00 indicates 02 hours and 30 minutes #PBS -l nodes=1:ppn=12,walltime=300:00:00 #! Specify ...
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Shell
953
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#!/bin/bash # Copyright 2020 Huawei Technologies Co., Ltd # # 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 ...
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Shell
953
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#!/usr/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # 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 ...
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Shell
953
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#!/bin/bash # Copyright 2022 Huawei Technologies Co., Ltd # # 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 ...