CI
7645430e58
Build pipeline: viash-hub.biobox.v0.1-8mh8l
Source commit: b84b29747d
Source message: Bump version to v0.1.0
1463 lines
64 KiB
Bash
Executable File
1463 lines
64 KiB
Bash
Executable File
#!/usr/bin/env bash
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# star_genome_generate v0.1.0
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#
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# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
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# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
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# Data Intuitive.
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#
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# The component may contain files which fall under a different license. The
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# authors of this component should specify the license in the header of such
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# files, or include a separate license file detailing the licenses of all included
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# files.
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set -e
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if [ -z "$VIASH_TEMP" ]; then
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VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
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VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$TMP}
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VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
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VIASH_TEMP=${VIASH_TEMP:-$TEMP}
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VIASH_TEMP=${VIASH_TEMP:-/tmp}
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fi
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# define helper functions
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# ViashQuote: put quotes around non flag values
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# $1 : unquoted string
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# return : possibly quoted string
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# examples:
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# ViashQuote --foo # returns --foo
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# ViashQuote bar # returns 'bar'
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# Viashquote --foo=bar # returns --foo='bar'
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function ViashQuote {
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if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
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echo "$1" | sed "s#=\(.*\)#='\1'#"
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elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
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echo "$1"
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else
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echo "'$1'"
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fi
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}
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# ViashRemoveFlags: Remove leading flag
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# $1 : string with a possible leading flag
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# return : string without possible leading flag
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# examples:
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# ViashRemoveFlags --foo=bar # returns bar
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function ViashRemoveFlags {
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echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
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}
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# ViashSourceDir: return the path of a bash file, following symlinks
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# usage : ViashSourceDir ${BASH_SOURCE[0]}
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# $1 : Should always be set to ${BASH_SOURCE[0]}
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# returns : The absolute path of the bash file
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function ViashSourceDir {
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SOURCE="$1"
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while [ -h "$SOURCE" ]; do
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DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
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SOURCE="$(readlink "$SOURCE")"
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[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
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done
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cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
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}
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# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
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# usage : ViashFindTargetDir 'ScriptPath'
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# $1 : The location from where to start the upward search
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# returns : The absolute path of the '.build.yaml' file
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function ViashFindTargetDir {
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SOURCE="$1"
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while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
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SOURCE=${SOURCE%/*}
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done
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echo $SOURCE
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}
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# see https://en.wikipedia.org/wiki/Syslog#Severity_level
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VIASH_LOGCODE_EMERGENCY=0
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VIASH_LOGCODE_ALERT=1
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VIASH_LOGCODE_CRITICAL=2
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VIASH_LOGCODE_ERROR=3
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VIASH_LOGCODE_WARNING=4
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VIASH_LOGCODE_NOTICE=5
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VIASH_LOGCODE_INFO=6
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VIASH_LOGCODE_DEBUG=7
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VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
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# ViashLog: Log events depending on the verbosity level
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# usage: ViashLog 1 alert Oh no something went wrong!
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# $1: required verbosity level
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# $2: display tag
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# $3+: messages to display
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# stdout: Your input, prepended by '[$2] '.
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function ViashLog {
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local required_level="$1"
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local display_tag="$2"
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shift 2
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if [ $VIASH_VERBOSITY -ge $required_level ]; then
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>&2 echo "[$display_tag]" "$@"
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fi
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}
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# ViashEmergency: log events when the system is unstable
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# usage: ViashEmergency Oh no something went wrong.
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# stdout: Your input, prepended by '[emergency] '.
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function ViashEmergency {
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ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
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}
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# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
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# usage: ViashAlert Oh no something went wrong.
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# stdout: Your input, prepended by '[alert] '.
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function ViashAlert {
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ViashLog $VIASH_LOGCODE_ALERT alert "$@"
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}
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# ViashCritical: log events when a critical condition occurs
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# usage: ViashCritical Oh no something went wrong.
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# stdout: Your input, prepended by '[critical] '.
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function ViashCritical {
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ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
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}
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# ViashError: log events when an error condition occurs
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# usage: ViashError Oh no something went wrong.
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# stdout: Your input, prepended by '[error] '.
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function ViashError {
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ViashLog $VIASH_LOGCODE_ERROR error "$@"
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}
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# ViashWarning: log potentially abnormal events
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# usage: ViashWarning Something may have gone wrong.
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# stdout: Your input, prepended by '[warning] '.
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function ViashWarning {
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ViashLog $VIASH_LOGCODE_WARNING warning "$@"
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}
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# ViashNotice: log significant but normal events
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# usage: ViashNotice This just happened.
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# stdout: Your input, prepended by '[notice] '.
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function ViashNotice {
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ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
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}
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# ViashInfo: log normal events
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# usage: ViashInfo This just happened.
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# stdout: Your input, prepended by '[info] '.
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function ViashInfo {
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ViashLog $VIASH_LOGCODE_INFO info "$@"
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}
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# ViashDebug: log all events, for debugging purposes
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# usage: ViashDebug This just happened.
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# stdout: Your input, prepended by '[debug] '.
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function ViashDebug {
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ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
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}
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# find source folder of this component
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VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
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# find the root of the built components & dependencies
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VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
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# define meta fields
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VIASH_META_NAME="star_genome_generate"
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VIASH_META_FUNCTIONALITY_NAME="star_genome_generate"
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VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
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VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
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VIASH_META_TEMP_DIR="$VIASH_TEMP"
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# ViashHelp: Display helpful explanation about this executable
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function ViashHelp {
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echo "star_genome_generate v0.1.0"
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echo ""
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echo "Create index for STAR"
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echo ""
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echo "Input:"
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echo " --genomeFastaFiles"
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echo " type: file, required parameter, multiple values allowed, file must exist"
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echo " Path(s) to the fasta files with the genome sequences, separated by"
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echo " spaces. These files should be plain text FASTA files, they *cannot* be"
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echo " zipped."
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echo ""
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echo " --sjdbGTFfile"
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echo " type: file, file must exist"
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echo " Path to the GTF file with annotations"
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echo ""
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echo " --sjdbOverhang"
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echo " type: integer"
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echo " example: 100"
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echo " Length of the donor/acceptor sequence on each side of the junctions,"
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echo " ideally = (mate_length - 1)"
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echo ""
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echo " --sjdbGTFchrPrefix"
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echo " type: string"
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echo " Prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL"
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echo " annotations with UCSC genomes)"
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echo ""
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echo " --sjdbGTFfeatureExon"
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echo " type: string"
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echo " example: exon"
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echo " Feature type in GTF file to be used as exons for building transcripts"
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echo ""
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echo " --sjdbGTFtagExonParentTranscript"
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echo " type: string"
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echo " example: transcript_id"
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echo " GTF attribute name for parent transcript ID (default \"transcript_id\""
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echo " works for GTF files)"
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echo ""
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echo " --sjdbGTFtagExonParentGene"
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echo " type: string"
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echo " example: gene_id"
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echo " GTF attribute name for parent gene ID (default \"gene_id\" works for GTF"
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echo " files)"
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echo ""
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echo " --sjdbGTFtagExonParentGeneName"
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echo " type: string, multiple values allowed"
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echo " example: gene_name"
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echo " GTF attribute name for parent gene name"
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echo ""
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echo " --sjdbGTFtagExonParentGeneType"
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echo " type: string, multiple values allowed"
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echo " example: gene_type;gene_biotype"
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echo " GTF attribute name for parent gene type"
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echo ""
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echo " --limitGenomeGenerateRAM"
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echo " type: long"
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echo " example: 31000000000"
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echo " Maximum available RAM (bytes) for genome generation"
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echo ""
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echo " --genomeSAindexNbases"
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echo " type: integer"
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echo " example: 14"
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echo " Length (bases) of the SA pre-indexing string. Typically between 10 and"
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echo " 15. Longer strings will use much more memory, but allow faster searches."
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echo " For small genomes, this parameter must be scaled down to min(14,"
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echo " log2(GenomeLength)/2 - 1)."
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echo ""
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echo " --genomeChrBinNbits"
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echo " type: integer"
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echo " example: 18"
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echo " Defined as log2(chrBin), where chrBin is the size of the bins for genome"
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echo " storage. Each chromosome will occupy an integer number of bins. For a"
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echo " genome with large number of contigs, it is recommended to scale this"
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echo " parameter as min(18,"
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echo " log2[max(GenomeLength/NumberOfReferences,ReadLength)])."
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echo ""
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echo " --genomeSAsparseD"
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echo " type: integer"
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echo " example: 1"
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echo " min: 0"
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echo " Suffux array sparsity, i.e. distance between indices. Use bigger numbers"
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echo " to decrease needed RAM at the cost of mapping speed reduction."
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echo ""
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echo " --genomeSuffixLengthMax"
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echo " type: integer"
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echo " example: -1"
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echo " Maximum length of the suffixes, has to be longer than read length. Use"
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echo " -1 for infinite length."
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echo ""
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echo " --genomeTransformType"
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echo " type: string"
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echo " example: None"
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echo " Type of genome transformation"
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echo " None ... no transformation"
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echo " Haploid ... replace reference alleles with alternative alleles from"
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echo " VCF file (e.g. consensus allele)"
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echo " Diploid ... create two haplotypes for each chromosome listed in VCF"
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echo " file, for genotypes 1|2, assumes perfect phasing (e.g. personal genome)"
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echo ""
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echo " --genomeTransformVCF"
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echo " type: file, file must exist"
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echo " path to VCF file for genome transformation"
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echo ""
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echo "Output:"
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echo " --index"
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echo " type: file, required parameter, output, file must exist"
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echo " default: STAR_index"
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echo " STAR index directory."
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}
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# initialise variables
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VIASH_MODE='run'
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VIASH_ENGINE_ID='docker'
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######## Helper functions for setting up Docker images for viash ########
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# expects: ViashDockerBuild
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# ViashDockerInstallationCheck: check whether Docker is installed correctly
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#
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# examples:
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# ViashDockerInstallationCheck
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function ViashDockerInstallationCheck {
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ViashDebug "Checking whether Docker is installed"
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if [ ! command -v docker &> /dev/null ]; then
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ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
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exit 1
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fi
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ViashDebug "Checking whether the Docker daemon is running"
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save=$-; set +e
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docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
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out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
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ViashCritical "- Try running 'dockerd' in the command line"
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ViashCritical "- See https://docs.docker.com/config/daemon/"
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exit 1
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fi
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}
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# ViashDockerRemoteTagCheck: check whether a Docker image is available
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# on a remote. Assumes `docker login` has been performed, if relevant.
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# ViashDockerRemoteTagCheck python:latest
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# echo $? # returns '0'
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# ViashDockerRemoteTagCheck sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerRemoteTagCheck {
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docker manifest inspect $1 > /dev/null 2> /dev/null
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}
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# ViashDockerLocalTagCheck: check whether a Docker image is available locally
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# docker pull python:latest
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# ViashDockerLocalTagCheck python:latest
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# echo $? # returns '0'
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# ViashDockerLocalTagCheck sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerLocalTagCheck {
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[ -n "$(docker images -q $1)" ]
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}
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# ViashDockerPull: pull a Docker image
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# ViashDockerPull python:latest
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# echo $? # returns '0'
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# ViashDockerPull sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerPull {
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ViashNotice "Checking if Docker image is available at '$1'"
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if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
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docker pull $1 && return 0 || return 1
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else
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save=$-; set +e
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docker pull $1 2> /dev/null > /dev/null
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out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
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fi
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return $out
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fi
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}
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# ViashDockerPush: push a Docker image
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
|
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# examples:
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# ViashDockerPush python:latest
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# echo $? # returns '0'
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# ViashDockerPush sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerPush {
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ViashNotice "Pushing image to '$1'"
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save=$-; set +e
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if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
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docker push $1
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out=$?
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else
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docker push $1 2> /dev/null > /dev/null
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out=$?
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fi
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[[ $save =~ e ]] && set -e
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if [ $out -eq 0 ]; then
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ViashNotice "Container '$1' push succeeded."
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else
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ViashError "Container '$1' push errored. You might not be logged in or have the necessary permissions."
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fi
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return $out
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}
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# ViashDockerPullElseBuild: pull a Docker image, else build it
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument.
|
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# examples:
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# ViashDockerPullElseBuild mynewcomponent
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function ViashDockerPullElseBuild {
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save=$-; set +e
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ViashDockerPull $1
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out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashDockerBuild $@
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fi
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}
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# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
|
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
|
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# $2 : docker setup strategy, see DockerSetupStrategy.scala
|
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# examples:
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# ViashDockerSetup mynewcomponent alwaysbuild
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function ViashDockerSetup {
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local image_id="$1"
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local setup_strategy="$2"
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if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
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ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
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ViashDockerPull $image_id
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elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
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ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
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ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
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ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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|
elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
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local save=$-; set +e
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ViashDockerLocalTagCheck $image_id
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local outCheck=$?
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[[ $save =~ e ]] && set -e
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if [ $outCheck -eq 0 ]; then
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ViashInfo "Image $image_id already exists"
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elif [ "$setup_strategy" == "ifneedbebuild" ]; then
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ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
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ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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|
elif [ "$setup_strategy" == "ifneedbepull" ]; then
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ViashDockerPull $image_id
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elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
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ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
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ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
|
|
else
|
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ViashError "Unrecognised Docker strategy: $setup_strategy"
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exit 1
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fi
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elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
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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 []
|
|
ENV STAR_VERSION 2.7.11b
|
|
ENV PACKAGES gcc g++ make wget zlib1g-dev unzip xxd
|
|
RUN apt-get update && \
|
|
apt-get install -y --no-install-recommends ${PACKAGES} && \
|
|
cd /tmp && \
|
|
wget --no-check-certificate https://github.com/alexdobin/STAR/archive/refs/tags/${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 / && \
|
|
rm -rf /tmp/STAR-${STAR_VERSION} /tmp/${STAR_VERSION}.zip && \
|
|
apt-get --purge autoremove -y ${PACKAGES} && \
|
|
apt-get clean
|
|
|
|
RUN STAR --version | sed 's#\(.*\)#star: "\1"#' > /var/software_versions.txt
|
|
|
|
LABEL org.opencontainers.image.description="Companion container for running component star star_genome_generate"
|
|
LABEL org.opencontainers.image.created="2024-06-24T09:12:41Z"
|
|
LABEL org.opencontainers.image.source="https://github.com/alexdobin/STAR"
|
|
LABEL org.opencontainers.image.revision="b84b29747d0635f2ac83ea63b496be9a9edb6724"
|
|
LABEL org.opencontainers.image.version="v0.1.0"
|
|
|
|
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
|
|
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
|
|
# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
|
|
# examples:
|
|
# ViashDockerAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar'
|
|
# ViashDockerAutodetectMountArg /path/to/bar # returns '--volume="/path/to:/viash_automount/path/to"'
|
|
function ViashDockerAutodetectMount {
|
|
abs_path=$(ViashAbsolutePath "$1")
|
|
if [ -d "$abs_path" ]; then
|
|
mount_source="$abs_path"
|
|
base_name=""
|
|
else
|
|
mount_source=`dirname "$abs_path"`
|
|
base_name=`basename "$abs_path"`
|
|
fi
|
|
mount_target="/viash_automount$mount_source"
|
|
if [ -z "$base_name" ]; then
|
|
echo "$mount_target"
|
|
else
|
|
echo "$mount_target/$base_name"
|
|
fi
|
|
}
|
|
function ViashDockerAutodetectMountArg {
|
|
abs_path=$(ViashAbsolutePath "$1")
|
|
if [ -d "$abs_path" ]; then
|
|
mount_source="$abs_path"
|
|
base_name=""
|
|
else
|
|
mount_source=`dirname "$abs_path"`
|
|
base_name=`basename "$abs_path"`
|
|
fi
|
|
mount_target="/viash_automount$mount_source"
|
|
ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
|
|
echo "--volume=\"$mount_source:$mount_target\""
|
|
}
|
|
function ViashDockerStripAutomount {
|
|
abs_path=$(ViashAbsolutePath "$1")
|
|
echo "${abs_path#/viash_automount}"
|
|
}
|
|
# initialise variables
|
|
VIASH_DIRECTORY_MOUNTS=()
|
|
|
|
# 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 "$1")"
|
|
shift 1
|
|
;;
|
|
--version)
|
|
echo "star_genome_generate v0.1.0"
|
|
exit
|
|
;;
|
|
--genomeFastaFiles)
|
|
if [ -z "$VIASH_PAR_GENOMEFASTAFILES" ]; then
|
|
VIASH_PAR_GENOMEFASTAFILES="$2"
|
|
else
|
|
VIASH_PAR_GENOMEFASTAFILES="$VIASH_PAR_GENOMEFASTAFILES;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeFastaFiles. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genomeFastaFiles=*)
|
|
if [ -z "$VIASH_PAR_GENOMEFASTAFILES" ]; then
|
|
VIASH_PAR_GENOMEFASTAFILES=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_GENOMEFASTAFILES="$VIASH_PAR_GENOMEFASTAFILES;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
--sjdbGTFfile)
|
|
[ -n "$VIASH_PAR_SJDBGTFFILE" ] && ViashError Bad arguments for option \'--sjdbGTFfile\': \'$VIASH_PAR_SJDBGTFFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBGTFFILE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFfile. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sjdbGTFfile=*)
|
|
[ -n "$VIASH_PAR_SJDBGTFFILE" ] && ViashError Bad arguments for option \'--sjdbGTFfile=*\': \'$VIASH_PAR_SJDBGTFFILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBGTFFILE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--sjdbOverhang)
|
|
[ -n "$VIASH_PAR_SJDBOVERHANG" ] && ViashError Bad arguments for option \'--sjdbOverhang\': \'$VIASH_PAR_SJDBOVERHANG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBOVERHANG="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbOverhang. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sjdbOverhang=*)
|
|
[ -n "$VIASH_PAR_SJDBOVERHANG" ] && ViashError Bad arguments for option \'--sjdbOverhang=*\': \'$VIASH_PAR_SJDBOVERHANG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBOVERHANG=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--sjdbGTFchrPrefix)
|
|
[ -n "$VIASH_PAR_SJDBGTFCHRPREFIX" ] && ViashError Bad arguments for option \'--sjdbGTFchrPrefix\': \'$VIASH_PAR_SJDBGTFCHRPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBGTFCHRPREFIX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFchrPrefix. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sjdbGTFchrPrefix=*)
|
|
[ -n "$VIASH_PAR_SJDBGTFCHRPREFIX" ] && ViashError Bad arguments for option \'--sjdbGTFchrPrefix=*\': \'$VIASH_PAR_SJDBGTFCHRPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBGTFCHRPREFIX=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--sjdbGTFfeatureExon)
|
|
[ -n "$VIASH_PAR_SJDBGTFFEATUREEXON" ] && ViashError Bad arguments for option \'--sjdbGTFfeatureExon\': \'$VIASH_PAR_SJDBGTFFEATUREEXON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBGTFFEATUREEXON="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFfeatureExon. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sjdbGTFfeatureExon=*)
|
|
[ -n "$VIASH_PAR_SJDBGTFFEATUREEXON" ] && ViashError Bad arguments for option \'--sjdbGTFfeatureExon=*\': \'$VIASH_PAR_SJDBGTFFEATUREEXON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBGTFFEATUREEXON=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--sjdbGTFtagExonParentTranscript)
|
|
[ -n "$VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT" ] && ViashError Bad arguments for option \'--sjdbGTFtagExonParentTranscript\': \'$VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFtagExonParentTranscript. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sjdbGTFtagExonParentTranscript=*)
|
|
[ -n "$VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT" ] && ViashError Bad arguments for option \'--sjdbGTFtagExonParentTranscript=*\': \'$VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--sjdbGTFtagExonParentGene)
|
|
[ -n "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENE" ] && ViashError Bad arguments for option \'--sjdbGTFtagExonParentGene\': \'$VIASH_PAR_SJDBGTFTAGEXONPARENTGENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTGENE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFtagExonParentGene. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sjdbGTFtagExonParentGene=*)
|
|
[ -n "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENE" ] && ViashError Bad arguments for option \'--sjdbGTFtagExonParentGene=*\': \'$VIASH_PAR_SJDBGTFTAGEXONPARENTGENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTGENE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--sjdbGTFtagExonParentGeneName)
|
|
if [ -z "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME" ]; then
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME="$2"
|
|
else
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME="$VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFtagExonParentGeneName. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sjdbGTFtagExonParentGeneName=*)
|
|
if [ -z "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME" ]; then
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME="$VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
--sjdbGTFtagExonParentGeneType)
|
|
if [ -z "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE" ]; then
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE="$2"
|
|
else
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE="$VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE;""$2"
|
|
fi
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sjdbGTFtagExonParentGeneType. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--sjdbGTFtagExonParentGeneType=*)
|
|
if [ -z "$VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE" ]; then
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE=$(ViashRemoveFlags "$1")
|
|
else
|
|
VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE="$VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE;"$(ViashRemoveFlags "$1")
|
|
fi
|
|
shift 1
|
|
;;
|
|
--limitGenomeGenerateRAM)
|
|
[ -n "$VIASH_PAR_LIMITGENOMEGENERATERAM" ] && ViashError Bad arguments for option \'--limitGenomeGenerateRAM\': \'$VIASH_PAR_LIMITGENOMEGENERATERAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIMITGENOMEGENERATERAM="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --limitGenomeGenerateRAM. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--limitGenomeGenerateRAM=*)
|
|
[ -n "$VIASH_PAR_LIMITGENOMEGENERATERAM" ] && ViashError Bad arguments for option \'--limitGenomeGenerateRAM=*\': \'$VIASH_PAR_LIMITGENOMEGENERATERAM\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIMITGENOMEGENERATERAM=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--genomeSAindexNbases)
|
|
[ -n "$VIASH_PAR_GENOMESAINDEXNBASES" ] && ViashError Bad arguments for option \'--genomeSAindexNbases\': \'$VIASH_PAR_GENOMESAINDEXNBASES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMESAINDEXNBASES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeSAindexNbases. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genomeSAindexNbases=*)
|
|
[ -n "$VIASH_PAR_GENOMESAINDEXNBASES" ] && ViashError Bad arguments for option \'--genomeSAindexNbases=*\': \'$VIASH_PAR_GENOMESAINDEXNBASES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMESAINDEXNBASES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--genomeChrBinNbits)
|
|
[ -n "$VIASH_PAR_GENOMECHRBINNBITS" ] && ViashError Bad arguments for option \'--genomeChrBinNbits\': \'$VIASH_PAR_GENOMECHRBINNBITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMECHRBINNBITS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeChrBinNbits. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genomeChrBinNbits=*)
|
|
[ -n "$VIASH_PAR_GENOMECHRBINNBITS" ] && ViashError Bad arguments for option \'--genomeChrBinNbits=*\': \'$VIASH_PAR_GENOMECHRBINNBITS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMECHRBINNBITS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--genomeSAsparseD)
|
|
[ -n "$VIASH_PAR_GENOMESASPARSED" ] && ViashError Bad arguments for option \'--genomeSAsparseD\': \'$VIASH_PAR_GENOMESASPARSED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMESASPARSED="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeSAsparseD. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genomeSAsparseD=*)
|
|
[ -n "$VIASH_PAR_GENOMESASPARSED" ] && ViashError Bad arguments for option \'--genomeSAsparseD=*\': \'$VIASH_PAR_GENOMESASPARSED\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMESASPARSED=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--genomeSuffixLengthMax)
|
|
[ -n "$VIASH_PAR_GENOMESUFFIXLENGTHMAX" ] && ViashError Bad arguments for option \'--genomeSuffixLengthMax\': \'$VIASH_PAR_GENOMESUFFIXLENGTHMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMESUFFIXLENGTHMAX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeSuffixLengthMax. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genomeSuffixLengthMax=*)
|
|
[ -n "$VIASH_PAR_GENOMESUFFIXLENGTHMAX" ] && ViashError Bad arguments for option \'--genomeSuffixLengthMax=*\': \'$VIASH_PAR_GENOMESUFFIXLENGTHMAX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMESUFFIXLENGTHMAX=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--genomeTransformType)
|
|
[ -n "$VIASH_PAR_GENOMETRANSFORMTYPE" ] && ViashError Bad arguments for option \'--genomeTransformType\': \'$VIASH_PAR_GENOMETRANSFORMTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMETRANSFORMTYPE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeTransformType. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genomeTransformType=*)
|
|
[ -n "$VIASH_PAR_GENOMETRANSFORMTYPE" ] && ViashError Bad arguments for option \'--genomeTransformType=*\': \'$VIASH_PAR_GENOMETRANSFORMTYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMETRANSFORMTYPE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--genomeTransformVCF)
|
|
[ -n "$VIASH_PAR_GENOMETRANSFORMVCF" ] && ViashError Bad arguments for option \'--genomeTransformVCF\': \'$VIASH_PAR_GENOMETRANSFORMVCF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMETRANSFORMVCF="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --genomeTransformVCF. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--genomeTransformVCF=*)
|
|
[ -n "$VIASH_PAR_GENOMETRANSFORMVCF" ] && ViashError Bad arguments for option \'--genomeTransformVCF=*\': \'$VIASH_PAR_GENOMETRANSFORMVCF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GENOMETRANSFORMVCF=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--index)
|
|
[ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'--index\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INDEX="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --index. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--index=*)
|
|
[ -n "$VIASH_PAR_INDEX" ] && ViashError Bad arguments for option \'--index=*\': \'$VIASH_PAR_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INDEX=$(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 "$1")"
|
|
shift 1
|
|
;;
|
|
---dockerfile)
|
|
VIASH_MODE='dockerfile'
|
|
shift 1
|
|
;;
|
|
---debug)
|
|
VIASH_MODE='debug'
|
|
shift 1
|
|
;;
|
|
---cpus)
|
|
[ -n "$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/star/star_genome_generate:v0.1.0'
|
|
fi
|
|
|
|
# print dockerfile
|
|
if [ "$VIASH_MODE" == "dockerfile" ]; then
|
|
ViashDockerfile "$VIASH_ENGINE_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_GENOMEFASTAFILES+x} ]; then
|
|
ViashError '--genomeFastaFiles' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_INDEX+x} ]; then
|
|
ViashError '--index' 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 ${VIASH_META_TEMP_DIR+x} ]; then
|
|
ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_GENOMEFASTAFILES" ]; then
|
|
IFS=';'
|
|
set -f
|
|
for file in $VIASH_PAR_GENOMEFASTAFILES; do
|
|
unset IFS
|
|
if [ ! -e "$file" ]; then
|
|
ViashError "Input file '$file' does not exist."
|
|
exit 1
|
|
fi
|
|
done
|
|
set +f
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SJDBGTFFILE" ] && [ ! -e "$VIASH_PAR_SJDBGTFFILE" ]; then
|
|
ViashError "Input file '$VIASH_PAR_SJDBGTFFILE' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOMETRANSFORMVCF" ] && [ ! -e "$VIASH_PAR_GENOMETRANSFORMVCF" ]; then
|
|
ViashError "Input file '$VIASH_PAR_GENOMETRANSFORMVCF' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
# check whether parameters values are of the right type
|
|
if [[ -n "$VIASH_PAR_SJDBOVERHANG" ]]; then
|
|
if ! [[ "$VIASH_PAR_SJDBOVERHANG" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--sjdbOverhang' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_LIMITGENOMEGENERATERAM" ]]; then
|
|
if ! [[ "$VIASH_PAR_LIMITGENOMEGENERATERAM" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--limitGenomeGenerateRAM' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_GENOMESAINDEXNBASES" ]]; then
|
|
if ! [[ "$VIASH_PAR_GENOMESAINDEXNBASES" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--genomeSAindexNbases' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_GENOMECHRBINNBITS" ]]; then
|
|
if ! [[ "$VIASH_PAR_GENOMECHRBINNBITS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--genomeChrBinNbits' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_GENOMESASPARSED" ]]; then
|
|
if ! [[ "$VIASH_PAR_GENOMESASPARSED" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--genomeSAsparseD' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [[ $VIASH_PAR_GENOMESASPARSED -lt 0 ]]; then
|
|
ViashError '--genomeSAsparseD' has be more than or equal to 0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_GENOMESUFFIXLENGTHMAX" ]]; then
|
|
if ! [[ "$VIASH_PAR_GENOMESUFFIXLENGTHMAX" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--genomeSuffixLengthMax' has to be an integer. 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 "$VIASH_PAR_INDEX" ] && [ ! -d "$(dirname "$VIASH_PAR_INDEX")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_INDEX")"
|
|
fi
|
|
|
|
if [ "$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_GENOMEFASTAFILES" ]; then
|
|
VIASH_TEST_GENOMEFASTAFILES=()
|
|
IFS=';'
|
|
for var in $VIASH_PAR_GENOMEFASTAFILES; do
|
|
unset IFS
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
|
var=$(ViashDockerAutodetectMount "$var")
|
|
VIASH_TEST_GENOMEFASTAFILES+=( "$var" )
|
|
done
|
|
VIASH_PAR_GENOMEFASTAFILES=$(IFS=';' ; echo "${VIASH_TEST_GENOMEFASTAFILES[*]}")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SJDBGTFFILE" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SJDBGTFFILE")" )
|
|
VIASH_PAR_SJDBGTFFILE=$(ViashDockerAutodetectMount "$VIASH_PAR_SJDBGTFFILE")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOMETRANSFORMVCF" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_GENOMETRANSFORMVCF")" )
|
|
VIASH_PAR_GENOMETRANSFORMVCF=$(ViashDockerAutodetectMount "$VIASH_PAR_GENOMETRANSFORMVCF")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_INDEX" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INDEX")" )
|
|
VIASH_PAR_INDEX=$(ViashDockerAutodetectMount "$VIASH_PAR_INDEX")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_INDEX" )
|
|
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-star_genome_generate-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'
|
|
#!/bin/bash
|
|
|
|
set -e
|
|
|
|
## VIASH START
|
|
# The following code has been auto-generated by Viash.
|
|
$( if [ ! -z ${VIASH_PAR_GENOMEFASTAFILES+x} ]; then echo "${VIASH_PAR_GENOMEFASTAFILES}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeFastaFiles='&'#" ; else echo "# par_genomeFastaFiles="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SJDBGTFFILE+x} ]; then echo "${VIASH_PAR_SJDBGTFFILE}" | sed "s#'#'\"'\"'#g;s#.*#par_sjdbGTFfile='&'#" ; else echo "# par_sjdbGTFfile="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SJDBOVERHANG+x} ]; then echo "${VIASH_PAR_SJDBOVERHANG}" | sed "s#'#'\"'\"'#g;s#.*#par_sjdbOverhang='&'#" ; else echo "# par_sjdbOverhang="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SJDBGTFCHRPREFIX+x} ]; then echo "${VIASH_PAR_SJDBGTFCHRPREFIX}" | sed "s#'#'\"'\"'#g;s#.*#par_sjdbGTFchrPrefix='&'#" ; else echo "# par_sjdbGTFchrPrefix="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SJDBGTFFEATUREEXON+x} ]; then echo "${VIASH_PAR_SJDBGTFFEATUREEXON}" | sed "s#'#'\"'\"'#g;s#.*#par_sjdbGTFfeatureExon='&'#" ; else echo "# par_sjdbGTFfeatureExon="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT+x} ]; then echo "${VIASH_PAR_SJDBGTFTAGEXONPARENTTRANSCRIPT}" | sed "s#'#'\"'\"'#g;s#.*#par_sjdbGTFtagExonParentTranscript='&'#" ; else echo "# par_sjdbGTFtagExonParentTranscript="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SJDBGTFTAGEXONPARENTGENE+x} ]; then echo "${VIASH_PAR_SJDBGTFTAGEXONPARENTGENE}" | sed "s#'#'\"'\"'#g;s#.*#par_sjdbGTFtagExonParentGene='&'#" ; else echo "# par_sjdbGTFtagExonParentGene="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME+x} ]; then echo "${VIASH_PAR_SJDBGTFTAGEXONPARENTGENENAME}" | sed "s#'#'\"'\"'#g;s#.*#par_sjdbGTFtagExonParentGeneName='&'#" ; else echo "# par_sjdbGTFtagExonParentGeneName="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE+x} ]; then echo "${VIASH_PAR_SJDBGTFTAGEXONPARENTGENETYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_sjdbGTFtagExonParentGeneType='&'#" ; else echo "# par_sjdbGTFtagExonParentGeneType="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_LIMITGENOMEGENERATERAM+x} ]; then echo "${VIASH_PAR_LIMITGENOMEGENERATERAM}" | sed "s#'#'\"'\"'#g;s#.*#par_limitGenomeGenerateRAM='&'#" ; else echo "# par_limitGenomeGenerateRAM="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GENOMESAINDEXNBASES+x} ]; then echo "${VIASH_PAR_GENOMESAINDEXNBASES}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeSAindexNbases='&'#" ; else echo "# par_genomeSAindexNbases="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GENOMECHRBINNBITS+x} ]; then echo "${VIASH_PAR_GENOMECHRBINNBITS}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeChrBinNbits='&'#" ; else echo "# par_genomeChrBinNbits="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GENOMESASPARSED+x} ]; then echo "${VIASH_PAR_GENOMESASPARSED}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeSAsparseD='&'#" ; else echo "# par_genomeSAsparseD="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GENOMESUFFIXLENGTHMAX+x} ]; then echo "${VIASH_PAR_GENOMESUFFIXLENGTHMAX}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeSuffixLengthMax='&'#" ; else echo "# par_genomeSuffixLengthMax="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GENOMETRANSFORMTYPE+x} ]; then echo "${VIASH_PAR_GENOMETRANSFORMTYPE}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeTransformType='&'#" ; else echo "# par_genomeTransformType="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_GENOMETRANSFORMVCF+x} ]; then echo "${VIASH_PAR_GENOMETRANSFORMVCF}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeTransformVCF='&'#" ; else echo "# par_genomeTransformVCF="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_INDEX+x} ]; then echo "${VIASH_PAR_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_index='&'#" ; else echo "# par_index="; 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
|
|
|
|
mkdir -p \$par_index
|
|
|
|
STAR \\
|
|
--runMode genomeGenerate \\
|
|
--genomeDir \$par_index \\
|
|
--genomeFastaFiles \$par_genomeFastaFiles \\
|
|
\${meta_cpus:+--runThreadN "\${meta_cpus}"} \\
|
|
\${par_sjdbGTFfile:+--sjdbGTFfile "\${par_sjdbGTFfile}"} \\
|
|
\${par_sjdbOverhang:+--sjdbOverhang "\${par_sjdbOverhang}"} \\
|
|
\${par_genomeSAindexNbases:+--genomeSAindexNbases "\${par_genomeSAindexNbases}"} \\
|
|
\${par_sjdbGTFchrPrefix:+--sjdbGTFchrPrefix "\${par_sjdbGTFchrPrefix}"} \\
|
|
\${par_sjdbGTFfeatureExon:+--sjdbGTFfeatureExon "\${par_sjdbGTFfeatureExon}"} \\
|
|
\${par_sjdbGTFtagExonParentTranscript:+--sjdbGTFtagExonParentTranscript "\${par_sjdbGTFtagExonParentTranscript}"} \\
|
|
\${par_sjdbGTFtagExonParentGene:+--sjdbGTFtagExonParentGene "\${par_sjdbGTFtagExonParentGene}"} \\
|
|
\${par_sjdbGTFtagExonParentGeneName:+--sjdbGTFtagExonParentGeneName "\${par_sjdbGTFtagExonParentGeneName}"} \\
|
|
\${par_sjdbGTFtagExonParentGeneType:+--sjdbGTFtagExonParentGeneType "\${sjdbGTFtagExonParentGeneType}"} \\
|
|
\${par_limitGenomeGenerateRAM:+--limitGenomeGenerateRAM "\${par_limitGenomeGenerateRAM}"} \\
|
|
\${par_genomeChrBinNbits:+--genomeChrBinNbits "\${par_genomeChrBinNbits}"} \\
|
|
\${par_genomeSAsparseD:+--genomeSAsparseD "\${par_genomeSAsparseD}"} \\
|
|
\${par_genomeSuffixLengthMax:+--genomeSuffixLengthMax "\${par_genomeSuffixLengthMax}"} \\
|
|
\${par_genomeTransformType:+--genomeTransformType "\${par_genomeTransformType}"} \\
|
|
\${par_genomeTransformVCF:+--genomeTransformVCF "\${par_genomeTransformVCF}"} \\
|
|
VIASHMAIN
|
|
bash "\$tempscript" &
|
|
wait "\$!"
|
|
|
|
VIASHEOF
|
|
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# strip viash automount from file paths
|
|
|
|
if [ ! -z "$VIASH_PAR_GENOMEFASTAFILES" ]; then
|
|
unset VIASH_TEST_GENOMEFASTAFILES
|
|
IFS=';'
|
|
for var in $VIASH_PAR_GENOMEFASTAFILES; do
|
|
unset IFS
|
|
if [ -z "$VIASH_TEST_GENOMEFASTAFILES" ]; then
|
|
VIASH_TEST_GENOMEFASTAFILES="$(ViashDockerStripAutomount "$var")"
|
|
else
|
|
VIASH_TEST_GENOMEFASTAFILES="$VIASH_TEST_GENOMEFASTAFILES;""$(ViashDockerStripAutomount "$var")"
|
|
fi
|
|
done
|
|
VIASH_PAR_GENOMEFASTAFILES="$VIASH_TEST_GENOMEFASTAFILES"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SJDBGTFFILE" ]; then
|
|
VIASH_PAR_SJDBGTFFILE=$(ViashDockerStripAutomount "$VIASH_PAR_SJDBGTFFILE")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_GENOMETRANSFORMVCF" ]; then
|
|
VIASH_PAR_GENOMETRANSFORMVCF=$(ViashDockerStripAutomount "$VIASH_PAR_GENOMETRANSFORMVCF")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_INDEX" ]; then
|
|
VIASH_PAR_INDEX=$(ViashDockerStripAutomount "$VIASH_PAR_INDEX")
|
|
fi
|
|
if [ ! -z "$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_INDEX" ] && [ ! -e "$VIASH_PAR_INDEX" ]; then
|
|
ViashError "Output file '$VIASH_PAR_INDEX' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
|
|
exit 0
|