CI
38a478d5ae
Build pipeline: viash-hub.biobox.main-t7scl
Source commit: a13b57d04a
Source message: Add bases2fastq (#167)
1784 lines
78 KiB
Bash
Executable File
1784 lines
78 KiB
Bash
Executable File
#!/usr/bin/env bash
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# busco_run main
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#
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# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
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# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
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# 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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#
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# Component authors:
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# * Dorien Roosen (author, maintainer)
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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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local source="$1"
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while [ -h "$source" ]; do
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local 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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local 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 $VIASH_META_RESOURCES_DIR`
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# define meta fields
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VIASH_META_NAME="busco_run"
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VIASH_META_FUNCTIONALITY_NAME="busco_run"
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VIASH_META_EXECUTABLE="$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 "busco_run main"
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echo ""
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echo "Assessment of genome assembly and annotation completeness with single copy"
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echo "orthologs"
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echo ""
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echo "Inputs:"
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echo " -i, --input"
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echo " type: file, required parameter, file must exist"
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echo " example: file.fasta"
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echo " Input sequence file in FASTA format. Can be an assembled genome or"
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echo " transcriptome (DNA), or protein sequences from an annotated gene set."
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echo " Also possible to use a path to a directory containing multiple input"
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echo " files."
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echo ""
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echo " -m, --mode"
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echo " type: string, required parameter"
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echo " example: proteins"
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echo " choices: [ genome, geno, transcriptome, tran, proteins, prot ]"
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echo " Specify which BUSCO analysis mode to run. There are three valid modes:"
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echo " - geno or genome, for genome assemblies (DNA)"
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echo " - tran or transcriptome, for transcriptome assemblies (DNA)"
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echo " - prot or proteins, for annotated gene sets (protein)"
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echo ""
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echo " -l, --lineage_dataset"
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echo " type: string"
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echo " example: stramenopiles_odb10"
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echo " Specify a BUSCO lineage dataset that is most closely related to the"
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echo " assembly or gene set being assessed."
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echo " The full list of available datasets can be viewed"
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echo " [here](https://busco-data.ezlab.org/v5/data/lineages/) or by running the"
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echo " busco/busco_list_datasets component."
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echo " When unsure, the \"--auto_lineage\" flag can be set to automatically find"
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echo " the optimal lineage path."
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echo " BUSCO will automatically download the requested dataset if it is not"
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echo " already present in the download folder."
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echo " You can optionally provide a path to a local dataset instead of a name,"
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echo " e.g. path/to/dataset."
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echo " Datasets can be downloaded using the busco/busco_download_dataset"
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echo " component."
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echo ""
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echo "Outputs:"
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echo " --short_summary_json"
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echo " type: file, output, file must exist"
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echo " example: short_summary.json"
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echo " Output file for short summary in JSON format."
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echo ""
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echo " --short_summary_txt"
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echo " type: file, output, file must exist"
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echo " example: short_summary.txt"
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echo " Output file for short summary in TXT format."
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echo ""
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echo " --full_table"
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echo " type: file, output, file must exist"
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echo " example: full_table.tsv"
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echo " Full table output in TSV format."
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echo ""
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echo " --missing_busco_list"
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echo " type: file, output, file must exist"
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echo " example: missing_busco_list.tsv"
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echo " Missing list output in TSV format."
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echo ""
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echo " --output_dir"
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echo " type: file, output, file must exist"
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echo " example: output_dir"
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echo " The full output directory, if so desired."
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echo ""
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echo "Resource and Run Settings:"
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echo " --force"
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echo " type: boolean_true"
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echo " Force rewriting of existing files. Must be used when output files with"
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echo " the provided name already exist."
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echo ""
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echo " -q, --quiet"
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echo " type: boolean_true"
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echo " Disable the info logs, displays only errors."
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echo ""
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echo " -r, --restart"
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echo " type: boolean_true"
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echo " Continue a run that had already partially completed. Restarting skips"
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echo " calls to tools that have completed but performs all pre- and"
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echo " post-processing steps."
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echo ""
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echo " --tar"
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echo " type: boolean_true"
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echo " Compress some subdirectories with many files to save space."
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echo ""
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echo "Lineage Dataset Settings:"
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echo " --auto_lineage"
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echo " type: boolean_true"
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echo " Run auto-lineage pipelilne to automatically determine BUSCO lineage"
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echo " dataset that is most closely related to the assembly or gene set being"
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echo " assessed."
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echo ""
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echo " --auto_lineage_euk"
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echo " type: boolean_true"
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echo " Run auto-placement just on eukaryota tree to find optimal lineage path."
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echo ""
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echo " --auto_lineage_prok"
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echo " type: boolean_true"
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echo " Run auto_lineage just on prokaryota trees to find optimum lineage path."
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echo ""
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echo " --datasets_version"
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echo " type: string"
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echo " example: odb10"
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echo " Specify the version of BUSCO datasets"
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echo ""
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echo "Augustus Settings:"
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echo " --augustus"
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echo " type: boolean_true"
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echo " Use augustus gene predictor for eukaryote runs."
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echo ""
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echo " --augustus_parameters"
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echo " type: string"
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echo " example: --PARAM1=VALUE1,--PARAM2=VALUE2"
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echo " Additional parameters to be passed to Augustus (see Augustus"
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echo " documentation:"
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echo " "
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echo "https://github.com/Gaius-Augustus/Augustus/blob/master/docs/RUNNING-AUGUSTUS.md)."
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echo " Parameters should be contained within a single string, without"
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echo " whitespace and seperated by commas."
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echo ""
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echo " --augustus_species"
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echo " type: string"
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echo " Specify the augustus species"
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echo ""
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echo " --long"
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echo " type: boolean_true"
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echo " Optimize Augustus self-training mode. This adds considerably to the run"
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echo " time, but can improve results for some non-model organisms."
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echo ""
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echo "BBTools Settings:"
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echo " --contig_break"
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echo " type: integer"
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echo " Number of contiguous Ns to signify a break between contigs in BBTools"
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echo " analysis."
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echo ""
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echo " --limit"
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echo " type: integer"
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echo " Number of candidate regions (contig or transcript) from the BLAST output"
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echo " to consider per BUSCO."
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echo " This option is only effective in pipelines using BLAST, i.e. the genome"
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echo " pipeline (see --augustus) or the prokaryota transcriptome pipeline."
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echo ""
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echo " --scaffold_composition"
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echo " type: boolean_true"
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echo " Writes ACGTN content per scaffold to a file scaffold_composition.txt."
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echo ""
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echo "BLAST Settings:"
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echo " --e_value"
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echo " type: double"
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echo " E-value cutoff for BLAST searches."
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echo ""
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echo "Protein Gene Prediction settings:"
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echo " --miniprot"
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echo " type: boolean_true"
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echo " Use Miniprot gene predictor."
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echo ""
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echo "MetaEuk Settings:"
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echo " --metaeuk"
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echo " type: boolean_true"
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echo " Use Metaeuk gene predictor."
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echo ""
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echo " --metaeuk_parameters"
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echo " type: string"
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echo " example: --max-overlap=15,--min-exon-aa=15"
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echo " Pass additional arguments to Metaeuk for the first run (see Metaeuk"
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echo " documentation https://github.com/soedinglab/metaeuk)."
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echo " All parameters should be contained within a single string with no white"
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echo " space, with each parameter separated by a comma."
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echo ""
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echo " --metaeuk_rerun_parameters"
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echo " type: string"
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echo " example: --max-overlap=15,--min-exon-aa=15"
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echo " Pass additional arguments to Metaeuk for the second run (see Metaeuk"
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echo " documentation https://github.com/soedinglab/metaeuk)."
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echo " All parameters should be contained within a single string with no white"
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echo " space, with each parameter separated by a comma."
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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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local save=$-; set +e
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local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
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local out=$?
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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
|
|
# examples:
|
|
# 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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|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# exit code $? : whether or not the image was found
|
|
# examples:
|
|
# 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 $1 && return 0 || return 1
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else
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local save=$-; set +e
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docker pull $1 2> /dev/null > /dev/null
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local out=$?
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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
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# exit code $? : whether or not the image was found
|
|
# examples:
|
|
# 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 '$1'"
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local save=$-; set +e
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local out
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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
|
|
#
|
|
# $1 : image identifier with format `[registry/]image[:tag]`
|
|
# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument.
|
|
# examples:
|
|
# ViashDockerPullElseBuild mynewcomponent
|
|
function ViashDockerPullElseBuild {
|
|
local save=$-; 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 quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
|
|
ENTRYPOINT []
|
|
RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_versions.txt
|
|
|
|
LABEL org.opencontainers.image.authors="Dorien Roosen"
|
|
LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
|
|
LABEL org.opencontainers.image.created="2024-11-26T14:03:20Z"
|
|
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
|
|
LABEL org.opencontainers.image.revision="a13b57d04a3f3741eedd1af10fd96a9bee126f55"
|
|
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 "$1")"
|
|
shift 1
|
|
;;
|
|
--version)
|
|
echo "busco_run main"
|
|
exit
|
|
;;
|
|
--input)
|
|
[ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --input. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--input=*)
|
|
[ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'--input=*\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INPUT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-i)
|
|
[ -n "$VIASH_PAR_INPUT" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_INPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--mode)
|
|
[ -n "$VIASH_PAR_MODE" ] && ViashError Bad arguments for option \'--mode\': \'$VIASH_PAR_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MODE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --mode. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--mode=*)
|
|
[ -n "$VIASH_PAR_MODE" ] && ViashError Bad arguments for option \'--mode=*\': \'$VIASH_PAR_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MODE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-m)
|
|
[ -n "$VIASH_PAR_MODE" ] && ViashError Bad arguments for option \'-m\': \'$VIASH_PAR_MODE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MODE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -m. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--lineage_dataset)
|
|
[ -n "$VIASH_PAR_LINEAGE_DATASET" ] && ViashError Bad arguments for option \'--lineage_dataset\': \'$VIASH_PAR_LINEAGE_DATASET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LINEAGE_DATASET="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --lineage_dataset. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--lineage_dataset=*)
|
|
[ -n "$VIASH_PAR_LINEAGE_DATASET" ] && ViashError Bad arguments for option \'--lineage_dataset=*\': \'$VIASH_PAR_LINEAGE_DATASET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LINEAGE_DATASET=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-l)
|
|
[ -n "$VIASH_PAR_LINEAGE_DATASET" ] && ViashError Bad arguments for option \'-l\': \'$VIASH_PAR_LINEAGE_DATASET\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LINEAGE_DATASET="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -l. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--short_summary_json)
|
|
[ -n "$VIASH_PAR_SHORT_SUMMARY_JSON" ] && ViashError Bad arguments for option \'--short_summary_json\': \'$VIASH_PAR_SHORT_SUMMARY_JSON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SHORT_SUMMARY_JSON="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --short_summary_json. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--short_summary_json=*)
|
|
[ -n "$VIASH_PAR_SHORT_SUMMARY_JSON" ] && ViashError Bad arguments for option \'--short_summary_json=*\': \'$VIASH_PAR_SHORT_SUMMARY_JSON\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SHORT_SUMMARY_JSON=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--short_summary_txt)
|
|
[ -n "$VIASH_PAR_SHORT_SUMMARY_TXT" ] && ViashError Bad arguments for option \'--short_summary_txt\': \'$VIASH_PAR_SHORT_SUMMARY_TXT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SHORT_SUMMARY_TXT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --short_summary_txt. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--short_summary_txt=*)
|
|
[ -n "$VIASH_PAR_SHORT_SUMMARY_TXT" ] && ViashError Bad arguments for option \'--short_summary_txt=*\': \'$VIASH_PAR_SHORT_SUMMARY_TXT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SHORT_SUMMARY_TXT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--full_table)
|
|
[ -n "$VIASH_PAR_FULL_TABLE" ] && ViashError Bad arguments for option \'--full_table\': \'$VIASH_PAR_FULL_TABLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FULL_TABLE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --full_table. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--full_table=*)
|
|
[ -n "$VIASH_PAR_FULL_TABLE" ] && ViashError Bad arguments for option \'--full_table=*\': \'$VIASH_PAR_FULL_TABLE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FULL_TABLE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--missing_busco_list)
|
|
[ -n "$VIASH_PAR_MISSING_BUSCO_LIST" ] && ViashError Bad arguments for option \'--missing_busco_list\': \'$VIASH_PAR_MISSING_BUSCO_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MISSING_BUSCO_LIST="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --missing_busco_list. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--missing_busco_list=*)
|
|
[ -n "$VIASH_PAR_MISSING_BUSCO_LIST" ] && ViashError Bad arguments for option \'--missing_busco_list=*\': \'$VIASH_PAR_MISSING_BUSCO_LIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MISSING_BUSCO_LIST=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--output_dir)
|
|
[ -n "$VIASH_PAR_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--output_dir\': \'$VIASH_PAR_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_DIR="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_dir. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output_dir=*)
|
|
[ -n "$VIASH_PAR_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--output_dir=*\': \'$VIASH_PAR_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_DIR=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--force)
|
|
[ -n "$VIASH_PAR_FORCE" ] && ViashError Bad arguments for option \'--force\': \'$VIASH_PAR_FORCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FORCE=true
|
|
shift 1
|
|
;;
|
|
--quiet)
|
|
[ -n "$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\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_QUIET=true
|
|
shift 1
|
|
;;
|
|
--restart)
|
|
[ -n "$VIASH_PAR_RESTART" ] && ViashError Bad arguments for option \'--restart\': \'$VIASH_PAR_RESTART\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_RESTART=true
|
|
shift 1
|
|
;;
|
|
-r)
|
|
[ -n "$VIASH_PAR_RESTART" ] && ViashError Bad arguments for option \'-r\': \'$VIASH_PAR_RESTART\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_RESTART=true
|
|
shift 1
|
|
;;
|
|
--tar)
|
|
[ -n "$VIASH_PAR_TAR" ] && ViashError Bad arguments for option \'--tar\': \'$VIASH_PAR_TAR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TAR=true
|
|
shift 1
|
|
;;
|
|
--auto_lineage)
|
|
[ -n "$VIASH_PAR_AUTO_LINEAGE" ] && ViashError Bad arguments for option \'--auto_lineage\': \'$VIASH_PAR_AUTO_LINEAGE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUTO_LINEAGE=true
|
|
shift 1
|
|
;;
|
|
--auto_lineage_euk)
|
|
[ -n "$VIASH_PAR_AUTO_LINEAGE_EUK" ] && ViashError Bad arguments for option \'--auto_lineage_euk\': \'$VIASH_PAR_AUTO_LINEAGE_EUK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUTO_LINEAGE_EUK=true
|
|
shift 1
|
|
;;
|
|
--auto_lineage_prok)
|
|
[ -n "$VIASH_PAR_AUTO_LINEAGE_PROK" ] && ViashError Bad arguments for option \'--auto_lineage_prok\': \'$VIASH_PAR_AUTO_LINEAGE_PROK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUTO_LINEAGE_PROK=true
|
|
shift 1
|
|
;;
|
|
--datasets_version)
|
|
[ -n "$VIASH_PAR_DATASETS_VERSION" ] && ViashError Bad arguments for option \'--datasets_version\': \'$VIASH_PAR_DATASETS_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DATASETS_VERSION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --datasets_version. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--datasets_version=*)
|
|
[ -n "$VIASH_PAR_DATASETS_VERSION" ] && ViashError Bad arguments for option \'--datasets_version=*\': \'$VIASH_PAR_DATASETS_VERSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_DATASETS_VERSION=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--augustus)
|
|
[ -n "$VIASH_PAR_AUGUSTUS" ] && ViashError Bad arguments for option \'--augustus\': \'$VIASH_PAR_AUGUSTUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUGUSTUS=true
|
|
shift 1
|
|
;;
|
|
--augustus_parameters)
|
|
[ -n "$VIASH_PAR_AUGUSTUS_PARAMETERS" ] && ViashError Bad arguments for option \'--augustus_parameters\': \'$VIASH_PAR_AUGUSTUS_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUGUSTUS_PARAMETERS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --augustus_parameters. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--augustus_parameters=*)
|
|
[ -n "$VIASH_PAR_AUGUSTUS_PARAMETERS" ] && ViashError Bad arguments for option \'--augustus_parameters=*\': \'$VIASH_PAR_AUGUSTUS_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUGUSTUS_PARAMETERS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--augustus_species)
|
|
[ -n "$VIASH_PAR_AUGUSTUS_SPECIES" ] && ViashError Bad arguments for option \'--augustus_species\': \'$VIASH_PAR_AUGUSTUS_SPECIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUGUSTUS_SPECIES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --augustus_species. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--augustus_species=*)
|
|
[ -n "$VIASH_PAR_AUGUSTUS_SPECIES" ] && ViashError Bad arguments for option \'--augustus_species=*\': \'$VIASH_PAR_AUGUSTUS_SPECIES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_AUGUSTUS_SPECIES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--long)
|
|
[ -n "$VIASH_PAR_LONG" ] && ViashError Bad arguments for option \'--long\': \'$VIASH_PAR_LONG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LONG=true
|
|
shift 1
|
|
;;
|
|
--contig_break)
|
|
[ -n "$VIASH_PAR_CONTIG_BREAK" ] && ViashError Bad arguments for option \'--contig_break\': \'$VIASH_PAR_CONTIG_BREAK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CONTIG_BREAK="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --contig_break. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--contig_break=*)
|
|
[ -n "$VIASH_PAR_CONTIG_BREAK" ] && ViashError Bad arguments for option \'--contig_break=*\': \'$VIASH_PAR_CONTIG_BREAK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CONTIG_BREAK=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--limit)
|
|
[ -n "$VIASH_PAR_LIMIT" ] && ViashError Bad arguments for option \'--limit\': \'$VIASH_PAR_LIMIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIMIT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --limit. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--limit=*)
|
|
[ -n "$VIASH_PAR_LIMIT" ] && ViashError Bad arguments for option \'--limit=*\': \'$VIASH_PAR_LIMIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LIMIT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--scaffold_composition)
|
|
[ -n "$VIASH_PAR_SCAFFOLD_COMPOSITION" ] && ViashError Bad arguments for option \'--scaffold_composition\': \'$VIASH_PAR_SCAFFOLD_COMPOSITION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SCAFFOLD_COMPOSITION=true
|
|
shift 1
|
|
;;
|
|
--e_value)
|
|
[ -n "$VIASH_PAR_E_VALUE" ] && ViashError Bad arguments for option \'--e_value\': \'$VIASH_PAR_E_VALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_E_VALUE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --e_value. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--e_value=*)
|
|
[ -n "$VIASH_PAR_E_VALUE" ] && ViashError Bad arguments for option \'--e_value=*\': \'$VIASH_PAR_E_VALUE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_E_VALUE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--miniprot)
|
|
[ -n "$VIASH_PAR_MINIPROT" ] && ViashError Bad arguments for option \'--miniprot\': \'$VIASH_PAR_MINIPROT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MINIPROT=true
|
|
shift 1
|
|
;;
|
|
--metaeuk)
|
|
[ -n "$VIASH_PAR_METAEUK" ] && ViashError Bad arguments for option \'--metaeuk\': \'$VIASH_PAR_METAEUK\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_METAEUK=true
|
|
shift 1
|
|
;;
|
|
--metaeuk_parameters)
|
|
[ -n "$VIASH_PAR_METAEUK_PARAMETERS" ] && ViashError Bad arguments for option \'--metaeuk_parameters\': \'$VIASH_PAR_METAEUK_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_METAEUK_PARAMETERS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --metaeuk_parameters. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--metaeuk_parameters=*)
|
|
[ -n "$VIASH_PAR_METAEUK_PARAMETERS" ] && ViashError Bad arguments for option \'--metaeuk_parameters=*\': \'$VIASH_PAR_METAEUK_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_METAEUK_PARAMETERS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--metaeuk_rerun_parameters)
|
|
[ -n "$VIASH_PAR_METAEUK_RERUN_PARAMETERS" ] && ViashError Bad arguments for option \'--metaeuk_rerun_parameters\': \'$VIASH_PAR_METAEUK_RERUN_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_METAEUK_RERUN_PARAMETERS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --metaeuk_rerun_parameters. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--metaeuk_rerun_parameters=*)
|
|
[ -n "$VIASH_PAR_METAEUK_RERUN_PARAMETERS" ] && ViashError Bad arguments for option \'--metaeuk_rerun_parameters=*\': \'$VIASH_PAR_METAEUK_RERUN_PARAMETERS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_METAEUK_RERUN_PARAMETERS=$(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/busco/busco_run: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_INPUT+x} ]; then
|
|
ViashError '--input' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_MODE+x} ]; then
|
|
ViashError '--mode' 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_FORCE+x} ]; then
|
|
VIASH_PAR_FORCE="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_QUIET+x} ]; then
|
|
VIASH_PAR_QUIET="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_RESTART+x} ]; then
|
|
VIASH_PAR_RESTART="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_TAR+x} ]; then
|
|
VIASH_PAR_TAR="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_AUTO_LINEAGE+x} ]; then
|
|
VIASH_PAR_AUTO_LINEAGE="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_AUTO_LINEAGE_EUK+x} ]; then
|
|
VIASH_PAR_AUTO_LINEAGE_EUK="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_AUTO_LINEAGE_PROK+x} ]; then
|
|
VIASH_PAR_AUTO_LINEAGE_PROK="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_AUGUSTUS+x} ]; then
|
|
VIASH_PAR_AUGUSTUS="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_LONG+x} ]; then
|
|
VIASH_PAR_LONG="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SCAFFOLD_COMPOSITION+x} ]; then
|
|
VIASH_PAR_SCAFFOLD_COMPOSITION="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_MINIPROT+x} ]; then
|
|
VIASH_PAR_MINIPROT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_METAEUK+x} ]; then
|
|
VIASH_PAR_METAEUK="false"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then
|
|
ViashError "Input file '$VIASH_PAR_INPUT' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
# check whether parameters values are of the right type
|
|
if [[ -n "$VIASH_PAR_FORCE" ]]; then
|
|
if ! [[ "$VIASH_PAR_FORCE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--force' 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 "$VIASH_PAR_RESTART" ]]; then
|
|
if ! [[ "$VIASH_PAR_RESTART" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--restart' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_TAR" ]]; then
|
|
if ! [[ "$VIASH_PAR_TAR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--tar' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_AUTO_LINEAGE" ]]; then
|
|
if ! [[ "$VIASH_PAR_AUTO_LINEAGE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--auto_lineage' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_AUTO_LINEAGE_EUK" ]]; then
|
|
if ! [[ "$VIASH_PAR_AUTO_LINEAGE_EUK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--auto_lineage_euk' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_AUTO_LINEAGE_PROK" ]]; then
|
|
if ! [[ "$VIASH_PAR_AUTO_LINEAGE_PROK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--auto_lineage_prok' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_AUGUSTUS" ]]; then
|
|
if ! [[ "$VIASH_PAR_AUGUSTUS" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--augustus' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_LONG" ]]; then
|
|
if ! [[ "$VIASH_PAR_LONG" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--long' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_CONTIG_BREAK" ]]; then
|
|
if ! [[ "$VIASH_PAR_CONTIG_BREAK" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--contig_break' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_LIMIT" ]]; then
|
|
if ! [[ "$VIASH_PAR_LIMIT" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--limit' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SCAFFOLD_COMPOSITION" ]]; then
|
|
if ! [[ "$VIASH_PAR_SCAFFOLD_COMPOSITION" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--scaffold_composition' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_E_VALUE" ]]; then
|
|
if ! [[ "$VIASH_PAR_E_VALUE" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--e_value' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MINIPROT" ]]; then
|
|
if ! [[ "$VIASH_PAR_MINIPROT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--miniprot' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_METAEUK" ]]; then
|
|
if ! [[ "$VIASH_PAR_METAEUK" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--metaeuk' 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
|
|
|
|
# check whether value is belongs to a set of choices
|
|
if [ ! -z "$VIASH_PAR_MODE" ]; then
|
|
VIASH_PAR_MODE_CHOICES=("genome;geno;transcriptome;tran;proteins;prot")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_MODE_CHOICES[*]};" =~ ";$VIASH_PAR_MODE;" ]]; then
|
|
ViashError '--mode' specified value of \'$VIASH_PAR_MODE\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
set +f
|
|
unset IFS
|
|
fi
|
|
|
|
# create parent directories of output files, if so desired
|
|
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_JSON" ] && [ ! -d "$(dirname "$VIASH_PAR_SHORT_SUMMARY_JSON")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_SHORT_SUMMARY_JSON")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_TXT" ] && [ ! -d "$(dirname "$VIASH_PAR_SHORT_SUMMARY_TXT")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_SHORT_SUMMARY_TXT")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FULL_TABLE" ] && [ ! -d "$(dirname "$VIASH_PAR_FULL_TABLE")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_FULL_TABLE")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MISSING_BUSCO_LIST" ] && [ ! -d "$(dirname "$VIASH_PAR_MISSING_BUSCO_LIST")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_MISSING_BUSCO_LIST")"
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_DIR")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_DIR")"
|
|
fi
|
|
|
|
if [ "$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 "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" )
|
|
VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_JSON" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SHORT_SUMMARY_JSON")" )
|
|
VIASH_PAR_SHORT_SUMMARY_JSON=$(ViashDockerAutodetectMount "$VIASH_PAR_SHORT_SUMMARY_JSON")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_SHORT_SUMMARY_JSON" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_TXT" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SHORT_SUMMARY_TXT")" )
|
|
VIASH_PAR_SHORT_SUMMARY_TXT=$(ViashDockerAutodetectMount "$VIASH_PAR_SHORT_SUMMARY_TXT")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_SHORT_SUMMARY_TXT" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FULL_TABLE" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FULL_TABLE")" )
|
|
VIASH_PAR_FULL_TABLE=$(ViashDockerAutodetectMount "$VIASH_PAR_FULL_TABLE")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_FULL_TABLE" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MISSING_BUSCO_LIST" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_MISSING_BUSCO_LIST")" )
|
|
VIASH_PAR_MISSING_BUSCO_LIST=$(ViashDockerAutodetectMount "$VIASH_PAR_MISSING_BUSCO_LIST")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_MISSING_BUSCO_LIST" )
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_DIR" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_DIR")" )
|
|
VIASH_PAR_OUTPUT_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_DIR")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_DIR" )
|
|
fi
|
|
if [ ! -z "$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-busco_run-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
|
|
|
|
## VIASH START
|
|
# The following code has been auto-generated by Viash.
|
|
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MODE+x} ]; then echo "${VIASH_PAR_MODE}" | sed "s#'#'\"'\"'#g;s#.*#par_mode='&'#" ; else echo "# par_mode="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_LINEAGE_DATASET+x} ]; then echo "${VIASH_PAR_LINEAGE_DATASET}" | sed "s#'#'\"'\"'#g;s#.*#par_lineage_dataset='&'#" ; else echo "# par_lineage_dataset="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SHORT_SUMMARY_JSON+x} ]; then echo "${VIASH_PAR_SHORT_SUMMARY_JSON}" | sed "s#'#'\"'\"'#g;s#.*#par_short_summary_json='&'#" ; else echo "# par_short_summary_json="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SHORT_SUMMARY_TXT+x} ]; then echo "${VIASH_PAR_SHORT_SUMMARY_TXT}" | sed "s#'#'\"'\"'#g;s#.*#par_short_summary_txt='&'#" ; else echo "# par_short_summary_txt="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FULL_TABLE+x} ]; then echo "${VIASH_PAR_FULL_TABLE}" | sed "s#'#'\"'\"'#g;s#.*#par_full_table='&'#" ; else echo "# par_full_table="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MISSING_BUSCO_LIST+x} ]; then echo "${VIASH_PAR_MISSING_BUSCO_LIST}" | sed "s#'#'\"'\"'#g;s#.*#par_missing_busco_list='&'#" ; else echo "# par_missing_busco_list="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_OUTPUT_DIR+x} ]; then echo "${VIASH_PAR_OUTPUT_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_output_dir='&'#" ; else echo "# par_output_dir="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_FORCE+x} ]; then echo "${VIASH_PAR_FORCE}" | sed "s#'#'\"'\"'#g;s#.*#par_force='&'#" ; else echo "# par_force="; 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 ${VIASH_PAR_RESTART+x} ]; then echo "${VIASH_PAR_RESTART}" | sed "s#'#'\"'\"'#g;s#.*#par_restart='&'#" ; else echo "# par_restart="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_TAR+x} ]; then echo "${VIASH_PAR_TAR}" | sed "s#'#'\"'\"'#g;s#.*#par_tar='&'#" ; else echo "# par_tar="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_AUTO_LINEAGE+x} ]; then echo "${VIASH_PAR_AUTO_LINEAGE}" | sed "s#'#'\"'\"'#g;s#.*#par_auto_lineage='&'#" ; else echo "# par_auto_lineage="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_AUTO_LINEAGE_EUK+x} ]; then echo "${VIASH_PAR_AUTO_LINEAGE_EUK}" | sed "s#'#'\"'\"'#g;s#.*#par_auto_lineage_euk='&'#" ; else echo "# par_auto_lineage_euk="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_AUTO_LINEAGE_PROK+x} ]; then echo "${VIASH_PAR_AUTO_LINEAGE_PROK}" | sed "s#'#'\"'\"'#g;s#.*#par_auto_lineage_prok='&'#" ; else echo "# par_auto_lineage_prok="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_DATASETS_VERSION+x} ]; then echo "${VIASH_PAR_DATASETS_VERSION}" | sed "s#'#'\"'\"'#g;s#.*#par_datasets_version='&'#" ; else echo "# par_datasets_version="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_AUGUSTUS+x} ]; then echo "${VIASH_PAR_AUGUSTUS}" | sed "s#'#'\"'\"'#g;s#.*#par_augustus='&'#" ; else echo "# par_augustus="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_AUGUSTUS_PARAMETERS+x} ]; then echo "${VIASH_PAR_AUGUSTUS_PARAMETERS}" | sed "s#'#'\"'\"'#g;s#.*#par_augustus_parameters='&'#" ; else echo "# par_augustus_parameters="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_AUGUSTUS_SPECIES+x} ]; then echo "${VIASH_PAR_AUGUSTUS_SPECIES}" | sed "s#'#'\"'\"'#g;s#.*#par_augustus_species='&'#" ; else echo "# par_augustus_species="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_LONG+x} ]; then echo "${VIASH_PAR_LONG}" | sed "s#'#'\"'\"'#g;s#.*#par_long='&'#" ; else echo "# par_long="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_CONTIG_BREAK+x} ]; then echo "${VIASH_PAR_CONTIG_BREAK}" | sed "s#'#'\"'\"'#g;s#.*#par_contig_break='&'#" ; else echo "# par_contig_break="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_LIMIT+x} ]; then echo "${VIASH_PAR_LIMIT}" | sed "s#'#'\"'\"'#g;s#.*#par_limit='&'#" ; else echo "# par_limit="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SCAFFOLD_COMPOSITION+x} ]; then echo "${VIASH_PAR_SCAFFOLD_COMPOSITION}" | sed "s#'#'\"'\"'#g;s#.*#par_scaffold_composition='&'#" ; else echo "# par_scaffold_composition="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_E_VALUE+x} ]; then echo "${VIASH_PAR_E_VALUE}" | sed "s#'#'\"'\"'#g;s#.*#par_e_value='&'#" ; else echo "# par_e_value="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MINIPROT+x} ]; then echo "${VIASH_PAR_MINIPROT}" | sed "s#'#'\"'\"'#g;s#.*#par_miniprot='&'#" ; else echo "# par_miniprot="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_METAEUK+x} ]; then echo "${VIASH_PAR_METAEUK}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk='&'#" ; else echo "# par_metaeuk="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_METAEUK_PARAMETERS+x} ]; then echo "${VIASH_PAR_METAEUK_PARAMETERS}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk_parameters='&'#" ; else echo "# par_metaeuk_parameters="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_METAEUK_RERUN_PARAMETERS+x} ]; then echo "${VIASH_PAR_METAEUK_RERUN_PARAMETERS}" | sed "s#'#'\"'\"'#g;s#.*#par_metaeuk_rerun_parameters='&'#" ; else echo "# par_metaeuk_rerun_parameters="; 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
|
|
|
|
unset_if_false=(
|
|
par_tar
|
|
par_force
|
|
par_quiet
|
|
par_restart
|
|
par_auto_lineage
|
|
par_auto_lineage_euk
|
|
par_auto_lineage_prok
|
|
par_augustus
|
|
par_long
|
|
par_scaffold_composition
|
|
par_miniprot
|
|
)
|
|
|
|
for par in \${unset_if_false[@]}; do
|
|
test_val="\${!par}"
|
|
[[ "\$test_val" == "false" ]] && unset \$par
|
|
done
|
|
|
|
tmp_dir=\$(mktemp -d -p "\$meta_temp_dir" busco_XXXXXXXXX)
|
|
prefix=\$(openssl rand -hex 8)
|
|
|
|
busco \\
|
|
--in "\$par_input" \\
|
|
--mode "\$par_mode" \\
|
|
--out "\$prefix" \\
|
|
--out_path "\$tmp_dir" \\
|
|
--opt-out-run-stats \\
|
|
\${meta_cpus:+--cpu "\${meta_cpus}"} \\
|
|
\${par_lineage_dataset:+--lineage_dataset "\$par_lineage_dataset"} \\
|
|
\${par_augustus:+--augustus} \\
|
|
\${par_augustus_parameters:+--augustus_parameters "\$par_augustus_parameters"} \\
|
|
\${par_augustus_species:+--augustus_species "\$par_augustus_species"} \\
|
|
\${par_auto_lineage:+--auto-lineage} \\
|
|
\${par_auto_lineage_euk:+--auto-lineage-euk} \\
|
|
\${par_auto_lineage_prok:+--auto-lineage-prok} \\
|
|
\${par_contig_break:+--contig_break \$par_contig_break} \\
|
|
\${par_datasets_version:+--datasets_version "\$par_datasets_version"} \\
|
|
\${par_e_value:+--evalue "\$par_e_value"} \\
|
|
\${par_force:+--force} \\
|
|
\${par_limit:+--limit "\$par_limit"} \\
|
|
\${par_long:+--long} \\
|
|
\${par_metaeuk:+--metaeuk} \\
|
|
\${par_metaeuk_parameters:+--metaeuk_parameters "\$par_metaeuk_parameters"} \\
|
|
\${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "\$par_metaeuk_rerun_parameters"} \\
|
|
\${par_miniprot:+--miniprot} \\
|
|
\${par_quiet:+--quiet} \\
|
|
\${par_restart:+--restart} \\
|
|
\${par_scaffold_composition:+--scaffold_composition} \\
|
|
\${par_tar:+--tar} \\
|
|
|
|
|
|
out_dir=\$(find "\$tmp_dir/\$prefix" -maxdepth 1 -name 'run_*')
|
|
|
|
if [[ -n "\$par_short_summary_json" ]]; then
|
|
cp "\$out_dir/short_summary.json" "\$par_short_summary_json"
|
|
fi
|
|
if [[ -n "\$par_short_summary_txt" ]]; then
|
|
cp "\$out_dir/short_summary.txt" "\$par_short_summary_txt"
|
|
fi
|
|
if [[ -n "\$par_full_table" ]]; then
|
|
cp "\$out_dir/full_table.tsv" "\$par_full_table"
|
|
fi
|
|
if [[ -n "\$par_missing_busco_list" ]]; then
|
|
cp "\$out_dir/missing_busco_list.tsv" "\$par_missing_busco_list"
|
|
fi
|
|
if [[ -n "\$par_output_dir" ]]; then
|
|
if [[ -d "\$par_output_dir" ]]; then
|
|
rm -r "\$par_output_dir"
|
|
fi
|
|
cp -r -L "\$out_dir" "\$par_output_dir"
|
|
fi
|
|
VIASHMAIN
|
|
bash "\$tempscript" &
|
|
wait "\$!"
|
|
|
|
VIASHEOF
|
|
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# strip viash automount from file paths
|
|
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_PAR_INPUT=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_JSON" ]; then
|
|
VIASH_PAR_SHORT_SUMMARY_JSON=$(ViashDockerStripAutomount "$VIASH_PAR_SHORT_SUMMARY_JSON")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_TXT" ]; then
|
|
VIASH_PAR_SHORT_SUMMARY_TXT=$(ViashDockerStripAutomount "$VIASH_PAR_SHORT_SUMMARY_TXT")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FULL_TABLE" ]; then
|
|
VIASH_PAR_FULL_TABLE=$(ViashDockerStripAutomount "$VIASH_PAR_FULL_TABLE")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MISSING_BUSCO_LIST" ]; then
|
|
VIASH_PAR_MISSING_BUSCO_LIST=$(ViashDockerStripAutomount "$VIASH_PAR_MISSING_BUSCO_LIST")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_DIR" ]; then
|
|
VIASH_PAR_OUTPUT_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_DIR")
|
|
fi
|
|
if [ ! -z "$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_SHORT_SUMMARY_JSON" ] && [ ! -e "$VIASH_PAR_SHORT_SUMMARY_JSON" ]; then
|
|
ViashError "Output file '$VIASH_PAR_SHORT_SUMMARY_JSON' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_SHORT_SUMMARY_TXT" ] && [ ! -e "$VIASH_PAR_SHORT_SUMMARY_TXT" ]; then
|
|
ViashError "Output file '$VIASH_PAR_SHORT_SUMMARY_TXT' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_FULL_TABLE" ] && [ ! -e "$VIASH_PAR_FULL_TABLE" ]; then
|
|
ViashError "Output file '$VIASH_PAR_FULL_TABLE' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_MISSING_BUSCO_LIST" ] && [ ! -e "$VIASH_PAR_MISSING_BUSCO_LIST" ]; then
|
|
ViashError "Output file '$VIASH_PAR_MISSING_BUSCO_LIST' does not exist."
|
|
exit 1
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT_DIR" ] && [ ! -e "$VIASH_PAR_OUTPUT_DIR" ]; then
|
|
ViashError "Output file '$VIASH_PAR_OUTPUT_DIR' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
|
|
exit 0
|