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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 # 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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#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 [ "${dataset_kind}" == "supervised" ] ; then mandatory_variables="my_ecf_file my_kwlist...
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Shell
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#!/bin/bash ## MAYBE: the first line is not needed # Run: `./slurm_submit.sh <script_name> <nthreads>` # Normally, no commands are allowed before #SBATCH. In this file we use a workaround. # Access `$SLURM_CPUS_PER_TASK` by escaping $-sign`\$SLURM_CPUS_PER_TASK` # output file and job name - by date # args: (1) python s...
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Shell
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#!/bin/bash module load Python/2.7.12-foss-2015b module load Java/11.0.2 indir=$1 output=$2 summarystats=/groups/umcg-wijmenga/tmp03/projects/eQTLGen/helpfiles/ePRSHelpFiles/SummaryStatisticsDatabase_freeze1b/ mkdir -p $output # fix snp ids mkdir -p $output/tmpgt/ cp -v $indir/* $output/tmpgt/ # kill b38 data pyt...
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Shell
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#!/bin/bash # COCO 2017 dataset http://cocodataset.org # Download command: bash data/scripts/get_coco.sh # Train command: python train.py --data coco.yaml # Default dataset location is next to /yolov5: # /parent_folder # /coco # /yolov5 # Download/unzip labels d='../' # unzip directory url=https://github.com...
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Shell
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#!/usr/bin/env bash stage=0 . ./cmd.sh ## You'll want to change cmd.sh to something that will work on your system. ## This relates to the queue. . utils/parse_options.sh # e.g. this parses the --stage option if supplied. if [ $stage -le 0 ]; then # data preparation local/prepare_data.sh for x in ci...
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Shell
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#!/usr/bin/env bash # Copyright 2017 Hossein Hadian # 2017 Chun Chieh Chang # 2017 Ashish Arora # This script prepares the dictionary. set -e dir=data/local/dict data_dir=data . ./utils/parse_options.sh || exit 1; base_dir=$(echo "$DIRECTORY" | cut -d "/" -f2) mkdir -p $dir ...
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Shell
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --time=1:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/project/labname-lab/authorid/brats_rerun/%x_%j_%N.out #SBATCH --job-name s7-dfp-mrnet #SBATCH --partition=debug #SBATCH --dependency=singleton...
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --time=1:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/project/labname-lab/authorid/brats_rerun/%x_%j_%N.out #SBATCH --job-name s9-dfp-mrnet #SBATCH --partition=debug #SBATCH --dependency=singleton...
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --time=1:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/project/labname-lab/authorid/brats_rerun/%x_%j_%N.out #SBATCH --job-name s8-dfp-mrnet #SBATCH --partition=debug #SBATCH --dependency=singleton...
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --time=1:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/project/labname-lab/authorid/brats_rerun/%x_%j_%N.out #SBATCH --job-name s6-dfp-mrnet #SBATCH --partition=debug #SBATCH --dependency=singleton...
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Shell
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#!/usr/bin/env bash . ./path.sh format=pdf # pdf svg output= . utils/parse_options.sh if [ $# != 3 ]; then echo "usage: $0 [--format pdf|svg] [--output <path-to-output>] <utt-id> <lattice-ark> <word-list>" echo "e.g.: $0 utt-0001 \"test/lat.*.gz\" tri1/graph/words.txt" exit 1; fi uttid=$1 lat=$2 words=$3...
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#!/usr/bin/env bash # Copyright 2016 Alibaba Robotics Corp. (Author: Xingyu Na) # Apache 2.0 # This runs MMI and MPE on top of the MLE system. It requires the alignments. dir=exp/tri5a . ./cmd.sh . ./path.sh steps/make_denlats.sh --cmd "$train_cmd" --nj 10 --transform-dir ${dir}_ali \ --config conf/decode.config ...
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#!/bin/bash #SBATCH --gres=gpu:1 #SBATCH --mem=32G #SBATCH --cpus-per-task=8 #SBATCH --time=1:00:00 #SBATCH --mail-user=email@email.com #SBATCH --mail-type=ALL #SBATCH --output=/project/labname-lab/authorid/brats_rerun/%x_%j_%N.out #SBATCH --job-name s10-dfp-mrnet #SBATCH --partition=debug #SBATCH --dependency=singleto...
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#!/bin/bash #! Sample PBS submission script for a MATLAB job #! Requesting resource (processors and wall-clock time): #! nodes=1:ppn=1 indicates a single processor. #! nodes=1:ppn=16 would request a whole node for BCp3. #! 02:30:00 indicates 02 hours and 30 minutes #PBS -l nodes=1:ppn=12,walltime=300:00:00 #! ...
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Shell
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#This script is not really supposed to be run directly #Instead, it should be sourced from the decoding script #It makes many assumption on existence of certain environmental #variables as well as certain directory structure. if [ "${dataset_kind}" == "supervised" ] ; then mandatory_variables="my_ecf_file my_kwlists...
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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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#!/usr/bin/env bash # Copyright 2017 John Morgan # Apache 2.0. . ./cmd.sh set -e . ./path.sh stage=0 . ./utils/parse_options.sh if [ ! -d data/local/lm ]; then mkdir -p data/local/lm fi corpus=$1 if [ ! -f $corpus ]; then echo "$0: input data $corpus not found." exit 1 fi if ! command ngram-count >/dev/n...
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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 nproteins=322 #split them between gorilla2 & 3 cat data/coevol_species_genomes.txt | while read i j k; do cd $j if [ ! -f $k.2bit ]; then echo "Generating ...
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Shell
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#!/bin/bash -u # Copyright 2020 Prisyach Tatyana (STC-innovations Ltd) . ./utils/parse_options.sh . ./path.sh . ./cmd.sh echo >&2 "$0" "$@" if [ $# -ne 3 ] ; then echo >&2 "$0" "$@" echo >&2 "$0: Error: wrong number of arguments" echo -e >&2 "Usage:\n $0 <gss-dir> <output-data-dir>" echo -e >&2 "eg:\n $...
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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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#============================# # 6.Derive PGS with PRSice # #============================# filepath="" cd $filepath module load apps/R # APOE region included Rscript program/PRSice.R \ --dir . \ --prsice program/PRSice_linux \ --base dat/genetics/base/Kunkle_Stage1_post-qc_semi_clumped.txt \ --target dat/genetics/...
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Shell
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#!/usr/bin/env bash dir=exp/tri6_nnet train_stage=-10 . conf/common_vars.sh . ./lang.conf # This parameter will be used when the training dies at a certain point. train_stage=-100 . ./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...
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Shell
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#!/usr/bin/env bash # Copyright 2014, University of Edinburgh (Author: Pawel Swietojanski) . ./path.sh nj=$1 job=$2 numch=$3 meetings=$4 sdir=$5 odir=$6 wdir=data/local/beamforming set -e set -u utils/split_scp.pl -j $nj $((job-1)) $meetings $meetings.$job while read line; do mkdir -p $odir/$line BeamformIt ...
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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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#!/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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#!/usr/bin/env bash numb_of_files=$1 numbproc=$2 refgen=$3 aux=$4 out=$5 sample=$6 quality=$7 echo 'Aligning reads to the reference genome ...' if [[ $numb_of_files == 1 ]]; then # IF SE READS bwa mem -v 1 -t $numbproc $refgen $aux/r1.2b.aln.fq | samtools sort --threads $numbproc -T ${aux}/${sample} > ${out}/${sa...
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#!/usr/bin/env bash # Copyright 2017 Johns Hopkins University (Author: Aswin Shanmugam Subramanian) # Apache 2.0 . ./cmd.sh . ./path.sh if [ $# != 4 ]; then echo "Wrong #arguments ($#, expected 3)" echo "Usage: local/run_nn-gev.sh <wav-in-dir> <wav-out-dir> <enhancement-type> <track>" exit 1; fi sdir=$1 odi...
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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 # 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 # Run model fitting, then create an archive with model fitting results # Use: fit_and_archive directory fit_names folder=$1 shift 1 # Pull git repository cd $HOME/Paramecium-model-fitting git pull # Remove the old archive rm /mnt/storage_s1/Paramecium/results_selection.tar.gz # Remove old yaml files for...
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Shell
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#!/usr/bin/env bash . ./path.sh format=pdf # pdf svg output= . utils/parse_options.sh if [ $# != 3 ]; then echo "usage: $0 [--format pdf|svg] [--output <path-to-output>] <utt-id> <lattice-ark> <word-list>" echo "e.g.: $0 utt-0001 \"test/lat.*.gz\" tri1/graph/words.txt" exit 1; fi uttid=$1 lat=$2 words=$3...
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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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#!/usr/bin/env bash # Copyright 2018 Chun-Chieh Chang # The original format of the dataset given is GEDI and page images. # This script is written to create line images from page images. # It also creates csv files from the GEDI files. database_train=/export/corpora5/handwriting_ocr/CASIA_HWDB/Offline/ database_compe...
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#!/bin/bash # script credit: https://github.com/naumenko-sa/bioscripts # reports holes in coverage: how many PB are below 20X per exon echo "target,gene,pos,min_coverage,bases_below20" cat $1 | awk -F "\t" '{print $1"-"$2"-"$3","$4","$2+$5","$6}' | \ awk -F ',' ' BEGIN{ prev_target=0; prev_pos=0; prev_c...
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#!/bin/bash if [ -z ${KALDI_ROOT+x} ]; then export KALDI_ROOT=`pwd -P`/../../.. fi if [ -z ${LD_LIBRARY_PATH+x} ]; then export LD_LIBRARY_PATH= fi export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$PWD:$PATH [ ! -f $KALDI_ROOT/tools/config/common_path.sh ] && echo >&2 "The standard file $KALDI_ROOT/tools/conf...
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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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# "queue.pl" uses qsub. The options to it are # options to qsub. If you have GridEngine installed, # change this to a queue you have access to. # Otherwise, use "run.pl", which will run jobs locally # (make sure your --num-jobs options are no more than # the number of cpus on your machine. #a) JHU cluster options ex...
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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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#!/usr/bin/env bash # Author: Ashish Arora # Apache 2.0 . ./cmd.sh . ./path.sh enhancement=gss . utils/parse_options.sh || exit 1; if [ $# != 3 ]; then echo "Wrong #arguments ($#, expected 3)" echo "Usage: local/add_location_to_uttid.sh [options] <json-transcription-in-dir>" echo " <p...
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#!/bin/bash # arguments HOST_DATA_DIR=$1 MASTER_CPUS=$2 NUM_WORKERS=$3 WORKER_CPUS=$4 WORKER_MEMORY=$5 ROUTE="../../dockers/spark" # building images if [[ "$(docker images -q spark-base-fis:2.4.5 2> /dev/null)" == "" ]]; then docker build $ROUTE/base -t spark-base-fis:2.4.5 docker build $ROUTE/master -t spark-ma...
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law ...
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law ...
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#/bin/bash # Copyright Johns Hopkins University # 2019 Fei Wu # Called by local/cslu_DataPrep.shi Assignment() { rnd=$((1+RANDOM % 100)) if [ $rnd -le $test_percentage ]; then target="test" else target="train" fi } audio= test_percentage=30 # Percent of data reserved as test set ...
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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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#!/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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#!/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 --workdir=/data/share/htp/TRNP1/MPRA_full_300919/MPRA_data/slurms #SBATCH --error=MPRA_I_deML_%J.err #SBATCH --output=MPRA_I_deML_%J.out #SBATCH --cpus-per-task=5 #SBATCH --mem=32G # Variables # maindir="/data/share/htp/TRNP1/MPRA_full_300919/MPRA_data/" fqdir="fastq" demldir="deML" declare -a lane...
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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/usr/env bash # RUN AS: bash prepare_run.sh samplesheet.csv BICRO66 fastqdir # head -1 samplesheet.csv as: BB78b,Caco2_Ctrl_2A,CATCAATC,Homo sapiens,5 inputfile=$1 #samplesheet.csv inputdir=`dirname $inputfile` run=$2 fastqdir=$3 # fullpath to dir containing FASTQ files if [[ ! -d runs ]]; then mkdir runs ...
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# "queue.pl" uses qsub. The options to it are # options to qsub. If you have GridEngine installed, # change this to a queue you have access to. # Otherwise, use "run.pl", which will run jobs locally # (make sure your --num-jobs options are no more than # the number of cpus on your machine. #a) JHU cluster options #e...
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#!/usr/bin/env bash cd /root mkdir certificates cd certificates openssl req -x509 -nodes -days 365 -subj "/C=XX/ST=XX/L=XX/O=XX/CN=XX" -newkey rsa:1024 -keyout mykey.key -out mycert.pem jupyter notebook --generate-config python -c "from notebook.auth import passwd; print passwd()" > /root/.jupyter/nbpasswd.txt echo "#...
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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 . ./cmd.sh split=dev data_dir=data/dev decode_dir=exp/sgmm2x_6a/decode_dev/ lang_dir=data/lang # Create the STM file # Always create this file before creating the CTM files so that # channel numbers are properly created. if [ ! -f $data_dir/stm ]; then /export/a11/guoguo/babel/103-bengali-li...
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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 # 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 [ $currenv != "deface" ]; then echo "Your act...
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Shell
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#!/bin/bash -l # Batch script to run a serial array job under SGE # Request 20 minutes of wallclock time (format hours:minutes:seconds). # one job ran on frontend was 2 min #$ -l h_rt=1:0:0 # Request 1 gigabyte of RAM (must be an integer followed by M, G, or T) # memory per node, so I am assuming per array task/orth...
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Shell
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#!/bin/bash # This a convenience script for checking that video and audio lengths # roughly match if there is suspicion of broken audio files or similar. if [ ! -d corpus ]; then echo "The directory 'corpus' (or a symbolic link to it) does not exist!" echo "Assuming therefore that there is nothing to check." ...
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Shell
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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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Shell
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#!/bin/bash #SBATCH --job-name=DIM_REDUCTION #SBATCH --output=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-03-12-deconvolution/jobs/output/DIM_REDUCTION.out #SBATCH --error=/groups/umcg-biogen/tmp03/output/2019-11-06-FreezeTwoDotOne/2020-03-12-deconvolution/jobs/output/DIM_REDUCTION.out #SBATCH --ti...
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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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MAIN_ROOT=$PWD/../../.. KALDI_ROOT=$MAIN_ROOT/tools/kaldi [ -f $KALDI_ROOT/tools/env.sh ] && . $KALDI_ROOT/tools/env.sh export PATH=$PWD/utils/:$KALDI_ROOT/tools/openfst/bin:$KALDI_ROOT/tools/sctk/bin:$PWD:$PATH [ ! -f $KALDI_ROOT/tools/config/common_path.sh ] && echo >&2 "The standard file $KALDI_ROOT/tools/config/co...
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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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# 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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#!/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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# 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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#borrows most functionality from script concatenating fastqc information rm ../read_summaries/reads.through.filtering_all.samples2.txt touch ../read_summaries/reads.through.filtering_all.samples2.txt echo -e "reads\tstep\tsample\treplicate" > ../read_summaries/reads.through.filtering_all.samples2.txt #add Sample colum...
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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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# 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 # Checking arguments if [ $# -le 1 ]; then echo "Use $0 <datadir> test1.wav [test2.wav] ..." echo " $0 data/test-corpus test1.wav test2.wav" exit 0; fi CORPUS=$1 shift for file in "$@"; do if [[ "$file" != *.wav ]]; then echo "Expecting .wav files, got $file" exit 1; fi if [ ...
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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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########################################################################################## ## UGER job submission script ## bulk RNA-seq analysis for 6 samples (d0, d21, d51 of NGN2 iNs in duplicate) ## Step 3 of 3: run htseq-count to generate gene counts for each of the 6 samples ## ## Author: Yu-Han Hsu, Kalliopi Tsa...
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Shell
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#!/bin/bash module load fsl/6.0.3 source $FSLDIR/etc/fslconf/fsl.sh MASKFACE_HOME=/scratch/cs/faceai/projects/faceai_testingdefacing/software/external/MaskFace/lin64.Dec2017 PATH=${MASKFACE_HOME}/bin:${PATH} export PATH MASKFACE_HOME module load matlab/r2018a function run_maskface() { # do some validation of the ...
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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 # 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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# Set environment variables. export MKL_NUM_THREADS=10 export NUMEXPR_NUM_THREADS=10 export OMP_NUM_THREADS=10 # Define constants. REPEATS=20 PROCESSES=3 # DRN WITH GABA for baseline_ in "-0.080" "-0.060" "-0.040" "-0.020" "0.000" "0.020" "0.040" "0.060" "0.080"; do deriv_input=../../data/simulations/GIF_network/...
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Shell
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#!/bin/bash # Download/update RefSeq complete genomes echo "#### Updating RefSeq complete $1 genomes" wget -cNrv -t 45 -A *.gbk,*.fna "ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/$1*" -P . # Download/update RefSeq draft genomes echo "#### Updating RefSeq draft $1 genomes" wget -cNrv -t 45 -A *.gbk.tgz,*.fna.tgz "ftp://...
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Shell
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#!/bin/bash JOB_PREFIX=$1 START=$2 END=$3 QOS_INPUT=$4 QOS_OPTIONS=("leftover" "regular" "priority" "panic" "ds", "dev") QOS="regular" if [[ " ${QOS_OPTIONS[@]} " =~ " $QOS_INPUT " ]]; then if [[ $QOS_INPUT = "panic" ]]; then QOS_INPUT="panic mode" fi QOS=$QOS_INPUT fi JOBS_DIR=/groups/umcg-biogen/...
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Shell
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#!/bin/bash set -e # This script should be run after the build/tests have successfully completed # Prune any local tags that aren't on the remote git fetch --prune origin "+refs/tags/*:refs/tags/*" cd $WORKSPACE # Let's get version from maven MVNVER=`xmllint --xpath "/*[local-name()='project']/*[local-name()='versi...
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Shell
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#!/bin/bash # Copyright (c) 2021. Huawei Technologies Co., Ltd. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicab...
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Shell
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masif_root=$(git rev-parse --show-toplevel) masif_source=$masif_root/source/ export PYTHONPATH=$PYTHONPATH:$masif_source:. PDB_ID=$(echo $1| cut -d"_" -f1) CHAIN1=$(echo $1| cut -d"_" -f2) CHAIN2=$(echo $1| cut -d"_" -f3) # Load your environment here. python -W ignore $masif_source/data_preparation/00-pdb_download.py ...
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Shell
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#!/bin/bash # Lanzar desde deploy OPTIONSEMITTER="$1" OPTIONSCONSUMER="$2" OUTPUT="/tmp/fishubulogs" mkdir -p $OUTPUT if [[ "$(docker images -q fishubu-base:1.0.0 2> /dev/null)" == "" ]]; then docker build -f ../../dockers/fishubu/base/Dockerfile -t fishubu-base:1.0.0 ../../ docker build -f ../../dockers/fi...
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Shell
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#!/bin/bash # simple bash script to create a gui 'launcher'. # Location of the launcher can be changed, copy-pasted and moved around # location of the bruker2nifti folder cannot be moved!! # get directory bruker2 nifty, and move there. DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" PARENTDIR="$(dirname "$DI...
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Shell
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#!/bin/bash module load fsl source $FSLDIR/etc/fslconf/fsl.sh function run_mrideface() { # do some validation of the input folder # create output folder outfolder=$1"/mri_deface" echo mkdir -p $outfolder mkdir -p $outfolder # run fsl deface infile=$1"/std/image_std.nii.gz" outfile=$outfolder"/defaced.nii.g...
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Shell
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#!/usr/bin/env bash # Gets lattice oracles if [ $# -lt 3 ]; then echo "Specify lattice dir, symbol table and text file for partition" exit 1; fi latticeDir=$1 textFile=$3 symTable=$2 oracleDir=$latticeDir/oracle echo $latticeDir echo $oracleDir . ./path.sh if [ ! -f $textFile -o ! -f $symTable -o ! -d $la...
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Shell
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#!/usr/bin/env bash # No sanity checks here, they need to be added data=data/test dir=exp/sgmm2x_6a_mmi_b0.2/decode_test_fmllr_it1 lang=data/lang LMWT=10 [ -f ./path.sh ] && . ./path.sh mkdir -p $dir/oracle cmd=run.pl filter_cmd="utils/convert_ctm.pl $data/segments $data/reco2file_and_channel" name=`basename $data...
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Shell
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#!/usr/bin/env bash # Copyright 2018 AIShell-Foundation(Authors:Jiayu DU, Xingyu NA, Bengu WU, Hao ZHENG) # 2018 Beijing Shell Shell Tech. Co. Ltd. (Author: Hui BU) # Apache 2.0 # AISHELL-2 provides: # * a Mandarin speech corpus (~1000hrs), free for non-commercial research/education use # * a baseline rec...
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Shell
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law ...
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Shell
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#MOLGENIS nodes=1 ppn=1 mem=1gb walltime=0:10:00 ### variables to help adding to database (have to use weave) #string project #string uniqueID ### #string alignedBamOrCram #string cramFileDir echo "## "$(date)" Start $0" newCram=${cramFileDir}${uniqueID}.cram original_cram_size=$(stat -c %s $alignedBamOrCram) new_...
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Shell
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#!/bin/bash # Copyright 2021 Huawei Technologies Co., Ltd # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law...
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Shell
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#!/bin/bash #$ -cwd #$ -o log.$JOB_ID.out #$ -j y # Resources requested: #$ -l h_data=8G,h_rt=04:00:00 #$ -t 1-7 # Email address to notify #$ -M videlock@mail #$ -m bea #$ -V samples=$(cat ../samps${SGE_TASK_ID}) . /u/local/Modules/default/init/modules.sh module load picard_tools module load R/3.5.1 ## Create ...
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Shell
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#!/bin/sh # simple bash script to create a gui 'launcher'. # Location of the launcher can be changed, copy-pasted and moved around # location of the bruker2nifti folder cannot be moved!! DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" PARENTDIR="$(dirname "$DIR")" cd $PARENTDIR echo echo 'Creating virtual e...
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Shell
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# you can change cmd.sh depending on what type of queue you are using. # If you have no queueing system and want to run on a local machine, you # can change all instances 'queue.pl' to run.pl (but be careful and run # commands one by one: most recipes will exhaust the memory on your # machine). queue.pl works with Gri...
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Shell
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#!/bin/bash workdir=/data/share/htp/TRNP1/paper_data/protein output=$workdir/fastas/TRNP1_coding/coding_seqs_sep2_extended slurm=$output/slurms mkdir -p $output mkdir -p $slurm #cat /data/share/htp/TRNP1/paper_data/protein/data/temporary_genomes.txt | while read i j k; cat /data/share/htp/TRNP1/paper_data/protein/da...
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Shell
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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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#!/usr/bin/env bash # Copyright 2018 Hossein Hadian # 2018 Ashish Arora # Apache 2.0 # This script performs data augmentation. nj=4 cmd=run.pl feat_dim=40 fliplr=false verticle_shift=0 echo "$0 $@" . ./cmd.sh . ./path.sh . ./utils/parse_options.sh || exit 1; srcdir=$1 outdir=$2 datadir=$3 mkdir -p $d...
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#!/usr/bin/env bash # Step 05 — fetch the CARLA map/asset Content (~31GB). # # Two official methods. We use the GIT method (preferred for development / # committing content), per user choice: # # git clone -b master https://bitbucket.org/carla-simulator/carla-content \ # ${CARLA_UE4_ROOT}/Unreal/CarlaUE4/Conten...
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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 ...