CI
71f1661df8
Build pipeline: viash-hub.biobox.main-w9wb7
Source commit: 219ba1d3d0
Source message: Add more fq components (#179)
* add fq_lint, move fq_subsample, improve unit tests
* update changelog
1340 lines
52 KiB
Bash
Executable File
1340 lines
52 KiB
Bash
Executable File
#!/usr/bin/env bash
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# bedtools_bamtobed main
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#
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# This wrapper script is auto-generated by viash 0.9.4 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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# * Theodoro Gasperin Terra Camargo (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 $VIASH_META_RESOURCES_DIR`
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# define meta fields
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VIASH_META_NAME="bedtools_bamtobed"
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VIASH_META_FUNCTIONALITY_NAME="bedtools_bamtobed"
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VIASH_META_EXECUTABLE="$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="$VIASH_TEMP"
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# initialise variables
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VIASH_MODE='run'
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VIASH_ENGINE_ID='docker'
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######## Helper functions for setting up Docker images for viash ########
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# expects: ViashDockerBuild
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# ViashDockerInstallationCheck: check whether Docker is installed correctly
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#
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# examples:
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# ViashDockerInstallationCheck
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function ViashDockerInstallationCheck {
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ViashDebug "Checking whether Docker is installed"
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if [ ! command -v docker &> /dev/null ]; then
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ViashCritical "Docker doesn't seem to be installed. See 'https://docs.docker.com/get-docker/' for instructions."
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exit 1
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fi
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ViashDebug "Checking whether the Docker daemon is running"
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local save=$-; 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
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# examples:
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# docker pull python:latest
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# ViashDockerLocalTagCheck python:latest
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# echo $? # returns '0'
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# ViashDockerLocalTagCheck sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerLocalTagCheck {
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[ -n "$(docker images -q $1)" ]
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}
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# ViashDockerPull: pull a Docker image
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# ViashDockerPull python:latest
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# echo $? # returns '0'
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# ViashDockerPull sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerPull {
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ViashNotice "Checking if Docker image is available at '$1'"
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if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
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docker pull $1 && return 0 || return 1
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else
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local save=$-; 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
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# exit code $? : whether or not the image was found
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# examples:
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# ViashDockerPush python:latest
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# echo $? # returns '0'
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# ViashDockerPush sdaizudceahifu
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# echo $? # returns '1'
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function ViashDockerPush {
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ViashNotice "Pushing image to '$1'"
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local save=$-; 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
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# ViashDockerBuild : a Bash function which builds a docker image, takes image identifier as argument.
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# examples:
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# ViashDockerPullElseBuild mynewcomponent
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function ViashDockerPullElseBuild {
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local save=$-; set +e
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ViashDockerPull $1
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local out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashDockerBuild $@
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fi
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}
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# ViashDockerSetup: create a Docker image, according to specified docker setup strategy
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# $2 : docker setup strategy, see DockerSetupStrategy.scala
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# examples:
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# ViashDockerSetup mynewcomponent alwaysbuild
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function ViashDockerSetup {
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local image_id="$1"
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local setup_strategy="$2"
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if [ "$setup_strategy" == "alwaysbuild" -o "$setup_strategy" == "build" -o "$setup_strategy" == "b" ]; then
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ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "alwayspull" -o "$setup_strategy" == "pull" -o "$setup_strategy" == "p" ]; then
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ViashDockerPull $image_id
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elif [ "$setup_strategy" == "alwayspullelsebuild" -o "$setup_strategy" == "pullelsebuild" ]; then
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ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "alwayspullelsecachedbuild" -o "$setup_strategy" == "pullelsecachedbuild" ]; then
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ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "alwayscachedbuild" -o "$setup_strategy" == "cachedbuild" -o "$setup_strategy" == "cb" ]; then
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ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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elif [[ "$setup_strategy" =~ ^ifneedbe ]]; then
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local save=$-; set +e
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ViashDockerLocalTagCheck $image_id
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local outCheck=$?
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[[ $save =~ e ]] && set -e
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if [ $outCheck -eq 0 ]; then
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ViashInfo "Image $image_id already exists"
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elif [ "$setup_strategy" == "ifneedbebuild" ]; then
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ViashDockerBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "ifneedbecachedbuild" ]; then
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ViashDockerBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "ifneedbepull" ]; then
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ViashDockerPull $image_id
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elif [ "$setup_strategy" == "ifneedbepullelsebuild" ]; then
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ViashDockerPullElseBuild $image_id --no-cache $(ViashDockerBuildArgs "$engine_id")
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elif [ "$setup_strategy" == "ifneedbepullelsecachedbuild" ]; then
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ViashDockerPullElseBuild $image_id $(ViashDockerBuildArgs "$engine_id")
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else
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ViashError "Unrecognised Docker strategy: $setup_strategy"
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exit 1
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fi
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elif [ "$setup_strategy" == "push" -o "$setup_strategy" == "forcepush" -o "$setup_strategy" == "alwayspush" ]; then
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ViashDockerPush "$image_id"
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elif [ "$setup_strategy" == "pushifnotpresent" -o "$setup_strategy" == "gentlepush" -o "$setup_strategy" == "maybepush" ]; then
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local save=$-; set +e
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ViashDockerRemoteTagCheck $image_id
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local outCheck=$?
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[[ $save =~ e ]] && set -e
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if [ $outCheck -eq 0 ]; then
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ViashNotice "Container '$image_id' exists, doing nothing."
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else
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ViashNotice "Container '$image_id' does not yet exist."
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ViashDockerPush "$image_id"
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fi
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elif [ "$setup_strategy" == "donothing" -o "$setup_strategy" == "meh" ]; then
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ViashNotice "Skipping setup."
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else
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ViashError "Unrecognised Docker strategy: $setup_strategy"
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exit 1
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fi
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}
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# ViashDockerCheckCommands: Check whether a docker container has the required commands
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#
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# $1 : image identifier with format `[registry/]image[:tag]`
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# $@ : commands to verify being present
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# examples:
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# ViashDockerCheckCommands bash:4.0 bash ps foo
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function ViashDockerCheckCommands {
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local image_id="$1"
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shift 1
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local commands="$@"
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local save=$-; set +e
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local missing # mark 'missing' as local in advance, otherwise the exit code of the command will be missing and always be '0'
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missing=$(docker run --rm --entrypoint=sh "$image_id" -c "for command in $commands; do command -v \$command >/dev/null 2>&1; if [ \$? -ne 0 ]; then echo \$command; exit 1; fi; done")
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local outCheck=$?
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[[ $save =~ e ]] && set -e
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if [ $outCheck -ne 0 ]; then
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ViashError "Docker container '$image_id' does not contain command '$missing'."
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exit 1
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fi
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}
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# ViashDockerBuild: build a docker image
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# $1 : image identifier with format `[registry/]image[:tag]`
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# $... : additional arguments to pass to docker build
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# $VIASH_META_TEMP_DIR : temporary directory to store dockerfile & optional resources in
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# $VIASH_META_NAME : name of the component
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# $VIASH_META_RESOURCES_DIR : directory containing the resources
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# $VIASH_VERBOSITY : verbosity level
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# exit code $? : whether or not the image was built successfully
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function ViashDockerBuild {
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local image_id="$1"
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shift 1
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# create temporary directory to store dockerfile & optional resources in
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local tmpdir=$(mktemp -d "$VIASH_META_TEMP_DIR/dockerbuild-$VIASH_META_NAME-XXXXXX")
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local dockerfile="$tmpdir/Dockerfile"
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function clean_up {
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rm -rf "$tmpdir"
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}
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trap clean_up EXIT
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# store dockerfile and resources
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ViashDockerfile "$VIASH_ENGINE_ID" > "$dockerfile"
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# generate the build command
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local docker_build_cmd="docker build -t '$image_id' $@ '$VIASH_META_RESOURCES_DIR' -f '$dockerfile'"
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# build the container
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ViashNotice "Building container '$image_id' with Dockerfile"
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ViashInfo "$docker_build_cmd"
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local save=$-; set +e
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if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
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eval $docker_build_cmd
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else
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eval $docker_build_cmd &> "$tmpdir/docker_build.log"
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fi
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# check exit code
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local out=$?
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[[ $save =~ e ]] && set -e
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if [ $out -ne 0 ]; then
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ViashError "Error occurred while building container '$image_id'"
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if [ $VIASH_VERBOSITY -lt $VIASH_LOGCODE_INFO ]; then
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ViashError "Transcript: --------------------------------"
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cat "$tmpdir/docker_build.log"
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ViashError "End of transcript --------------------------"
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fi
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exit 1
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fi
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}
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######## End of helper functions for setting up Docker images for viash ########
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# ViashDockerFile: print the dockerfile to stdout
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# $1 : engine identifier
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# return : dockerfile required to run this component
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# examples:
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# ViashDockerFile
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function ViashDockerfile {
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local engine_id="$1"
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if [[ "$engine_id" == "docker" ]]; then
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cat << 'VIASHDOCKER'
|
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FROM debian:stable-slim
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ENTRYPOINT []
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RUN apt-get update && \
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DEBIAN_FRONTEND=noninteractive apt-get install -y bedtools procps && \
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rm -rf /var/lib/apt/lists/*
|
|
|
|
RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var/software_versions.txt
|
|
|
|
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
|
|
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtobed"
|
|
LABEL org.opencontainers.image.created="2025-06-23T06:29:27Z"
|
|
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
|
|
LABEL org.opencontainers.image.revision="219ba1d3d0d7fbc66393595534bb6c333b08b238"
|
|
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)
|
|
|
|
|
|
# ViashHelp: Display helpful explanation about this executable
|
|
function ViashHelp {
|
|
echo "bedtools_bamtobed main"
|
|
echo ""
|
|
echo "Converts BAM alignments to BED6 or BEDPE format."
|
|
echo ""
|
|
echo "Inputs:"
|
|
echo " -i, --input"
|
|
echo " type: file, required parameter, file must exist"
|
|
echo " Input BAM file."
|
|
echo ""
|
|
echo "Outputs:"
|
|
echo " -o, --output"
|
|
echo " type: file, required parameter, output, file must exist"
|
|
echo " Output BED file."
|
|
echo ""
|
|
echo "Options:"
|
|
echo " --bedpe"
|
|
echo " type: boolean_true"
|
|
echo " Write BEDPE format. Requires BAM to be grouped or sorted by query."
|
|
echo ""
|
|
echo " --mate1"
|
|
echo " type: boolean_true"
|
|
echo " When writing BEDPE (-bedpe) format, always report mate one as the first"
|
|
echo " BEDPE \"block\"."
|
|
echo ""
|
|
echo " --bed12"
|
|
echo " type: boolean_true"
|
|
echo " Write \"blocked\" BED format (aka \"BED12\"). Forces -split."
|
|
echo " See http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1"
|
|
echo ""
|
|
echo " --split"
|
|
echo " type: boolean_true"
|
|
echo " Report \"split\" BAM alignments as separate BED entries."
|
|
echo " Splits only on N CIGAR operations."
|
|
echo ""
|
|
echo " --splitD"
|
|
echo " type: boolean_true"
|
|
echo " Split alignments based on N and D CIGAR operators."
|
|
echo " Forces -split."
|
|
echo ""
|
|
echo " -ed, --edit_distance"
|
|
echo " type: boolean_true"
|
|
echo " Use BAM edit distance (NM tag) for BED score."
|
|
echo " - Default for BED is to use mapping quality."
|
|
echo " - Default for BEDPE is to use the minimum of"
|
|
echo " the two mapping qualities for the pair."
|
|
echo " - When -ed is used with -bedpe, the total edit"
|
|
echo " distance from the two mates is reported."
|
|
echo ""
|
|
echo " --tag"
|
|
echo " type: string"
|
|
echo " example: SM"
|
|
echo " Use other NUMERIC BAM alignment tag for BED score."
|
|
echo " Default for BED is to use mapping quality. Disallowed with BEDPE output."
|
|
echo ""
|
|
echo " --color"
|
|
echo " type: string"
|
|
echo " example: 250,250,250"
|
|
echo " An R,G,B string for the color used with BED12 format."
|
|
echo " Default is (255,0,0)."
|
|
echo ""
|
|
echo " --cigar"
|
|
echo " type: boolean_true"
|
|
echo " Add the CIGAR string to the BED entry as a 7th column."
|
|
echo ""
|
|
echo "Viash built in Computational Requirements:"
|
|
echo " ---cpus=INT"
|
|
echo " Number of CPUs to use"
|
|
echo " ---memory=STRING"
|
|
echo " Amount of memory to use. Examples: 4GB, 3MiB."
|
|
echo ""
|
|
echo "Viash built in Docker:"
|
|
echo " ---setup=STRATEGY"
|
|
echo " Setup the docker container. Options are: alwaysbuild, alwayscachedbuild, ifneedbebuild, ifneedbecachedbuild, alwayspull, alwayspullelsebuild, alwayspullelsecachedbuild, ifneedbepull, ifneedbepullelsebuild, ifneedbepullelsecachedbuild, push, pushifnotpresent, donothing."
|
|
echo " Default: ifneedbepullelsecachedbuild"
|
|
echo " ---dockerfile"
|
|
echo " Print the dockerfile to stdout."
|
|
echo " ---docker_run_args=ARG"
|
|
echo " Provide runtime arguments to Docker. See the documentation on \`docker run\` for more information."
|
|
echo " ---docker_image_id"
|
|
echo " Print the docker image id to stdout."
|
|
echo " ---debug"
|
|
echo " Enter the docker container for debugging purposes."
|
|
echo ""
|
|
echo "Viash built in Engines:"
|
|
echo " ---engine=ENGINE_ID"
|
|
echo " Specify the engine to use. Options are: docker, native."
|
|
echo " Default: docker"
|
|
}
|
|
|
|
# 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 "$1")"
|
|
shift 1
|
|
;;
|
|
--version)
|
|
echo "bedtools_bamtobed main"
|
|
exit
|
|
;;
|
|
--input)
|
|
[ -n "$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"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output=*)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-o)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'-o\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--bedpe)
|
|
[ -n "$VIASH_PAR_BEDPE" ] && ViashError Bad arguments for option \'--bedpe\': \'$VIASH_PAR_BEDPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BEDPE=true
|
|
shift 1
|
|
;;
|
|
--mate1)
|
|
[ -n "$VIASH_PAR_MATE1" ] && ViashError Bad arguments for option \'--mate1\': \'$VIASH_PAR_MATE1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MATE1=true
|
|
shift 1
|
|
;;
|
|
--bed12)
|
|
[ -n "$VIASH_PAR_BED12" ] && ViashError Bad arguments for option \'--bed12\': \'$VIASH_PAR_BED12\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_BED12=true
|
|
shift 1
|
|
;;
|
|
--split)
|
|
[ -n "$VIASH_PAR_SPLIT" ] && ViashError Bad arguments for option \'--split\': \'$VIASH_PAR_SPLIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SPLIT=true
|
|
shift 1
|
|
;;
|
|
--splitD)
|
|
[ -n "$VIASH_PAR_SPLITD" ] && ViashError Bad arguments for option \'--splitD\': \'$VIASH_PAR_SPLITD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SPLITD=true
|
|
shift 1
|
|
;;
|
|
--edit_distance)
|
|
[ -n "$VIASH_PAR_EDIT_DISTANCE" ] && ViashError Bad arguments for option \'--edit_distance\': \'$VIASH_PAR_EDIT_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EDIT_DISTANCE=true
|
|
shift 1
|
|
;;
|
|
-ed)
|
|
[ -n "$VIASH_PAR_EDIT_DISTANCE" ] && ViashError Bad arguments for option \'-ed\': \'$VIASH_PAR_EDIT_DISTANCE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_EDIT_DISTANCE=true
|
|
shift 1
|
|
;;
|
|
--tag)
|
|
[ -n "$VIASH_PAR_TAG" ] && ViashError Bad arguments for option \'--tag\': \'$VIASH_PAR_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TAG="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --tag. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--tag=*)
|
|
[ -n "$VIASH_PAR_TAG" ] && ViashError Bad arguments for option \'--tag=*\': \'$VIASH_PAR_TAG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_TAG=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--color)
|
|
[ -n "$VIASH_PAR_COLOR" ] && ViashError Bad arguments for option \'--color\': \'$VIASH_PAR_COLOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COLOR="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --color. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--color=*)
|
|
[ -n "$VIASH_PAR_COLOR" ] && ViashError Bad arguments for option \'--color=*\': \'$VIASH_PAR_COLOR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_COLOR=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--cigar)
|
|
[ -n "$VIASH_PAR_CIGAR" ] && ViashError Bad arguments for option \'--cigar\': \'$VIASH_PAR_CIGAR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_CIGAR=true
|
|
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/bedtools/bedtools_bamtobed: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_OUTPUT+x} ]; then
|
|
ViashError '--output' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_NAME+x} ]; then
|
|
ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
|
|
ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
|
|
ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
|
|
ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_CONFIG+x} ]; then
|
|
ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
|
|
ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
|
|
# filling in defaults
|
|
if [ -z ${VIASH_PAR_BEDPE+x} ]; then
|
|
VIASH_PAR_BEDPE="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_MATE1+x} ]; then
|
|
VIASH_PAR_MATE1="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_BED12+x} ]; then
|
|
VIASH_PAR_BED12="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SPLIT+x} ]; then
|
|
VIASH_PAR_SPLIT="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SPLITD+x} ]; then
|
|
VIASH_PAR_SPLITD="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_EDIT_DISTANCE+x} ]; then
|
|
VIASH_PAR_EDIT_DISTANCE="false"
|
|
fi
|
|
if [ -z ${VIASH_PAR_CIGAR+x} ]; then
|
|
VIASH_PAR_CIGAR="false"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$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 "$VIASH_PAR_BEDPE" ]]; then
|
|
if ! [[ "$VIASH_PAR_BEDPE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--bedpe' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MATE1" ]]; then
|
|
if ! [[ "$VIASH_PAR_MATE1" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--mate1' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_BED12" ]]; then
|
|
if ! [[ "$VIASH_PAR_BED12" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--bed12' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SPLIT" ]]; then
|
|
if ! [[ "$VIASH_PAR_SPLIT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--split' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SPLITD" ]]; then
|
|
if ! [[ "$VIASH_PAR_SPLITD" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--splitD' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_EDIT_DISTANCE" ]]; then
|
|
if ! [[ "$VIASH_PAR_EDIT_DISTANCE" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--edit_distance' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_CIGAR" ]]; then
|
|
if ! [[ "$VIASH_PAR_CIGAR" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
|
ViashError '--cigar' has to be a boolean_true. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_CPUS" ]]; then
|
|
if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
|
|
if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
|
|
# create parent directories of output files, if so desired
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT")" ]; then
|
|
mkdir -p "$(dirname "$VIASH_PAR_OUTPUT")"
|
|
fi
|
|
|
|
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
|
|
if [ "$VIASH_MODE" == "run" ]; then
|
|
VIASH_CMD="bash"
|
|
else
|
|
ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
|
|
exit 1
|
|
fi
|
|
fi
|
|
|
|
if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
|
# detect volumes from file arguments
|
|
VIASH_CHOWN_VARS=()
|
|
if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT")" )
|
|
VIASH_PAR_INPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT")
|
|
fi
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ]; then
|
|
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" )
|
|
VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT")
|
|
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT" )
|
|
fi
|
|
if [ ! -z "$VIASH_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-bedtools_bamtobed-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 ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_BEDPE+x} ]; then echo "${VIASH_PAR_BEDPE}" | sed "s#'#'\"'\"'#g;s#.*#par_bedpe='&'#" ; else echo "# par_bedpe="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_MATE1+x} ]; then echo "${VIASH_PAR_MATE1}" | sed "s#'#'\"'\"'#g;s#.*#par_mate1='&'#" ; else echo "# par_mate1="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_BED12+x} ]; then echo "${VIASH_PAR_BED12}" | sed "s#'#'\"'\"'#g;s#.*#par_bed12='&'#" ; else echo "# par_bed12="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SPLIT+x} ]; then echo "${VIASH_PAR_SPLIT}" | sed "s#'#'\"'\"'#g;s#.*#par_split='&'#" ; else echo "# par_split="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_SPLITD+x} ]; then echo "${VIASH_PAR_SPLITD}" | sed "s#'#'\"'\"'#g;s#.*#par_splitD='&'#" ; else echo "# par_splitD="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_EDIT_DISTANCE+x} ]; then echo "${VIASH_PAR_EDIT_DISTANCE}" | sed "s#'#'\"'\"'#g;s#.*#par_edit_distance='&'#" ; else echo "# par_edit_distance="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_TAG+x} ]; then echo "${VIASH_PAR_TAG}" | sed "s#'#'\"'\"'#g;s#.*#par_tag='&'#" ; else echo "# par_tag="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_COLOR+x} ]; then echo "${VIASH_PAR_COLOR}" | sed "s#'#'\"'\"'#g;s#.*#par_color='&'#" ; else echo "# par_color="; fi )
|
|
$( if [ ! -z ${VIASH_PAR_CIGAR+x} ]; then echo "${VIASH_PAR_CIGAR}" | sed "s#'#'\"'\"'#g;s#.*#par_cigar='&'#" ; else echo "# par_cigar="; 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
|
|
|
|
set -eo pipefail
|
|
|
|
# Unset parameters
|
|
unset_if_false=(
|
|
par_bedpe
|
|
par_mate1
|
|
par_bed12
|
|
par_split
|
|
par_splitD
|
|
par_edit_distance
|
|
par_tag
|
|
par_color
|
|
par_cigar
|
|
)
|
|
|
|
for par in \${unset_if_false[@]}; do
|
|
test_val="\${!par}"
|
|
[[ "\$test_val" == "false" ]] && unset \$par
|
|
done
|
|
|
|
# Execute bedtools sort with the provided arguments
|
|
bedtools bamtobed \\
|
|
\${par_bedpe:+-bedpe} \\
|
|
\${par_mate1:+-mate1} \\
|
|
\${par_bed12:+-bed12} \\
|
|
\${par_split:+-split} \\
|
|
\${par_splitD:+-splitD} \\
|
|
\${par_edit_distance:+-ed} \\
|
|
\${par_tag:+-tag "\$par_tag"} \\
|
|
\${par_cigar:+-cigar} \\
|
|
\${par_color:+-color "\$par_color"} \\
|
|
-i "\$par_input" \\
|
|
> "\$par_output"
|
|
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 "$VIASH_PAR_OUTPUT" ]; then
|
|
VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT")
|
|
fi
|
|
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
|
|
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
|
|
fi
|
|
if [ ! -z "$VIASH_META_EXECUTABLE" ]; then
|
|
VIASH_META_EXECUTABLE=$(ViashDockerStripAutomount "$VIASH_META_EXECUTABLE")
|
|
fi
|
|
if [ ! -z "$VIASH_META_CONFIG" ]; then
|
|
VIASH_META_CONFIG=$(ViashDockerStripAutomount "$VIASH_META_CONFIG")
|
|
fi
|
|
if [ ! -z "$VIASH_META_TEMP_DIR" ]; then
|
|
VIASH_META_TEMP_DIR=$(ViashDockerStripAutomount "$VIASH_META_TEMP_DIR")
|
|
fi
|
|
fi
|
|
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$VIASH_PAR_OUTPUT" ] && [ ! -e "$VIASH_PAR_OUTPUT" ]; then
|
|
ViashError "Output file '$VIASH_PAR_OUTPUT' does not exist."
|
|
exit 1
|
|
fi
|
|
|
|
|
|
exit 0
|