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99b76ba2a1c85ccbd300666d333f00ccda88da62
biobox/target/executable/rsem/rsem_prepare_reference/rsem_prepare_reference
CI 99b76ba2a1 Build branch main with version main (237a2e3) 
Build pipeline: viash-hub.biobox.main-dqhhg

Source commit: 237a2e3a22

Source message: Fixes the typo raised in issue #132 (#157)

* Fixes the typo raised in issue #132

* Add changelog entry

* fix typo, modify script

---------

Co-authored-by: jakubmajercik <jakub.majercik@gmail.com>
2024-09-27 10:17:59 +00:00

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#!/usr/bin/env bash
# rsem_prepare_reference main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.
#
# Component authors:
# * Sai Nirmayi Yasa (author, maintainer)
set -e
if [ -z "$VIASH_TEMP" ]; then
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$TMP}
VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$TEMP}
VIASH_TEMP=${VIASH_TEMP:-/tmp}
fi
# define helper functions
# ViashQuote: put quotes around non flag values
# $1 : unquoted string
# return : possibly quoted string
# examples:
# ViashQuote --foo # returns --foo
# ViashQuote bar # returns 'bar'
# Viashquote --foo=bar # returns --foo='bar'
function ViashQuote {
if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
echo "$1" | sed "s#=\(.*\)#='\1'#"
elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
echo "$1"
else
echo "'$1'"
fi
}
# ViashRemoveFlags: Remove leading flag
# $1 : string with a possible leading flag
# return : string without possible leading flag
# examples:
# ViashRemoveFlags --foo=bar # returns bar
function ViashRemoveFlags {
echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
}
# ViashSourceDir: return the path of a bash file, following symlinks
# usage : ViashSourceDir ${BASH_SOURCE[0]}
# $1 : Should always be set to ${BASH_SOURCE[0]}
# returns : The absolute path of the bash file
function ViashSourceDir {
local source="$1"
while [ -h "$source" ]; do
local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
source="$(readlink "$source")"
[[ $source != /* ]] && source="$dir/$source"
done
cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
}
# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
# usage : ViashFindTargetDir 'ScriptPath'
# $1 : The location from where to start the upward search
# returns : The absolute path of the '.build.yaml' file
function ViashFindTargetDir {
local source="$1"
while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
source=${source%/*}
done
echo $source
}
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
VIASH_LOGCODE_EMERGENCY=0
VIASH_LOGCODE_ALERT=1
VIASH_LOGCODE_CRITICAL=2
VIASH_LOGCODE_ERROR=3
VIASH_LOGCODE_WARNING=4
VIASH_LOGCODE_NOTICE=5
VIASH_LOGCODE_INFO=6
VIASH_LOGCODE_DEBUG=7
VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
# ViashLog: Log events depending on the verbosity level
# usage: ViashLog 1 alert Oh no something went wrong!
# $1: required verbosity level
# $2: display tag
# $3+: messages to display
# stdout: Your input, prepended by '[$2] '.
function ViashLog {
local required_level="$1"
local display_tag="$2"
shift 2
if [ $VIASH_VERBOSITY -ge $required_level ]; then
>&2 echo "[$display_tag]" "$@"
fi
}
# ViashEmergency: log events when the system is unstable
# usage: ViashEmergency Oh no something went wrong.
# stdout: Your input, prepended by '[emergency] '.
function ViashEmergency {
ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
}
# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
# usage: ViashAlert Oh no something went wrong.
# stdout: Your input, prepended by '[alert] '.
function ViashAlert {
ViashLog $VIASH_LOGCODE_ALERT alert "$@"
}
# ViashCritical: log events when a critical condition occurs
# usage: ViashCritical Oh no something went wrong.
# stdout: Your input, prepended by '[critical] '.
function ViashCritical {
ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
}
# ViashError: log events when an error condition occurs
# usage: ViashError Oh no something went wrong.
# stdout: Your input, prepended by '[error] '.
function ViashError {
ViashLog $VIASH_LOGCODE_ERROR error "$@"
}
# ViashWarning: log potentially abnormal events
# usage: ViashWarning Something may have gone wrong.
# stdout: Your input, prepended by '[warning] '.
function ViashWarning {
ViashLog $VIASH_LOGCODE_WARNING warning "$@"
}
# ViashNotice: log significant but normal events
# usage: ViashNotice This just happened.
# stdout: Your input, prepended by '[notice] '.
function ViashNotice {
ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
}
# ViashInfo: log normal events
# usage: ViashInfo This just happened.
# stdout: Your input, prepended by '[info] '.
function ViashInfo {
ViashLog $VIASH_LOGCODE_INFO info "$@"
}
# ViashDebug: log all events, for debugging purposes
# usage: ViashDebug This just happened.
# stdout: Your input, prepended by '[debug] '.
function ViashDebug {
ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
}
# find source folder of this component
VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
# find the root of the built components & dependencies
VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
# define meta fields
VIASH_META_NAME="rsem_prepare_reference"
VIASH_META_FUNCTIONALITY_NAME="rsem_prepare_reference"
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "rsem_prepare_reference main"
echo ""
echo "RSEM is a software package for estimating gene and isoform expression levels"
echo "from RNA-Seq data. This component prepares transcript references for RSEM."
echo ""
echo "Inputs:"
echo " --reference_fasta_files"
echo " type: file, required parameter, multiple values allowed, file must exist"
echo " example: read1.fasta"
echo " Semi-colon separated list of Multi-FASTA formatted files OR a directory"
echo " name. If a directory name is specified, RSEM will read all files with"
echo " suffix \".fa\" or \".fasta\" in this directory. The files should contain"
echo " either the sequences of transcripts or an entire genome, depending on"
echo " whether the '--gtf' option is used."
echo ""
echo " --reference_name"
echo " type: string, required parameter"
echo " example: /ref/mm9"
echo " The name of the reference used. RSEM will generate several"
echo " reference-related files that are prefixed by this name. This name can"
echo " contain path information (e.g. '/ref/mm9')."
echo ""
echo "Outputs:"
echo " --output"
echo " type: file, required parameter, output, file must exist"
echo " Directory containing reference files generated by RSEM."
echo ""
echo "Other options:"
echo " --gtf"
echo " type: file, file must exist"
echo " example: annotations.gtf"
echo " Assume that 'reference_fasta_files' contains the sequence of a genome,"
echo " and extract transcript reference sequences using the gene annotations"
echo " specified in the GTF file. If this and '--gff3' options are not"
echo " provided, RSEM will assume 'reference_fasta_files' contains the"
echo " reference transcripts. In this case, RSEM assumes that name of each"
echo " sequence in the Multi-FASTA files is its transcript_id."
echo ""
echo " --gff3"
echo " type: file, file must exist"
echo " example: annotations.gff"
echo " GFF3 annotation file. Converted to GTF format with the file name"
echo " 'reference_name.gtf'. Please make sure that 'reference_name.gtf' does"
echo " not exist."
echo ""
echo " --gff3_rna_patterns"
echo " type: string, multiple values allowed"
echo " example: mRNA;rRNA"
echo " List of transcript categories (separated by semi-colon). Only"
echo " transcripts that match the string will be extracted."
echo ""
echo " --gff3_genes_as_transcripts"
echo " type: boolean_true"
echo " This option is designed for untypical organisms, such as viruses, whose"
echo " GFF3 files only contain genes. RSEM will assume each gene as a unique"
echo " transcript when it converts the GFF3 file into GTF format."
echo ""
echo " --trusted_sources"
echo " type: string, multiple values allowed"
echo " example: ENSEMBL;HAVANA"
echo " List of trusted sources (separated by semi-colon). Only transcripts"
echo " coming from these sources will be extracted. If this option is off, all"
echo " sources are accepted."
echo ""
echo " --transcript_to_gene_map"
echo " type: file, file must exist"
echo " example: isoforms.txt"
echo " Use information from this file to map from transcript (isoform) ids to"
echo " gene ids. Each line of this file should be of the form:"
echo " gene_id transcript_id"
echo " with the two fields separated by a tab character."
echo " If you are using a GTF file for the \"UCSC Genes\" gene set from the UCSC"
echo " Genome Browser, then the \"knownIsoforms.txt\" file (obtained from the"
echo " \"Downloads\" section of the UCSC Genome Browser site) is of this format."
echo " If this option is off, then the mapping of isoforms to genes depends on"
echo " whether the '--gtf' option is specified. If '--gtf' is specified, then"
echo " RSEM uses the \"gene_id\" and \"transcript_id\" attributes in the GTF file."
echo " Otherwise, RSEM assumes that each sequence in the reference sequence"
echo " files is a separate gene."
echo ""
echo " --allele_to_gene_map"
echo " type: file, file must exist"
echo " Use information from <file> to provide gene_id and transcript_id"
echo " information for each allele-specific transcript. Each line of <file>"
echo " should be of the form:"
echo " gene_id transcript_id allele_id"
echo " with the fields separated by a tab character."
echo " This option is designed for quantifying allele-specific expression. It"
echo " is only valid if '--gtf' option is not specified. allele_id should be"
echo " the sequence names presented in the Multi-FASTA-formatted files."
echo ""
echo " --polyA"
echo " type: boolean_true"
echo " Add poly(A) tails to the end of all reference isoforms. The length of"
echo " poly(A) tail added is specified by '--polyA-length' option. STAR aligner"
echo " users may not want to use this option."
echo ""
echo " --polyA_length"
echo " type: integer"
echo " example: 125"
echo " The length of the poly(A) tails to be added."
echo ""
echo " --no_polyA_subset"
echo " type: file, file must exist"
echo " example: transcript_ids.txt"
echo " Only meaningful if '--polyA' is specified. Do not add poly(A) tails to"
echo " those transcripts listed in this file containing a list of"
echo " transcript_ids."
echo ""
echo " --bowtie"
echo " type: boolean_true"
echo " Build Bowtie indices."
echo ""
echo " --bowtie2"
echo " type: boolean_true"
echo " Build Bowtie 2 indices."
echo ""
echo " --star"
echo " type: boolean_true"
echo " Build STAR indices."
echo ""
echo " --star_sjdboverhang"
echo " type: integer"
echo " example: 100"
echo " Length of the genomic sequence around annotated junction. It is only"
echo " used for STAR to build splice junctions database and not needed for"
echo " Bowtie or Bowtie2. It will be passed as the --sjdbOverhang option to"
echo " STAR. According to STAR's manual, its ideal value is max(ReadLength)-1,"
echo " e.g. for 2x101 paired-end reads, the ideal value is 101-1=100. In most"
echo " cases, the default value of 100 will work as well as the ideal value."
echo " (Default is 100)"
echo ""
echo " --hisat2_hca"
echo " type: boolean_true"
echo " Build HISAT2 indices on the transcriptome according to Human Cell Atlas"
echo " (HCA) SMART-Seq2 pipeline."
echo ""
echo " -q, --quiet"
echo " type: boolean_true"
echo " Suppress the output of logging information."
echo ""
echo "Prior-enhanced RSEM options:"
echo " --prep_pRSEM"
echo " type: boolean_true"
echo " A Boolean indicating whether to prepare reference files for pRSEM,"
echo " including building Bowtie indices for a genome and selecting training"
echo " set isoforms. The index files will be used for aligning ChIP-seq reads"
echo " in prior-enhanced RSEM and the training set isoforms will be used for"
echo " learning prior. A path to Bowtie executables and a mappability file in"
echo " bigWig format are required when this option is on. Currently, Bowtie2 is"
echo " not supported for prior-enhanced RSEM."
echo ""
echo " --mappability_bigwig_file"
echo " type: file, file must exist"
echo " Full path to a whole-genome mappability file in bigWig format. This file"
echo " is required for running prior-enhanced RSEM. It is used for selecting a"
echo " training set of isoforms for prior-learning. This file can be either"
echo " downloaded from UCSC Genome Browser or generated by GEM (Derrien et al.,"
echo " 2012, PLoS One)."
}
# initialise variables
VIASH_MODE='run'
VIASH_ENGINE_ID='docker'
######## Helper functions for setting up Docker images for viash ########
# expects: ViashDockerBuild
# ViashDockerInstallationCheck: check whether Docker is installed correctly
#
# examples:
# ViashDockerInstallationCheck
function ViashDockerInstallationCheck {
ViashDebug "Checking whether Docker is installed"
if [ ! command -v docker &> /dev/null ]; then
ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
exit 1
fi
ViashDebug "Checking whether the Docker daemon is running"
local save=$-; set +e
local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
ViashCritical "- Try running 'dockerd' in the command line"
ViashCritical "- See https://docs.docker.com/config/daemon/"
exit 1
fi
}
# ViashDockerRemoteTagCheck: check whether a Docker image is available
# on a remote. Assumes `docker login` has been performed, if relevant.
#
# $1 : image identifier with format `[registry/]image[:tag]`
# exit code $? : whether or not the image was found
# examples:
# ViashDockerRemoteTagCheck python:latest
# echo $? # returns '0'
# ViashDockerRemoteTagCheck sdaizudceahifu
# echo $? # returns '1'
function ViashDockerRemoteTagCheck {
docker manifest inspect $1 > /dev/null 2> /dev/null
}
# ViashDockerLocalTagCheck: check whether a Docker image is available locally
#
# $1 : image identifier with format `[registry/]image[:tag]`
# exit code $? : whether or not the image was found
# examples:
# docker pull python:latest
# ViashDockerLocalTagCheck python:latest
# echo $? # returns '0'
# ViashDockerLocalTagCheck sdaizudceahifu
# echo $? # returns '1'
function ViashDockerLocalTagCheck {
[ -n "$(docker images -q $1)" ]
}
# ViashDockerPull: pull a Docker image
#
# $1 : image identifier with format `[registry/]image[:tag]`
# exit code $? : whether or not the image was found
# examples:
# ViashDockerPull python:latest
# echo $? # returns '0'
# ViashDockerPull sdaizudceahifu
# echo $? # returns '1'
function ViashDockerPull {
ViashNotice "Checking if Docker image is available at '$1'"
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
docker pull $1 && return 0 || return 1
else
local save=$-; set +e
docker pull $1 2> /dev/null > /dev/null
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
fi
return $out
fi
}
# ViashDockerPush: push a Docker image
#
# $1 : image identifier with format `[registry/]image[:tag]`
# exit code $? : whether or not the image was found
# examples:
# ViashDockerPush python:latest
# echo $? # returns '0'
# ViashDockerPush sdaizudceahifu
# echo $? # returns '1'
function ViashDockerPush {
ViashNotice "Pushing image to '$1'"
local save=$-; set +e
local out
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
docker push $1
out=$?
else
docker push $1 2> /dev/null > /dev/null
out=$?
fi
[[ $save =~ e ]] && set -e
if [ $out -eq 0 ]; then
ViashNotice "Container '$1' push succeeded."
else
ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
fi
return $out
}
# ViashDockerPullElseBuild: pull a Docker image, else build it
#
# $1 : image identifier with format `[registry/]image[:tag]`
# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument.
# examples:
# ViashDockerPullElseBuild mynewcomponent
function ViashDockerPullElseBuild {
local save=$-; set +e
ViashDockerPull $1
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashDockerBuild $@
fi
}
# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
#
# $1 : image identifier with format `[registry/]image[:tag]`
# $2 : docker setup strategy, see DockerSetupStrategy.scala
# examples:
# ViashDockerSetup mynewcomponent alwaysbuild
function ViashDockerSetup {
local image_id="$1"
local setup_strategy="$2"
if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
ViashDockerPull $image_id
elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
local save=$-; set +e
ViashDockerLocalTagCheck $image_id
local outCheck=$?
[[ $save =~ e ]] && set -e
if [ $outCheck -eq 0 ]; then
ViashInfo "Image $image_id already exists"
elif [ "$setup_strategy" == "ifneedbebuild" ]; then
ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "ifneedbepull" ]; then
ViashDockerPull $image_id
elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
else
ViashError "Unrecognised Docker strategy: $setup_strategy"
exit 1
fi
elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
ViashDockerPush "$image_id"
elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
local save=$-; set +e
ViashDockerRemoteTagCheck $image_id
local outCheck=$?
[[ $save =~ e ]] && set -e
if [ $outCheck -eq 0 ]; then
ViashNotice "Container '$image_id' exists, doing nothing."
else
ViashNotice "Container '$image_id' does not yet exist."
ViashDockerPush "$image_id"
fi
elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
ViashNotice "Skipping setup."
else
ViashError "Unrecognised Docker strategy: $setup_strategy"
exit 1
fi
}
# ViashDockerCheckCommands: Check whether a docker container has the required commands
#
# $1 : image identifier with format `[registry/]image[:tag]`
# $@ : commands to verify being present
# examples:
# ViashDockerCheckCommands bash:4.0 bash ps foo
function ViashDockerCheckCommands {
local image_id="$1"
shift 1
local commands="$@"
local save=$-; set +e
local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
local outCheck=$?
[[ $save =~ e ]] && set -e
if [ $outCheck -ne 0 ]; then
ViashError "Docker container '$image_id' does not contain command '$missing'."
exit 1
fi
}
# ViashDockerBuild: build a docker image
# $1 : image identifier with format `[registry/]image[:tag]`
# $... : additional arguments to pass to docker build
# $VIASH_META_TEMP_DIR : temporary directory to store dockerfile & optional resources in
# $VIASH_META_NAME : name of the component
# $VIASH_META_RESOURCES_DIR : directory containing the resources
# $VIASH_VERBOSITY : verbosity level
# exit code $? : whether or not the image was built successfully
function ViashDockerBuild {
local image_id="$1"
shift 1
# create temporary directory to store dockerfile & optional resources in
local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
local dockerfile="$tmpdir/Dockerfile"
function clean_up {
rm -rf "$tmpdir"
}
trap clean_up EXIT
# store dockerfile and resources
ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
# generate the build command
local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
# build the container
ViashNotice "Building container '$image_id' with Dockerfile"
ViashInfo "$docker_build_cmd"
local save=$-; set +e
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
eval $docker_build_cmd
else
eval $docker_build_cmd &> "$tmpdir/docker_build.log"
fi
# check exit code
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashError "Error occurred while building container '$image_id'"
if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
ViashError "Transcript: --------------------------------"
cat "$tmpdir/docker_build.log"
ViashError "End of transcript --------------------------"
fi
exit 1
fi
}
######## End of helper functions for setting up Docker images for viash ########
# ViashDockerFile: print the dockerfile to stdout
# $1 : engine identifier
# return : dockerfile required to run this component
# examples:
# ViashDockerFile
function ViashDockerfile {
local engine_id="$1"
if [[ "$engine_id" == "docker" ]]; then
cat << 'VIASHDOCKER'
FROM ubuntu:22.04
ENTRYPOINT []
RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential gcc g++ make wget zlib1g-dev unzip xxd perl r-base bowtie2 pip git && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "bowtie"
ENV STAR_VERSION=2.7.11b
ENV RSEM_VERSION=1.3.3
ENV BOWTIE_VERSION=1.3.1
ENV TZ=Europe/Brussels
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && \
cd /tmp && \
wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${STAR_VERSION}.zip && \
unzip ${STAR_VERSION}.zip && \
cd STAR-${STAR_VERSION}/source && \
make STARstatic CXXFLAGS_SIMD=-std=c++11 && \
cp STAR /usr/local/bin && \
cd /tmp && \
wget --no-check-certificate https://github.com/deweylab/RSEM/archive/refs/tags/v${RSEM_VERSION}.zip && \
unzip v${RSEM_VERSION}.zip && \
cd RSEM-${RSEM_VERSION} && \
make && \
make install && \
cd /tmp && \
wget --no-check-certificate -O bowtie-${BOWTIE_VERSION}-linux-x86_64.zip https://sourceforge.net/projects/bowtie-bio/files/bowtie/${BOWTIE_VERSION}/bowtie-${BOWTIE_VERSION}-linux-x86_64.zip/download && \
unzip bowtie-${BOWTIE_VERSION}-linux-x86_64.zip && \
cp bowtie-${BOWTIE_VERSION}-linux-x86_64/bowtie* /usr/local/bin && \
cd /tmp && \
git clone https://github.com/DaehwanKimLab/hisat2.git /tmp/hisat2 && \
cd /tmp/hisat2 && \
make && \
cp -r hisat2* /usr/local/bin && \
cd && \
rm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip /tmp/bowtie-${BOWTIE_VERSION}-linux-x86_64 /tmp/hisat2 && \
apt-get --purge autoremove -y ${PACKAGES} && \
apt-get clean
RUN echo "RSEM: `rsem-calculate-expression --version | sed -e 's/Current version: RSEM v//g'`" > /var/software_versions.txt && \
echo "STAR: `STAR --version`" >> /var/software_versions.txt && \
echo "bowtie2: `bowtie2 --version | grep -oP '\d+\.\d+\.\d+'`" >> /var/software_versions.txt && \
echo "bowtie: `bowtie --version | grep -oP 'bowtie-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt && \
echo "HISAT2: `hisat2 --version | grep -oP 'hisat2-align-s version \K\d+\.\d+\.\d+'`" >> /var/software_versions.txt
LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_prepare_reference"
LABEL org.opencontainers.image.created="2024-09-27T09:55:17Z"
LABEL org.opencontainers.image.source="https://github.com/deweylab/RSEM"
LABEL org.opencontainers.image.revision="237a2e3a229ee589d1ebbc282526f87398e26f58"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
fi
}
# ViashDockerBuildArgs: return the arguments to pass to docker build
# $1 : engine identifier
# return : arguments to pass to docker build
function ViashDockerBuildArgs {
local engine_id="$1"
if [[ "$engine_id" == "docker" ]]; then
echo ""
fi
}
# ViashAbsolutePath: generate absolute path from relative path
# borrowed from https://stackoverflow.com/a/21951256
# $1 : relative filename
# return : absolute path
# examples:
# ViashAbsolutePath some_file.txt # returns /path/to/some_file.txt
# ViashAbsolutePath /foo/bar/.. # returns /foo
function ViashAbsolutePath {
local thePath
local parr
local outp
local len
if [[ ! "$1" =~ ^/ ]]; then
thePath="$PWD/$1"
else
thePath="$1"
fi
echo "$thePath" | (
IFS=/
read -a parr
declare -a outp
for i in "${parr[@]}"; do
case "$i" in
''|.) continue ;;
..)
len=${#outp[@]}
if ((len==0)); then
continue
else
unset outp[$((len-1))]
fi
;;
*)
len=${#outp[@]}
outp[$len]="$i"
;;
esac
done
echo /"${outp[*]}"
)
}
# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
# $1 : The parameter value
# returns : New parameter
# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
# examples:
# ViashDockerAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar'
# ViashDockerAutodetectMountArg /path/to/bar # returns '--volume="/path/to:/viash_automount/path/to"'
function ViashDockerAutodetectMount {
local abs_path=$(ViashAbsolutePath "$1")
local mount_source
local base_name
if [ -d "$abs_path" ]; then
mount_source="$abs_path"
base_name=""
else
mount_source=`dirname "$abs_path"`
base_name=`basename "$abs_path"`
fi
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
if [ -z "$base_name" ]; then
echo "$mount_target"
else
echo "$mount_target/$base_name"
fi
}
function ViashDockerAutodetectMountArg {
local abs_path=$(ViashAbsolutePath "$1")
local mount_source
local base_name
if [ -d "$abs_path" ]; then
mount_source="$abs_path"
base_name=""
else
mount_source=`dirname "$abs_path"`
base_name=`basename "$abs_path"`
fi
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
echo "--volume=\"$mount_source:$mount_target\""
}
function ViashDockerStripAutomount {
local abs_path=$(ViashAbsolutePath "$1")
echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
}
# initialise variables
VIASH_DIRECTORY_MOUNTS=()
# configure default docker automount prefix if it is unset
if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
# initialise array
VIASH_POSITIONAL_ARGS=''
while [[ $# -gt 0 ]]; do
case "$1" in
-h|--help)
ViashHelp
exit
;;
---v|---verbose)
let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
shift 1
;;
---verbosity)
VIASH_VERBOSITY="$2"
shift 2
;;
---verbosity=*)
VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
shift 1
;;
--version)
echo "rsem_prepare_reference main"
exit
;;
--reference_fasta_files)
if [ -z "$VIASH_PAR_REFERENCE_FASTA_FILES" ]; then
VIASH_PAR_REFERENCE_FASTA_FILES="$2"
else
VIASH_PAR_REFERENCE_FASTA_FILES="$VIASH_PAR_REFERENCE_FASTA_FILES;""$2"
fi
[ $# -lt 2 ] && ViashError Not enough arguments passed to --reference_fasta_files. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--reference_fasta_files=*)
if [ -z "$VIASH_PAR_REFERENCE_FASTA_FILES" ]; then
VIASH_PAR_REFERENCE_FASTA_FILES=$(ViashRemoveFlags "$1")
else
VIASH_PAR_REFERENCE_FASTA_FILES="$VIASH_PAR_REFERENCE_FASTA_FILES;"$(ViashRemoveFlags "$1")
fi
shift 1
;;
--reference_name)
[ -n "$VIASH_PAR_REFERENCE_NAME" ] && ViashError Bad arguments for option \'--reference_name\': \'$VIASH_PAR_REFERENCE_NAME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REFERENCE_NAME="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --reference_name. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--reference_name=*)
[ -n "$VIASH_PAR_REFERENCE_NAME" ] && ViashError Bad arguments for option \'--reference_name=*\': \'$VIASH_PAR_REFERENCE_NAME\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_REFERENCE_NAME=$(ViashRemoveFlags "$1")
shift 1
;;
--output)
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPUT="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--output=*)
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
shift 1
;;
--gtf)
[ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_GTF="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--gtf=*)
[ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf=*\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_GTF=$(ViashRemoveFlags "$1")
shift 1
;;
--gff3)
[ -n "$VIASH_PAR_GFF3" ] && ViashError Bad arguments for option \'--gff3\': \'$VIASH_PAR_GFF3\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_GFF3="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --gff3. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--gff3=*)
[ -n "$VIASH_PAR_GFF3" ] && ViashError Bad arguments for option \'--gff3=*\': \'$VIASH_PAR_GFF3\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_GFF3=$(ViashRemoveFlags "$1")
shift 1
;;
--gff3_rna_patterns)
if [ -z "$VIASH_PAR_GFF3_RNA_PATTERNS" ]; then
VIASH_PAR_GFF3_RNA_PATTERNS="$2"
else
VIASH_PAR_GFF3_RNA_PATTERNS="$VIASH_PAR_GFF3_RNA_PATTERNS;""$2"
fi
[ $# -lt 2 ] && ViashError Not enough arguments passed to --gff3_rna_patterns. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--gff3_rna_patterns=*)
if [ -z "$VIASH_PAR_GFF3_RNA_PATTERNS" ]; then
VIASH_PAR_GFF3_RNA_PATTERNS=$(ViashRemoveFlags "$1")
else
VIASH_PAR_GFF3_RNA_PATTERNS="$VIASH_PAR_GFF3_RNA_PATTERNS;"$(ViashRemoveFlags "$1")
fi
shift 1
;;
--gff3_genes_as_transcripts)
[ -n "$VIASH_PAR_GFF3_GENES_AS_TRANSCRIPTS" ] && ViashError Bad arguments for option \'--gff3_genes_as_transcripts\': \'$VIASH_PAR_GFF3_GENES_AS_TRANSCRIPTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_GFF3_GENES_AS_TRANSCRIPTS=true
shift 1
;;
--trusted_sources)
if [ -z "$VIASH_PAR_TRUSTED_SOURCES" ]; then
VIASH_PAR_TRUSTED_SOURCES="$2"
else
VIASH_PAR_TRUSTED_SOURCES="$VIASH_PAR_TRUSTED_SOURCES;""$2"
fi
[ $# -lt 2 ] && ViashError Not enough arguments passed to --trusted_sources. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--trusted_sources=*)
if [ -z "$VIASH_PAR_TRUSTED_SOURCES" ]; then
VIASH_PAR_TRUSTED_SOURCES=$(ViashRemoveFlags "$1")
else
VIASH_PAR_TRUSTED_SOURCES="$VIASH_PAR_TRUSTED_SOURCES;"$(ViashRemoveFlags "$1")
fi
shift 1
;;
--transcript_to_gene_map)
[ -n "$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP" ] && ViashError Bad arguments for option \'--transcript_to_gene_map\': \'$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_TRANSCRIPT_TO_GENE_MAP="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --transcript_to_gene_map. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--transcript_to_gene_map=*)
[ -n "$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP" ] && ViashError Bad arguments for option \'--transcript_to_gene_map=*\': \'$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_TRANSCRIPT_TO_GENE_MAP=$(ViashRemoveFlags "$1")
shift 1
;;
--allele_to_gene_map)
[ -n "$VIASH_PAR_ALLELE_TO_GENE_MAP" ] && ViashError Bad arguments for option \'--allele_to_gene_map\': \'$VIASH_PAR_ALLELE_TO_GENE_MAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ALLELE_TO_GENE_MAP="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --allele_to_gene_map. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--allele_to_gene_map=*)
[ -n "$VIASH_PAR_ALLELE_TO_GENE_MAP" ] && ViashError Bad arguments for option \'--allele_to_gene_map=*\': \'$VIASH_PAR_ALLELE_TO_GENE_MAP\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ALLELE_TO_GENE_MAP=$(ViashRemoveFlags "$1")
shift 1
;;
--polyA)
[ -n "$VIASH_PAR_POLYA" ] && ViashError Bad arguments for option \'--polyA\': \'$VIASH_PAR_POLYA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_POLYA=true
shift 1
;;
--polyA_length)
[ -n "$VIASH_PAR_POLYA_LENGTH" ] && ViashError Bad arguments for option \'--polyA_length\': \'$VIASH_PAR_POLYA_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_POLYA_LENGTH="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --polyA_length. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--polyA_length=*)
[ -n "$VIASH_PAR_POLYA_LENGTH" ] && ViashError Bad arguments for option \'--polyA_length=*\': \'$VIASH_PAR_POLYA_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_POLYA_LENGTH=$(ViashRemoveFlags "$1")
shift 1
;;
--no_polyA_subset)
[ -n "$VIASH_PAR_NO_POLYA_SUBSET" ] && ViashError Bad arguments for option \'--no_polyA_subset\': \'$VIASH_PAR_NO_POLYA_SUBSET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_POLYA_SUBSET="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --no_polyA_subset. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--no_polyA_subset=*)
[ -n "$VIASH_PAR_NO_POLYA_SUBSET" ] && ViashError Bad arguments for option \'--no_polyA_subset=*\': \'$VIASH_PAR_NO_POLYA_SUBSET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_NO_POLYA_SUBSET=$(ViashRemoveFlags "$1")
shift 1
;;
--bowtie)
[ -n "$VIASH_PAR_BOWTIE" ] && ViashError Bad arguments for option \'--bowtie\': \'$VIASH_PAR_BOWTIE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BOWTIE=true
shift 1
;;
--bowtie2)
[ -n "$VIASH_PAR_BOWTIE2" ] && ViashError Bad arguments for option \'--bowtie2\': \'$VIASH_PAR_BOWTIE2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BOWTIE2=true
shift 1
;;
--star)
[ -n "$VIASH_PAR_STAR" ] && ViashError Bad arguments for option \'--star\': \'$VIASH_PAR_STAR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR=true
shift 1
;;
--star_sjdboverhang)
[ -n "$VIASH_PAR_STAR_SJDBOVERHANG" ] && ViashError Bad arguments for option \'--star_sjdboverhang\': \'$VIASH_PAR_STAR_SJDBOVERHANG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_SJDBOVERHANG="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --star_sjdboverhang. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--star_sjdboverhang=*)
[ -n "$VIASH_PAR_STAR_SJDBOVERHANG" ] && ViashError Bad arguments for option \'--star_sjdboverhang=*\': \'$VIASH_PAR_STAR_SJDBOVERHANG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STAR_SJDBOVERHANG=$(ViashRemoveFlags "$1")
shift 1
;;
--hisat2_hca)
[ -n "$VIASH_PAR_HISAT2_HCA" ] && ViashError Bad arguments for option \'--hisat2_hca\': \'$VIASH_PAR_HISAT2_HCA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_HISAT2_HCA=true
shift 1
;;
--quiet)
[ -n "$VIASH_PAR_QUIET" ] && ViashError Bad arguments for option \'--quiet\': \'$VIASH_PAR_QUIET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_QUIET=true
shift 1
;;
-q)
[ -n "$VIASH_PAR_QUIET" ] && ViashError Bad arguments for option \'-q\': \'$VIASH_PAR_QUIET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_QUIET=true
shift 1
;;
--prep_pRSEM)
[ -n "$VIASH_PAR_PREP_PRSEM" ] && ViashError Bad arguments for option \'--prep_pRSEM\': \'$VIASH_PAR_PREP_PRSEM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_PREP_PRSEM=true
shift 1
;;
--mappability_bigwig_file)
[ -n "$VIASH_PAR_MAPPABILITY_BIGWIG_FILE" ] && ViashError Bad arguments for option \'--mappability_bigwig_file\': \'$VIASH_PAR_MAPPABILITY_BIGWIG_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MAPPABILITY_BIGWIG_FILE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --mappability_bigwig_file. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--mappability_bigwig_file=*)
[ -n "$VIASH_PAR_MAPPABILITY_BIGWIG_FILE" ] && ViashError Bad arguments for option \'--mappability_bigwig_file=*\': \'$VIASH_PAR_MAPPABILITY_BIGWIG_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MAPPABILITY_BIGWIG_FILE=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
;;
---engine=*)
VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
shift 1
;;
---setup)
VIASH_MODE='setup'
VIASH_SETUP_STRATEGY="$2"
shift 2
;;
---setup=*)
VIASH_MODE='setup'
VIASH_SETUP_STRATEGY="$(ViashRemoveFlags "$1")"
shift 1
;;
---dockerfile)
VIASH_MODE='dockerfile'
shift 1
;;
---docker_run_args)
VIASH_DOCKER_RUN_ARGS+=("$2")
shift 2
;;
---docker_run_args=*)
VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
shift 1
;;
---docker_image_id)
VIASH_MODE='docker_image_id'
shift 1
;;
---debug)
VIASH_MODE='debug'
shift 1
;;
---cpus)
[ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_CPUS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
---cpus=*)
[ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_CPUS=$(ViashRemoveFlags "$1")
shift 1
;;
---memory)
[ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_MEMORY="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
---memory=*)
[ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
shift 1
;;
*) # positional arg or unknown option
# since the positional args will be eval'd, can we always quote, instead of using ViashQuote
VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
[[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
shift # past argument
;;
esac
done
# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
VIASH_ENGINE_TYPE='native'
elif [ "$VIASH_ENGINE_ID" == "docker" ] ; then
VIASH_ENGINE_TYPE='docker'
else
ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: docker, native."
exit 1
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# check if docker is installed properly
ViashDockerInstallationCheck
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/biobox/rsem/rsem_prepare_reference:main'
fi
# print dockerfile
if [ "$VIASH_MODE" == "dockerfile" ]; then
ViashDockerfile "$VIASH_ENGINE_ID"
exit 0
elif [ "$VIASH_MODE" == "docker_image_id" ]; then
echo "$VIASH_DOCKER_IMAGE_ID"
exit 0
# enter docker container
elif [[ "$VIASH_MODE" == "debug" ]]; then
VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} -v '$(pwd)':/pwd --workdir /pwd -t $VIASH_DOCKER_IMAGE_ID"
ViashNotice "+ $VIASH_CMD"
eval $VIASH_CMD
exit
# build docker image
elif [ "$VIASH_MODE" == "setup" ]; then
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" "$VIASH_SETUP_STRATEGY"
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
exit 0
fi
# check if docker image exists
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" 'ps' 'bash'
fi
# setting computational defaults
# helper function for parsing memory strings
function ViashMemoryAsBytes {
local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
if [[ $memory =~ $memory_regex ]]; then
local number=${memory/[^0-9]*/}
local symbol=${memory/*[0-9]/}
case $symbol in
b) memory_b=$number ;;
kb|k) memory_b=$(( $number * 1000 )) ;;
mb|m) memory_b=$(( $number * 1000 * 1000 )) ;;
gb|g) memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
tb|t) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
pb|p) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
kib|ki) memory_b=$(( $number * 1024 )) ;;
mib|mi) memory_b=$(( $number * 1024 * 1024 )) ;;
gib|gi) memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
tib|ti) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
pib|pi) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
esac
echo "$memory_b"
fi
}
# compute memory in different units
if [ ! -z ${VIASH_META_MEMORY+x} ]; then
VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
# do not define other variables if memory_b is an empty string
if [ ! -z "$VIASH_META_MEMORY_B" ]; then
VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
else
# unset memory if string is empty
unset $VIASH_META_MEMORY_B
fi
fi
# unset nproc if string is empty
if [ -z "$VIASH_META_CPUS" ]; then
unset $VIASH_META_CPUS
fi
# check whether required parameters exist
if [ -z ${VIASH_PAR_REFERENCE_FASTA_FILES+x} ]; then
ViashError '--reference_fasta_files' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_PAR_REFERENCE_NAME+x} ]; then
ViashError '--reference_name' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_PAR_OUTPUT+x} ]; then
ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
# filling in defaults
if [ -z ${VIASH_PAR_GFF3_GENES_AS_TRANSCRIPTS+x} ]; then
VIASH_PAR_GFF3_GENES_AS_TRANSCRIPTS="false"
fi
if [ -z ${VIASH_PAR_POLYA+x} ]; then
VIASH_PAR_POLYA="false"
fi
if [ -z ${VIASH_PAR_BOWTIE+x} ]; then
VIASH_PAR_BOWTIE="false"
fi
if [ -z ${VIASH_PAR_BOWTIE2+x} ]; then
VIASH_PAR_BOWTIE2="false"
fi
if [ -z ${VIASH_PAR_STAR+x} ]; then
VIASH_PAR_STAR="false"
fi
if [ -z ${VIASH_PAR_HISAT2_HCA+x} ]; then
VIASH_PAR_HISAT2_HCA="false"
fi
if [ -z ${VIASH_PAR_QUIET+x} ]; then
VIASH_PAR_QUIET="false"
fi
if [ -z ${VIASH_PAR_PREP_PRSEM+x} ]; then
VIASH_PAR_PREP_PRSEM="false"
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_REFERENCE_FASTA_FILES" ]; then
IFS=';'
set -f
for file in $VIASH_PAR_REFERENCE_FASTA_FILES; do
unset IFS
if [ ! -e "$file" ]; then
ViashError "Input file '$file' does not exist."
exit 1
fi
done
set +f
fi
if [ ! -z "$VIASH_PAR_GTF" ] && [ ! -e "$VIASH_PAR_GTF" ]; then
ViashError "Input file '$VIASH_PAR_GTF' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_GFF3" ] && [ ! -e "$VIASH_PAR_GFF3" ]; then
ViashError "Input file '$VIASH_PAR_GFF3' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP" ] && [ ! -e "$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP" ]; then
ViashError "Input file '$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_ALLELE_TO_GENE_MAP" ] && [ ! -e "$VIASH_PAR_ALLELE_TO_GENE_MAP" ]; then
ViashError "Input file '$VIASH_PAR_ALLELE_TO_GENE_MAP' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_NO_POLYA_SUBSET" ] && [ ! -e "$VIASH_PAR_NO_POLYA_SUBSET" ]; then
ViashError "Input file '$VIASH_PAR_NO_POLYA_SUBSET' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_MAPPABILITY_BIGWIG_FILE" ] && [ ! -e "$VIASH_PAR_MAPPABILITY_BIGWIG_FILE" ]; then
ViashError "Input file '$VIASH_PAR_MAPPABILITY_BIGWIG_FILE' does not exist."
exit 1
fi
# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_GFF3_GENES_AS_TRANSCRIPTS" ]]; then
if ! [[ "$VIASH_PAR_GFF3_GENES_AS_TRANSCRIPTS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--gff3_genes_as_transcripts' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_POLYA" ]]; then
if ! [[ "$VIASH_PAR_POLYA" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--polyA' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_POLYA_LENGTH" ]]; then
if ! [[ "$VIASH_PAR_POLYA_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--polyA_length' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_BOWTIE" ]]; then
if ! [[ "$VIASH_PAR_BOWTIE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--bowtie' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_BOWTIE2" ]]; then
if ! [[ "$VIASH_PAR_BOWTIE2" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--bowtie2' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_STAR" ]]; then
if ! [[ "$VIASH_PAR_STAR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--star' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_STAR_SJDBOVERHANG" ]]; then
if ! [[ "$VIASH_PAR_STAR_SJDBOVERHANG" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--star_sjdboverhang' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_HISAT2_HCA" ]]; then
if ! [[ "$VIASH_PAR_HISAT2_HCA" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--hisat2_hca' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_QUIET" ]]; then
if ! [[ "$VIASH_PAR_QUIET" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--quiet' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_PREP_PRSEM" ]]; then
if ! [[ "$VIASH_PAR_PREP_PRSEM" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--prep_pRSEM' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
if [ "$VIASH_MODE" == "run" ]; then
VIASH_CMD="bash"
else
ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
exit 1
fi
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# detect volumes from file arguments
VIASH_CHOWN_VARS=()
if [ ! -z "$VIASH_PAR_REFERENCE_FASTA_FILES" ]; then
VIASH_TEST_REFERENCE_FASTA_FILES=()
IFS=';'
for var in $VIASH_PAR_REFERENCE_FASTA_FILES; do
unset IFS
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
var=$(ViashDockerAutodetectMount "$var")
VIASH_TEST_REFERENCE_FASTA_FILES+=( "$var" )
done
VIASH_PAR_REFERENCE_FASTA_FILES=$(IFS=';' ; echo "${VIASH_TEST_REFERENCE_FASTA_FILES[*]}")
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
fi
if [ ! -z "$VIASH_PAR_GTF" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GTF")" )
VIASH_PAR_GTF=$(ViashDockerAutodetectMount "$VIASH_PAR_GTF")
fi
if [ ! -z "$VIASH_PAR_GFF3" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GFF3")" )
VIASH_PAR_GFF3=$(ViashDockerAutodetectMount "$VIASH_PAR_GFF3")
fi
if [ ! -z "$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP")" )
VIASH_PAR_TRANSCRIPT_TO_GENE_MAP=$(ViashDockerAutodetectMount "$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP")
fi
if [ ! -z "$VIASH_PAR_ALLELE_TO_GENE_MAP" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_ALLELE_TO_GENE_MAP")" )
VIASH_PAR_ALLELE_TO_GENE_MAP=$(ViashDockerAutodetectMount "$VIASH_PAR_ALLELE_TO_GENE_MAP")
fi
if [ ! -z "$VIASH_PAR_NO_POLYA_SUBSET" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_NO_POLYA_SUBSET")" )
VIASH_PAR_NO_POLYA_SUBSET=$(ViashDockerAutodetectMount "$VIASH_PAR_NO_POLYA_SUBSET")
fi
if [ ! -z "$VIASH_PAR_MAPPABILITY_BIGWIG_FILE" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_MAPPABILITY_BIGWIG_FILE")" )
VIASH_PAR_MAPPABILITY_BIGWIG_FILE=$(ViashDockerAutodetectMount "$VIASH_PAR_MAPPABILITY_BIGWIG_FILE")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
fi
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_EXECUTABLE")" )
VIASH_META_EXECUTABLE=$(ViashDockerAutodetectMount "$VIASH_META_EXECUTABLE")
fi
if [ ! -z "$VIASH_META_CONFIG" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_CONFIG")" )
VIASH_META_CONFIG=$(ViashDockerAutodetectMount "$VIASH_META_CONFIG")
fi
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_TEMP_DIR")" )
VIASH_META_TEMP_DIR=$(ViashDockerAutodetectMount "$VIASH_META_TEMP_DIR")
fi
# get unique mounts
VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_DIRECTORY_MOUNTS[@]}"; do echo "$val"; done | sort -u))
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# change file ownership
function ViashPerformChown {
if (( ${#VIASH_CHOWN_VARS[@]} )); then
set +e
VIASH_CMD="docker run --entrypoint=bash --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID -c 'chown $(id -u):$(id -g) --silent --recursive ${VIASH_CHOWN_VARS[@]}'"
ViashDebug "+ $VIASH_CMD"
eval $VIASH_CMD
set -e
fi
}
trap ViashPerformChown EXIT
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# helper function for filling in extra docker args
if [ ! -z "$VIASH_META_MEMORY_B" ]; then
VIASH_DOCKER_RUN_ARGS+=("--memory=${VIASH_META_MEMORY_B}")
fi
if [ ! -z "$VIASH_META_CPUS" ]; then
VIASH_DOCKER_RUN_ARGS+=("--cpus=${VIASH_META_CPUS}")
fi
fi
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
VIASH_CMD="docker run --entrypoint=bash ${VIASH_DOCKER_RUN_ARGS[@]} ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_DOCKER_IMAGE_ID"
fi
# set dependency paths
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-rsem_prepare_reference-XXXXXX").sh
function clean_up {
rm "\$tempscript"
}
function interrupt {
echo -e "\nCTRL-C Pressed..."
exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_REFERENCE_FASTA_FILES+x} ]; then echo "${VIASH_PAR_REFERENCE_FASTA_FILES}" | sed "s#'#'\"'\"'#g;s#.*#par_reference_fasta_files='&'#" ; else echo "# par_reference_fasta_files="; fi )
$( if [ ! -z ${VIASH_PAR_REFERENCE_NAME+x} ]; then echo "${VIASH_PAR_REFERENCE_NAME}" | sed "s#'#'\"'\"'#g;s#.*#par_reference_name='&'#" ; else echo "# par_reference_name="; fi )
$( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
$( if [ ! -z ${VIASH_PAR_GTF+x} ]; then echo "${VIASH_PAR_GTF}" | sed "s#'#'\"'\"'#g;s#.*#par_gtf='&'#" ; else echo "# par_gtf="; fi )
$( if [ ! -z ${VIASH_PAR_GFF3+x} ]; then echo "${VIASH_PAR_GFF3}" | sed "s#'#'\"'\"'#g;s#.*#par_gff3='&'#" ; else echo "# par_gff3="; fi )
$( if [ ! -z ${VIASH_PAR_GFF3_RNA_PATTERNS+x} ]; then echo "${VIASH_PAR_GFF3_RNA_PATTERNS}" | sed "s#'#'\"'\"'#g;s#.*#par_gff3_rna_patterns='&'#" ; else echo "# par_gff3_rna_patterns="; fi )
$( if [ ! -z ${VIASH_PAR_GFF3_GENES_AS_TRANSCRIPTS+x} ]; then echo "${VIASH_PAR_GFF3_GENES_AS_TRANSCRIPTS}" | sed "s#'#'\"'\"'#g;s#.*#par_gff3_genes_as_transcripts='&'#" ; else echo "# par_gff3_genes_as_transcripts="; fi )
$( if [ ! -z ${VIASH_PAR_TRUSTED_SOURCES+x} ]; then echo "${VIASH_PAR_TRUSTED_SOURCES}" | sed "s#'#'\"'\"'#g;s#.*#par_trusted_sources='&'#" ; else echo "# par_trusted_sources="; fi )
$( if [ ! -z ${VIASH_PAR_TRANSCRIPT_TO_GENE_MAP+x} ]; then echo "${VIASH_PAR_TRANSCRIPT_TO_GENE_MAP}" | sed "s#'#'\"'\"'#g;s#.*#par_transcript_to_gene_map='&'#" ; else echo "# par_transcript_to_gene_map="; fi )
$( if [ ! -z ${VIASH_PAR_ALLELE_TO_GENE_MAP+x} ]; then echo "${VIASH_PAR_ALLELE_TO_GENE_MAP}" | sed "s#'#'\"'\"'#g;s#.*#par_allele_to_gene_map='&'#" ; else echo "# par_allele_to_gene_map="; fi )
$( if [ ! -z ${VIASH_PAR_POLYA+x} ]; then echo "${VIASH_PAR_POLYA}" | sed "s#'#'\"'\"'#g;s#.*#par_polyA='&'#" ; else echo "# par_polyA="; fi )
$( if [ ! -z ${VIASH_PAR_POLYA_LENGTH+x} ]; then echo "${VIASH_PAR_POLYA_LENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_polyA_length='&'#" ; else echo "# par_polyA_length="; fi )
$( if [ ! -z ${VIASH_PAR_NO_POLYA_SUBSET+x} ]; then echo "${VIASH_PAR_NO_POLYA_SUBSET}" | sed "s#'#'\"'\"'#g;s#.*#par_no_polyA_subset='&'#" ; else echo "# par_no_polyA_subset="; fi )
$( if [ ! -z ${VIASH_PAR_BOWTIE+x} ]; then echo "${VIASH_PAR_BOWTIE}" | sed "s#'#'\"'\"'#g;s#.*#par_bowtie='&'#" ; else echo "# par_bowtie="; fi )
$( if [ ! -z ${VIASH_PAR_BOWTIE2+x} ]; then echo "${VIASH_PAR_BOWTIE2}" | sed "s#'#'\"'\"'#g;s#.*#par_bowtie2='&'#" ; else echo "# par_bowtie2="; fi )
$( if [ ! -z ${VIASH_PAR_STAR+x} ]; then echo "${VIASH_PAR_STAR}" | sed "s#'#'\"'\"'#g;s#.*#par_star='&'#" ; else echo "# par_star="; fi )
$( if [ ! -z ${VIASH_PAR_STAR_SJDBOVERHANG+x} ]; then echo "${VIASH_PAR_STAR_SJDBOVERHANG}" | sed "s#'#'\"'\"'#g;s#.*#par_star_sjdboverhang='&'#" ; else echo "# par_star_sjdboverhang="; fi )
$( if [ ! -z ${VIASH_PAR_HISAT2_HCA+x} ]; then echo "${VIASH_PAR_HISAT2_HCA}" | sed "s#'#'\"'\"'#g;s#.*#par_hisat2_hca='&'#" ; else echo "# par_hisat2_hca="; fi )
$( if [ ! -z ${VIASH_PAR_QUIET+x} ]; then echo "${VIASH_PAR_QUIET}" | sed "s#'#'\"'\"'#g;s#.*#par_quiet='&'#" ; else echo "# par_quiet="; fi )
$( if [ ! -z ${VIASH_PAR_PREP_PRSEM+x} ]; then echo "${VIASH_PAR_PREP_PRSEM}" | sed "s#'#'\"'\"'#g;s#.*#par_prep_pRSEM='&'#" ; else echo "# par_prep_pRSEM="; fi )
$( if [ ! -z ${VIASH_PAR_MAPPABILITY_BIGWIG_FILE+x} ]; then echo "${VIASH_PAR_MAPPABILITY_BIGWIG_FILE}" | sed "s#'#'\"'\"'#g;s#.*#par_mappability_bigwig_file='&'#" ; else echo "# par_mappability_bigwig_file="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
## VIASH END
#!/bin/bash
set -eo pipefail
unset_if_false=( par_gff3_genes_as_transcripts par_polyA par_bowtie par_bowtie2 par_star par_hisat2_hca par_quiet par_prep_pRSEM )
for par in \${unset_if_false[@]}; do
test_val="\${!par}"
[[ "\$test_val" == "false" ]] && unset \$par
done
# replace ';' with ','
par_reference_fasta_files=\$(echo \$par_reference_fasta_files | tr ';' ',')
par_gff3_rna_patterns=\$(echo \$par_gff3_rna_patterns | tr ';' ',')
par_trusted_sources=\$(echo \$par_trusted_sources | tr ';' ',')
echo "\$par_reference_fasta_files"
rsem-prepare-reference \\
\${par_gtf:+--gtf "\${par_gtf}"} \\
\${par_gff3:+--gff3 "\${par_gff3}"} \\
\${par_gff3_rna_patterns:+--gff3-RNA-patterns "\${par_gff3_rna_patterns}"} \\
\${par_gff3_genes_as_transcripts:+--gff3-genes-as-transcripts "\${par_gff3_genes_as_transcripts}"} \\
\${par_trusted_sources:+--trusted-sources "\${par_trusted_sources}"} \\
\${par_transcript_to_gene_map:+--transcript-to-gene-map "\${par_transcript_to_gene_map}"} \\
\${par_allele_to_gene_map:+--allele-to-gene-map "\${par_allele_to_gene_map}"} \\
\${par_polyA:+--polyA} \\
\${par_polyA_length:+--polyA-length "\${par_polyA_length}"} \\
\${par_no_polyA_subset:+--no-polyA-subset "\${par_no_polyA_subset}"} \\
\${par_bowtie:+--bowtie} \\
\${par_bowtie2:+--bowtie2} \\
\${par_star:+--star} \\
\${par_star_sjdboverhang:+--star-sjdboverhang "\${par_star_sjdboverhang}"} \\
\${par_hisat2_hca:+--hisat2-hca} \\
\${par_quiet:+--quiet} \\
\${par_prep_pRSEM:+--prep-pRSEM} \\
\${par_mappability_bigwig_file:+--mappability-bigwig-file "\${par_mappability_bigwig_file}"} \\
\${meta_cpus:+--num-threads "\${meta_cpus}"} \\
"\${par_reference_fasta_files}" \\
"\${par_reference_name}"
mkdir -p "\${par_output}"
mv \${par_reference_name}.* "\${par_output}/"
VIASHMAIN
bash "\$tempscript" &
wait "\$!"
VIASHEOF
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# strip viash automount from file paths
if [ ! -z "$VIASH_PAR_REFERENCE_FASTA_FILES" ]; then
unset VIASH_TEST_REFERENCE_FASTA_FILES
IFS=';'
for var in $VIASH_PAR_REFERENCE_FASTA_FILES; do
unset IFS
if [ -z "$VIASH_TEST_REFERENCE_FASTA_FILES" ]; then
VIASH_TEST_REFERENCE_FASTA_FILES="$(ViashDockerStripAutomount "$var")"
else
VIASH_TEST_REFERENCE_FASTA_FILES="$VIASH_TEST_REFERENCE_FASTA_FILES;""$(ViashDockerStripAutomount "$var")"
fi
done
VIASH_PAR_REFERENCE_FASTA_FILES="$VIASH_TEST_REFERENCE_FASTA_FILES"
fi
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
fi
if [ ! -z "$VIASH_PAR_GTF" ]; then
VIASH_PAR_GTF=$(ViashDockerStripAutomount "$VIASH_PAR_GTF")
fi
if [ ! -z "$VIASH_PAR_GFF3" ]; then
VIASH_PAR_GFF3=$(ViashDockerStripAutomount "$VIASH_PAR_GFF3")
fi
if [ ! -z "$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP" ]; then
VIASH_PAR_TRANSCRIPT_TO_GENE_MAP=$(ViashDockerStripAutomount "$VIASH_PAR_TRANSCRIPT_TO_GENE_MAP")
fi
if [ ! -z "$VIASH_PAR_ALLELE_TO_GENE_MAP" ]; then
VIASH_PAR_ALLELE_TO_GENE_MAP=$(ViashDockerStripAutomount "$VIASH_PAR_ALLELE_TO_GENE_MAP")
fi
if [ ! -z "$VIASH_PAR_NO_POLYA_SUBSET" ]; then
VIASH_PAR_NO_POLYA_SUBSET=$(ViashDockerStripAutomount "$VIASH_PAR_NO_POLYA_SUBSET")
fi
if [ ! -z "$VIASH_PAR_MAPPABILITY_BIGWIG_FILE" ]; then
VIASH_PAR_MAPPABILITY_BIGWIG_FILE=$(ViashDockerStripAutomount "$VIASH_PAR_MAPPABILITY_BIGWIG_FILE")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
fi
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
fi
if [ ! -z "$VIASH_META_CONFIG" ]; then
VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
fi
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
fi
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then
ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
exit 1
fi
exit 0
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