CI
cd0af18851
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
1776 lines
74 KiB
Bash
Executable File
1776 lines
74 KiB
Bash
Executable File
#!/usr/bin/env bash
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# densmap dev
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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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# * Jakub Majercik (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 $VIASH_META_RESOURCES_DIR`
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# define meta fields
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VIASH_META_NAME="densmap"
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VIASH_META_FUNCTIONALITY_NAME="densmap"
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VIASH_META_EXECUTABLE="$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 "densmap dev"
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echo ""
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echo "A modification of UMAP that adds an extra cost term in order to preserve"
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echo "information"
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echo "about the relative local density of the data. It is performed on the same inputs"
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echo "as UMAP."
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echo ""
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echo "Inputs:"
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echo " --input"
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echo " type: file, required parameter, file must exist"
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echo " example: input.h5mu"
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echo " Input h5mu file"
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echo ""
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echo " --modality"
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echo " type: string"
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echo " default: rna"
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echo ""
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echo " --uns_neighbors"
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echo " type: string"
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echo " default: neighbors"
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echo " The \`.uns\` neighbors slot as output by the \`find_neighbors\` component."
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echo ""
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echo " --obsm_pca"
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echo " type: string, required parameter"
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echo " The slot in \`.obsm\` where the PCA results are stored."
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echo ""
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echo " --obsm_knn_indices"
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echo " type: string, required parameter"
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echo " The slot in \`.obsm\` where the kNN indices are stored."
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echo ""
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echo " --obsm_knn_distances"
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echo " type: string, required parameter"
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echo " The slot in \`.obsm\` where the kNN distances are stored."
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echo ""
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echo "Outputs:"
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echo " -o, --output"
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echo " type: file, required parameter, output, file must exist"
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echo " example: output.h5mu"
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echo " Output h5mu file."
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echo ""
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echo " --output_compression"
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echo " type: string"
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echo " example: gzip"
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echo " choices: [ gzip, lzf ]"
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echo " The compression format to be used on the output h5mu object."
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echo ""
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echo " --obsm_output"
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echo " type: string"
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echo " default: X_densmap"
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echo " The .obsm key to use for storing the densMAP results.."
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echo ""
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echo "Arguments UMAP:"
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echo " --min_dist"
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echo " type: double"
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echo " default: 0.5"
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echo " min: 0.0"
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echo " max: 10.0"
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echo " The effective minimum distance between embedded points. Smaller values"
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echo " will result"
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echo " in a more clustered/clumped embedding where nearby points on the"
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echo " manifold are drawn"
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echo " closer together, while larger values will result on a more even"
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echo " dispersal of points."
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echo " The value should be set relative to the spread value, which determines"
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echo " the scale at"
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echo " which embedded points will be spread out."
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echo ""
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echo " --spread"
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echo " type: double"
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echo " default: 1.0"
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echo " min: 0.0"
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echo " max: 10.0"
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echo " The effective scale of embedded points. In combination with \`min_dist\`"
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echo " this"
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echo " determines how clustered/clumped the embedded points are."
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echo ""
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echo " --num_components"
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echo " type: integer"
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echo " default: 2"
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echo " min: 1"
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echo " The number of dimensions of the embedding."
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echo ""
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echo " --max_iter"
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echo " type: integer"
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echo " default: 0"
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echo " min: 0"
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echo " max: 1000"
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echo " The number of iterations (epochs) of the optimization. Called \`n_epochs\`"
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echo " in the original UMAP. Default is set to 500 if"
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echo " neighbors['connectivities'].shape[0] <= 10000, else 200."
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echo ""
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echo " --alpha"
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echo " type: double"
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echo " default: 1.0"
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echo " The initial learning rate for the embedding optimization."
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echo ""
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echo " --gamma"
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echo " type: double"
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echo " default: 1.0"
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echo " Weighting applied to negative samples in low dimensional embedding"
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echo " optimization."
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echo " Values higher than one will result in greater weight being given to"
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echo " negative samples."
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echo ""
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echo " --negative_sample_rate"
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echo " type: integer"
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echo " default: 5"
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echo " The number of negative samples to select per positive sample"
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echo " in the optimization process. Increasing this value will result"
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echo " in greater repulsive force being applied, greater optimization"
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echo " cost, but slightly more accuracy."
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echo ""
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echo " --init_pos"
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echo " type: string"
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echo " default: spectral"
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echo " choices: [ paga, spectral, random ]"
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echo " How to initialize the low dimensional embedding. Called \`init\` in the"
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echo " original UMAP. Options are:"
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echo " * Any key from \`.obsm\`"
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echo " * \`'paga'\`: positions from \`paga()\`"
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echo " * \`'spectral'\`: use a spectral embedding of the graph"
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echo " * \`'random'\`: assign initial embedding positions at random."
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echo ""
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echo "Arguments densMAP:"
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echo " --lambda"
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echo " type: double"
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echo " default: 2.0"
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echo " min: 0.01"
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echo " max: 10.0"
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echo " Controls the regularization weight of the density correlation term in"
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echo " densMAP."
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echo " Higher values prioritize density preservation over the UMAP objective,"
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echo " and vice versa"
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echo " for values closer to zero. Setting this parameter to zero is equivalent"
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echo " to running"
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echo " the original UMAP algorithm."
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echo ""
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echo " --fraction"
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echo " type: double"
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echo " default: 0.3"
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echo " Controls the fraction of epochs (between 0 and 1) where the"
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echo " density-augmented objective"
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echo " is used in densMAP. The first (1 - dens_frac) fraction of epochs"
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echo " optimize the original"
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echo " UMAP objective before introducing the density correlation term."
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echo ""
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echo " --var_shift"
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echo " type: double"
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echo " default: 0.1"
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echo " A small constant added to the variance of local radii in the embedding"
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echo " when calculating"
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echo " the density correlation objective to prevent numerical instability from"
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echo " dividing by a"
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echo " small number."
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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
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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")
|
|
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 python:3.12-slim
|
|
ENTRYPOINT []
|
|
RUN apt-get update && \
|
|
DEBIAN_FRONTEND=noninteractive apt-get install -y procps && \
|
|
rm -rf /var/lib/apt/lists/*
|
|
|
|
RUN pip install --upgrade pip && \
|
|
pip install --upgrade --no-cache-dir "anndata==0.10.8" "mudata~=0.2.4" "pandas!=2.1.2" "numpy<2.0.0" "umap-learn"
|
|
|
|
LABEL org.opencontainers.image.authors="Jakub Majercik"
|
|
LABEL org.opencontainers.image.description="Companion container for running component dimred densmap"
|
|
LABEL org.opencontainers.image.created="2024-10-17T17:49:02Z"
|
|
LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
|
|
LABEL org.opencontainers.image.revision="2dbe3b7231f9abb4baa628e76e8abc686e627087"
|
|
LABEL org.opencontainers.image.version="dev"
|
|
|
|
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 "$1")"
|
|
shift 1
|
|
;;
|
|
--version)
|
|
echo "densmap dev"
|
|
exit
|
|
;;
|
|
--input)
|
|
[ -n "$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 "$1")
|
|
shift 1
|
|
;;
|
|
--modality)
|
|
[ -n "$VIASH_PAR_MODALITY" ] && ViashError Bad arguments for option \'--modality\': \'$VIASH_PAR_MODALITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MODALITY="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --modality. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--modality=*)
|
|
[ -n "$VIASH_PAR_MODALITY" ] && ViashError Bad arguments for option \'--modality=*\': \'$VIASH_PAR_MODALITY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MODALITY=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--uns_neighbors)
|
|
[ -n "$VIASH_PAR_UNS_NEIGHBORS" ] && ViashError Bad arguments for option \'--uns_neighbors\': \'$VIASH_PAR_UNS_NEIGHBORS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UNS_NEIGHBORS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --uns_neighbors. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--uns_neighbors=*)
|
|
[ -n "$VIASH_PAR_UNS_NEIGHBORS" ] && ViashError Bad arguments for option \'--uns_neighbors=*\': \'$VIASH_PAR_UNS_NEIGHBORS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_UNS_NEIGHBORS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--obsm_pca)
|
|
[ -n "$VIASH_PAR_OBSM_PCA" ] && ViashError Bad arguments for option \'--obsm_pca\': \'$VIASH_PAR_OBSM_PCA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OBSM_PCA="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --obsm_pca. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--obsm_pca=*)
|
|
[ -n "$VIASH_PAR_OBSM_PCA" ] && ViashError Bad arguments for option \'--obsm_pca=*\': \'$VIASH_PAR_OBSM_PCA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OBSM_PCA=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--obsm_knn_indices)
|
|
[ -n "$VIASH_PAR_OBSM_KNN_INDICES" ] && ViashError Bad arguments for option \'--obsm_knn_indices\': \'$VIASH_PAR_OBSM_KNN_INDICES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OBSM_KNN_INDICES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --obsm_knn_indices. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--obsm_knn_indices=*)
|
|
[ -n "$VIASH_PAR_OBSM_KNN_INDICES" ] && ViashError Bad arguments for option \'--obsm_knn_indices=*\': \'$VIASH_PAR_OBSM_KNN_INDICES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OBSM_KNN_INDICES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--obsm_knn_distances)
|
|
[ -n "$VIASH_PAR_OBSM_KNN_DISTANCES" ] && ViashError Bad arguments for option \'--obsm_knn_distances\': \'$VIASH_PAR_OBSM_KNN_DISTANCES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OBSM_KNN_DISTANCES="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --obsm_knn_distances. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--obsm_knn_distances=*)
|
|
[ -n "$VIASH_PAR_OBSM_KNN_DISTANCES" ] && ViashError Bad arguments for option \'--obsm_knn_distances=*\': \'$VIASH_PAR_OBSM_KNN_DISTANCES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OBSM_KNN_DISTANCES=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--output)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output=*)
|
|
[ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output=*\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
-o)
|
|
[ -n "$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"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to -o. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output_compression)
|
|
[ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_COMPRESSION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --output_compression. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--output_compression=*)
|
|
[ -n "$VIASH_PAR_OUTPUT_COMPRESSION" ] && ViashError Bad arguments for option \'--output_compression=*\': \'$VIASH_PAR_OUTPUT_COMPRESSION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OUTPUT_COMPRESSION=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--obsm_output)
|
|
[ -n "$VIASH_PAR_OBSM_OUTPUT" ] && ViashError Bad arguments for option \'--obsm_output\': \'$VIASH_PAR_OBSM_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OBSM_OUTPUT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --obsm_output. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--obsm_output=*)
|
|
[ -n "$VIASH_PAR_OBSM_OUTPUT" ] && ViashError Bad arguments for option \'--obsm_output=*\': \'$VIASH_PAR_OBSM_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_OBSM_OUTPUT=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--min_dist)
|
|
[ -n "$VIASH_PAR_MIN_DIST" ] && ViashError Bad arguments for option \'--min_dist\': \'$VIASH_PAR_MIN_DIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_DIST="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --min_dist. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--min_dist=*)
|
|
[ -n "$VIASH_PAR_MIN_DIST" ] && ViashError Bad arguments for option \'--min_dist=*\': \'$VIASH_PAR_MIN_DIST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MIN_DIST=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--spread)
|
|
[ -n "$VIASH_PAR_SPREAD" ] && ViashError Bad arguments for option \'--spread\': \'$VIASH_PAR_SPREAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SPREAD="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --spread. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--spread=*)
|
|
[ -n "$VIASH_PAR_SPREAD" ] && ViashError Bad arguments for option \'--spread=*\': \'$VIASH_PAR_SPREAD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_SPREAD=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--num_components)
|
|
[ -n "$VIASH_PAR_NUM_COMPONENTS" ] && ViashError Bad arguments for option \'--num_components\': \'$VIASH_PAR_NUM_COMPONENTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_COMPONENTS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --num_components. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--num_components=*)
|
|
[ -n "$VIASH_PAR_NUM_COMPONENTS" ] && ViashError Bad arguments for option \'--num_components=*\': \'$VIASH_PAR_NUM_COMPONENTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NUM_COMPONENTS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--max_iter)
|
|
[ -n "$VIASH_PAR_MAX_ITER" ] && ViashError Bad arguments for option \'--max_iter\': \'$VIASH_PAR_MAX_ITER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_ITER="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --max_iter. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--max_iter=*)
|
|
[ -n "$VIASH_PAR_MAX_ITER" ] && ViashError Bad arguments for option \'--max_iter=*\': \'$VIASH_PAR_MAX_ITER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_MAX_ITER=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--alpha)
|
|
[ -n "$VIASH_PAR_ALPHA" ] && ViashError Bad arguments for option \'--alpha\': \'$VIASH_PAR_ALPHA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ALPHA="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --alpha. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--alpha=*)
|
|
[ -n "$VIASH_PAR_ALPHA" ] && ViashError Bad arguments for option \'--alpha=*\': \'$VIASH_PAR_ALPHA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_ALPHA=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--gamma)
|
|
[ -n "$VIASH_PAR_GAMMA" ] && ViashError Bad arguments for option \'--gamma\': \'$VIASH_PAR_GAMMA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GAMMA="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --gamma. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--gamma=*)
|
|
[ -n "$VIASH_PAR_GAMMA" ] && ViashError Bad arguments for option \'--gamma=*\': \'$VIASH_PAR_GAMMA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_GAMMA=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--negative_sample_rate)
|
|
[ -n "$VIASH_PAR_NEGATIVE_SAMPLE_RATE" ] && ViashError Bad arguments for option \'--negative_sample_rate\': \'$VIASH_PAR_NEGATIVE_SAMPLE_RATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NEGATIVE_SAMPLE_RATE="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --negative_sample_rate. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--negative_sample_rate=*)
|
|
[ -n "$VIASH_PAR_NEGATIVE_SAMPLE_RATE" ] && ViashError Bad arguments for option \'--negative_sample_rate=*\': \'$VIASH_PAR_NEGATIVE_SAMPLE_RATE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_NEGATIVE_SAMPLE_RATE=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--init_pos)
|
|
[ -n "$VIASH_PAR_INIT_POS" ] && ViashError Bad arguments for option \'--init_pos\': \'$VIASH_PAR_INIT_POS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INIT_POS="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --init_pos. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--init_pos=*)
|
|
[ -n "$VIASH_PAR_INIT_POS" ] && ViashError Bad arguments for option \'--init_pos=*\': \'$VIASH_PAR_INIT_POS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_INIT_POS=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--lambda)
|
|
[ -n "$VIASH_PAR_LAMBDA" ] && ViashError Bad arguments for option \'--lambda\': \'$VIASH_PAR_LAMBDA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LAMBDA="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --lambda. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--lambda=*)
|
|
[ -n "$VIASH_PAR_LAMBDA" ] && ViashError Bad arguments for option \'--lambda=*\': \'$VIASH_PAR_LAMBDA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_LAMBDA=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--fraction)
|
|
[ -n "$VIASH_PAR_FRACTION" ] && ViashError Bad arguments for option \'--fraction\': \'$VIASH_PAR_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FRACTION="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fraction. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--fraction=*)
|
|
[ -n "$VIASH_PAR_FRACTION" ] && ViashError Bad arguments for option \'--fraction=*\': \'$VIASH_PAR_FRACTION\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_FRACTION=$(ViashRemoveFlags "$1")
|
|
shift 1
|
|
;;
|
|
--var_shift)
|
|
[ -n "$VIASH_PAR_VAR_SHIFT" ] && ViashError Bad arguments for option \'--var_shift\': \'$VIASH_PAR_VAR_SHIFT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_VAR_SHIFT="$2"
|
|
[ $# -lt 2 ] && ViashError Not enough arguments passed to --var_shift. Use "--help" to get more information on the parameters. && exit 1
|
|
shift 2
|
|
;;
|
|
--var_shift=*)
|
|
[ -n "$VIASH_PAR_VAR_SHIFT" ] && ViashError Bad arguments for option \'--var_shift=*\': \'$VIASH_PAR_VAR_SHIFT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
|
VIASH_PAR_VAR_SHIFT=$(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/openpipeline/dimred/densmap:dev'
|
|
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 "$VIASH_DOCKER_IMAGE_ID" 'bash'
|
|
exit 0
|
|
fi
|
|
|
|
# check if docker image exists
|
|
ViashDockerSetup "$VIASH_DOCKER_IMAGE_ID" ifneedbepullelsecachedbuild
|
|
ViashDockerCheckCommands "$VIASH_DOCKER_IMAGE_ID" '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_OBSM_PCA+x} ]; then
|
|
ViashError '--obsm_pca' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_OBSM_KNN_INDICES+x} ]; then
|
|
ViashError '--obsm_knn_indices' is a required argument. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [ -z ${VIASH_PAR_OBSM_KNN_DISTANCES+x} ]; then
|
|
ViashError '--obsm_knn_distances' 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_MODALITY+x} ]; then
|
|
VIASH_PAR_MODALITY="rna"
|
|
fi
|
|
if [ -z ${VIASH_PAR_UNS_NEIGHBORS+x} ]; then
|
|
VIASH_PAR_UNS_NEIGHBORS="neighbors"
|
|
fi
|
|
if [ -z ${VIASH_PAR_OBSM_OUTPUT+x} ]; then
|
|
VIASH_PAR_OBSM_OUTPUT="X_densmap"
|
|
fi
|
|
if [ -z ${VIASH_PAR_MIN_DIST+x} ]; then
|
|
VIASH_PAR_MIN_DIST="0.5"
|
|
fi
|
|
if [ -z ${VIASH_PAR_SPREAD+x} ]; then
|
|
VIASH_PAR_SPREAD="1.0"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NUM_COMPONENTS+x} ]; then
|
|
VIASH_PAR_NUM_COMPONENTS="2"
|
|
fi
|
|
if [ -z ${VIASH_PAR_MAX_ITER+x} ]; then
|
|
VIASH_PAR_MAX_ITER="0"
|
|
fi
|
|
if [ -z ${VIASH_PAR_ALPHA+x} ]; then
|
|
VIASH_PAR_ALPHA="1.0"
|
|
fi
|
|
if [ -z ${VIASH_PAR_GAMMA+x} ]; then
|
|
VIASH_PAR_GAMMA="1.0"
|
|
fi
|
|
if [ -z ${VIASH_PAR_NEGATIVE_SAMPLE_RATE+x} ]; then
|
|
VIASH_PAR_NEGATIVE_SAMPLE_RATE="5"
|
|
fi
|
|
if [ -z ${VIASH_PAR_INIT_POS+x} ]; then
|
|
VIASH_PAR_INIT_POS="spectral"
|
|
fi
|
|
if [ -z ${VIASH_PAR_LAMBDA+x} ]; then
|
|
VIASH_PAR_LAMBDA="2.0"
|
|
fi
|
|
if [ -z ${VIASH_PAR_FRACTION+x} ]; then
|
|
VIASH_PAR_FRACTION="0.3"
|
|
fi
|
|
if [ -z ${VIASH_PAR_VAR_SHIFT+x} ]; then
|
|
VIASH_PAR_VAR_SHIFT="0.1"
|
|
fi
|
|
|
|
# check whether required files exist
|
|
if [ ! -z "$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 "$VIASH_PAR_MIN_DIST" ]]; then
|
|
if ! [[ "$VIASH_PAR_MIN_DIST" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--min_dist' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_MIN_DIST '>=' 0.0 | bc` -eq 1 ]]; then
|
|
ViashError '--min_dist' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_MIN_DIST -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--min_dist' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--min_dist' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_MIN_DIST '<=' 10.0 | bc` -eq 1 ]]; then
|
|
ViashError '--min_dist' has to be less than or equal to 10.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_MIN_DIST -v n2=10.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--min_dist' has be less than or equal to 10.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--min_dist' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_SPREAD" ]]; then
|
|
if ! [[ "$VIASH_PAR_SPREAD" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--spread' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_SPREAD '>=' 0.0 | bc` -eq 1 ]]; then
|
|
ViashError '--spread' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_SPREAD -v n2=0.0 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--spread' has be more than or equal to 0.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--spread' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_SPREAD '<=' 10.0 | bc` -eq 1 ]]; then
|
|
ViashError '--spread' has to be less than or equal to 10.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_SPREAD -v n2=10.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--spread' has be less than or equal to 10.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--spread' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NUM_COMPONENTS" ]]; then
|
|
if ! [[ "$VIASH_PAR_NUM_COMPONENTS" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--num_components' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [[ $VIASH_PAR_NUM_COMPONENTS -lt 1 ]]; then
|
|
ViashError '--num_components' has be more than or equal to 1. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_MAX_ITER" ]]; then
|
|
if ! [[ "$VIASH_PAR_MAX_ITER" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--max_iter' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [[ $VIASH_PAR_MAX_ITER -lt 0 ]]; then
|
|
ViashError '--max_iter' has be more than or equal to 0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if [[ $VIASH_PAR_MAX_ITER -gt 1000 ]]; then
|
|
ViashError '--max_iter' has be less than or equal to 1000. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_ALPHA" ]]; then
|
|
if ! [[ "$VIASH_PAR_ALPHA" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--alpha' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_GAMMA" ]]; then
|
|
if ! [[ "$VIASH_PAR_GAMMA" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--gamma' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_NEGATIVE_SAMPLE_RATE" ]]; then
|
|
if ! [[ "$VIASH_PAR_NEGATIVE_SAMPLE_RATE" =~ ^[-+]?[0-9]+$ ]]; then
|
|
ViashError '--negative_sample_rate' has to be an integer. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_LAMBDA" ]]; then
|
|
if ! [[ "$VIASH_PAR_LAMBDA" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--lambda' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_LAMBDA '>=' 0.01 | bc` -eq 1 ]]; then
|
|
ViashError '--lambda' has be more than or equal to 0.01. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_LAMBDA -v n2=0.01 'BEGIN { print (n1 >= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--lambda' has be more than or equal to 0.01. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--lambda' specifies a minimum value but the value was not verified as neither \'bc\' or \`awk\` are present on the system.
|
|
fi
|
|
if command -v bc &> /dev/null; then
|
|
if ! [[ `echo $VIASH_PAR_LAMBDA '<=' 10.0 | bc` -eq 1 ]]; then
|
|
ViashError '--lambda' has to be less than or equal to 10.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
elif command -v awk &> /dev/null; then
|
|
if ! [[ `awk -v n1=$VIASH_PAR_LAMBDA -v n2=10.0 'BEGIN { print (n1 <= n2) ? "1" : "0" }'` -eq 1 ]]; then
|
|
ViashError '--lambda' has be less than or equal to 10.0. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
else
|
|
ViashWarning '--lambda' specifies a maximum value but the value was not verified as neither \'bc\' or \'awk\' are present on the system.
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_FRACTION" ]]; then
|
|
if ! [[ "$VIASH_PAR_FRACTION" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--fraction' has to be a double. Use "--help" to get more information on the parameters.
|
|
exit 1
|
|
fi
|
|
fi
|
|
if [[ -n "$VIASH_PAR_VAR_SHIFT" ]]; then
|
|
if ! [[ "$VIASH_PAR_VAR_SHIFT" =~ ^[-+]?(\.[0-9]+|[0-9]+(\.[0-9]*)?)([eE][-+]?[0-9]+)?$ ]]; then
|
|
ViashError '--var_shift' has to be a double. 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 "$VIASH_PAR_OUTPUT_COMPRESSION" ]; then
|
|
VIASH_PAR_OUTPUT_COMPRESSION_CHOICES=("gzip;lzf")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_OUTPUT_COMPRESSION_CHOICES[*]};" =~ ";$VIASH_PAR_OUTPUT_COMPRESSION;" ]]; then
|
|
ViashError '--output_compression' specified value of \'$VIASH_PAR_OUTPUT_COMPRESSION\' 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
|
|
|
|
if [ ! -z "$VIASH_PAR_INIT_POS" ]; then
|
|
VIASH_PAR_INIT_POS_CHOICES=("paga;spectral;random")
|
|
IFS=';'
|
|
set -f
|
|
if ! [[ ";${VIASH_PAR_INIT_POS_CHOICES[*]};" =~ ";$VIASH_PAR_INIT_POS;" ]]; then
|
|
ViashError '--init_pos' specified value of \'$VIASH_PAR_INIT_POS\' 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 "$VIASH_PAR_OUTPUT" ] && [ ! -d "$(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-densmap-XXXXXX").py
|
|
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'
|
|
from umap import UMAP
|
|
import mudata as mu
|
|
import sys
|
|
import anndata as ad
|
|
|
|
## VIASH START
|
|
# The following code has been auto-generated by Viash.
|
|
par = {
|
|
'input': $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "r'${VIASH_PAR_INPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'modality': $( if [ ! -z ${VIASH_PAR_MODALITY+x} ]; then echo "r'${VIASH_PAR_MODALITY//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'uns_neighbors': $( if [ ! -z ${VIASH_PAR_UNS_NEIGHBORS+x} ]; then echo "r'${VIASH_PAR_UNS_NEIGHBORS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'obsm_pca': $( if [ ! -z ${VIASH_PAR_OBSM_PCA+x} ]; then echo "r'${VIASH_PAR_OBSM_PCA//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'obsm_knn_indices': $( if [ ! -z ${VIASH_PAR_OBSM_KNN_INDICES+x} ]; then echo "r'${VIASH_PAR_OBSM_KNN_INDICES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'obsm_knn_distances': $( if [ ! -z ${VIASH_PAR_OBSM_KNN_DISTANCES+x} ]; then echo "r'${VIASH_PAR_OBSM_KNN_DISTANCES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'output_compression': $( if [ ! -z ${VIASH_PAR_OUTPUT_COMPRESSION+x} ]; then echo "r'${VIASH_PAR_OUTPUT_COMPRESSION//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'obsm_output': $( if [ ! -z ${VIASH_PAR_OBSM_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OBSM_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'min_dist': $( if [ ! -z ${VIASH_PAR_MIN_DIST+x} ]; then echo "float(r'${VIASH_PAR_MIN_DIST//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'spread': $( if [ ! -z ${VIASH_PAR_SPREAD+x} ]; then echo "float(r'${VIASH_PAR_SPREAD//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'num_components': $( if [ ! -z ${VIASH_PAR_NUM_COMPONENTS+x} ]; then echo "int(r'${VIASH_PAR_NUM_COMPONENTS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'max_iter': $( if [ ! -z ${VIASH_PAR_MAX_ITER+x} ]; then echo "int(r'${VIASH_PAR_MAX_ITER//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'alpha': $( if [ ! -z ${VIASH_PAR_ALPHA+x} ]; then echo "float(r'${VIASH_PAR_ALPHA//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'gamma': $( if [ ! -z ${VIASH_PAR_GAMMA+x} ]; then echo "float(r'${VIASH_PAR_GAMMA//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'negative_sample_rate': $( if [ ! -z ${VIASH_PAR_NEGATIVE_SAMPLE_RATE+x} ]; then echo "int(r'${VIASH_PAR_NEGATIVE_SAMPLE_RATE//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'init_pos': $( if [ ! -z ${VIASH_PAR_INIT_POS+x} ]; then echo "r'${VIASH_PAR_INIT_POS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'lambda': $( if [ ! -z ${VIASH_PAR_LAMBDA+x} ]; then echo "float(r'${VIASH_PAR_LAMBDA//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'fraction': $( if [ ! -z ${VIASH_PAR_FRACTION+x} ]; then echo "float(r'${VIASH_PAR_FRACTION//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'var_shift': $( if [ ! -z ${VIASH_PAR_VAR_SHIFT+x} ]; then echo "float(r'${VIASH_PAR_VAR_SHIFT//\'/\'\"\'\"r\'}')"; else echo None; fi )
|
|
}
|
|
meta = {
|
|
'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'functionality_name': $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "r'${VIASH_META_FUNCTIONALITY_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'resources_dir': $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "r'${VIASH_META_RESOURCES_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'executable': $( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "r'${VIASH_META_EXECUTABLE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'config': $( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "r'${VIASH_META_CONFIG//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'temp_dir': $( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "r'${VIASH_META_TEMP_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
|
'cpus': $( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "int(r'${VIASH_META_CPUS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_b': $( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "int(r'${VIASH_META_MEMORY_B//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_kb': $( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_mb': $( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_gb': $( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_tb': $( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_pb': $( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_kib': $( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_mib': $( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_gib': $( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_tib': $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
|
'memory_pib': $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PIB//\'/\'\"\'\"r\'}')"; else echo None; fi )
|
|
}
|
|
dep = {
|
|
|
|
}
|
|
|
|
## VIASH END
|
|
|
|
sys.path.append(meta["resources_dir"])
|
|
# START TEMPORARY WORKAROUND setup_logger
|
|
# reason: resources aren't available when using Nextflow fusion
|
|
# from setup_logger import setup_logger
|
|
def setup_logger():
|
|
import logging
|
|
from sys import stdout
|
|
|
|
logger = logging.getLogger()
|
|
logger.setLevel(logging.INFO)
|
|
console_handler = logging.StreamHandler(stdout)
|
|
logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
|
|
console_handler.setFormatter(logFormatter)
|
|
logger.addHandler(console_handler)
|
|
|
|
return logger
|
|
# END TEMPORARY WORKAROUND setup_logger
|
|
logger = setup_logger()
|
|
|
|
logger.info("Reading %s", par["input"])
|
|
mdata = mu.read_h5mu(par["input"])
|
|
|
|
if par['modality'] not in mdata.mod:
|
|
raise ValueError(f"Modality '{par['modality']}' not found in the input data.")
|
|
|
|
logger.info("Computing densMAP for modality '%s'", par['modality'])
|
|
data = mdata.mod[par['modality']]
|
|
|
|
neigh_key = par["uns_neighbors"]
|
|
|
|
if neigh_key not in data.uns:
|
|
raise ValueError(f"'{neigh_key}' was not found in .mod['{par['modality']}'].uns. Set the correct key or run 'find_neighbors' first.")
|
|
|
|
temp_uns = { neigh_key: data.uns[neigh_key] }
|
|
|
|
if 'use_rep' not in temp_uns[neigh_key]['params']:
|
|
raise ValueError(f"'use_rep' was not found in .mod['{par['modality']}'].uns['{neigh_key}'].params. Set the correct key or run PCA first.")
|
|
|
|
|
|
X_densmap = UMAP(
|
|
min_dist=par["min_dist"],
|
|
spread=par["spread"],
|
|
n_components=par["num_components"],
|
|
n_epochs=par["max_iter"],
|
|
learning_rate=par["alpha"],
|
|
repulsion_strength=par["gamma"],
|
|
negative_sample_rate=par["negative_sample_rate"],
|
|
init=par["init_pos"],
|
|
metric=data.uns["neighbors"].get("metric", "euclidean"),
|
|
metric_kwds=data.uns["neighbors"].get("metric_kwds", {}),
|
|
densmap=True,
|
|
dens_lambda=par["lambda"],
|
|
dens_frac=par["fraction"],
|
|
dens_var_shift=par["var_shift"],
|
|
precomputed_knn=(
|
|
data.obsm[par["obsm_knn_indices"]],
|
|
data.obsm[par["obsm_knn_distances"]],
|
|
)
|
|
).fit_transform(data.obsm[par["obsm_pca"]])
|
|
|
|
logger.info(f"Writing densMAP embeddings to .mod[{par['modality']}].obsm[{par['obsm_output']}]")
|
|
data.obsm[par['obsm_output']] = X_densmap
|
|
|
|
logger.info(f"Writing densMAP metadata to .mod[{par['modality']}].uns['densmap']")
|
|
data.uns['densmap'] = {
|
|
'params': {
|
|
'min_dist': par["min_dist"],
|
|
'spread': par["spread"],
|
|
'n_components': par["num_components"],
|
|
'n_epochs': par["max_iter"],
|
|
'learning_rate': par["alpha"],
|
|
'repulsion_strength': par["gamma"],
|
|
'negative_sample_rate': par["negative_sample_rate"],
|
|
'init': par["init_pos"],
|
|
'metric': data.uns["neighbors"].get("metric", "euclidean"),
|
|
'metric_kwds': data.uns["neighbors"].get("metric_kwds", {}),
|
|
'dens_lambda': par["lambda"],
|
|
'dens_frac': par["fraction"],
|
|
'dens_var_shift': par["var_shift"],
|
|
'knn_indices_key': par["obsm_knn_indices"],
|
|
'knn_distances_key': par["obsm_knn_distances"],
|
|
}
|
|
}
|
|
|
|
logger.info("Writing to %s.", par["output"])
|
|
mdata.write_h5mu(filename=par["output"], compression=par["output_compression"])
|
|
|
|
logger.info("Finished")
|
|
VIASHMAIN
|
|
python -B "\$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
|