Build branch main with version main (2b29a47)

Build pipeline: viash-hub.biobox.main-bjgnf Source commit: 2b29a47575 Source message: Bedtools GroupBY (#123) * Initial Commit * Update config.vsh.yaml * config file * script.sh * adding some tests * more test * Update CHANGELOG.md * deleted test_data * bug fix * Update config.vsh.yaml * adding more links * exit on error * $TMPDIR * Update script.sh * Update config.vsh.yaml * Suggested change on column option --------- Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com>
2024-09-02 13:18:11 +00:00
parent b17c19f92e
commit 18d6cad4c4
232 changed files with 32974 additions and 2381 deletions
--- a/target/executable/busco/busco_download_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_download_datasets/.config.vsh.yaml
@@ -157,15 +157,15 @@ build_info:
  engine: "docker|native"
  output: "target/executable/busco/busco_download_datasets"
  executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
-  viash_version: "0.9.0-RC6"
-  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
+  viash_version: "0.9.0-RC7"
+  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
  version: "main"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0-RC7"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/busco/busco_download_datasets/busco_download_datasets
+++ b/target/executable/busco/busco_download_datasets/busco_download_datasets
@@ -2,7 +2,7 @@

 # busco_download_datasets main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
 # derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
 # Data Intuitive.
 # 
@@ -57,24 +57,24 @@ function ViashRemoveFlags {
 # $1      : Should always be set to ${BASH_SOURCE[0]}
 # returns : The absolute path of the bash file
 function ViashSourceDir {
-  SOURCE="$1"
-  while [ -h "$SOURCE" ]; do
-    DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  local source="$1"
+  while [ -h "$source" ]; do
+    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
+    source="$(readlink "$source")"
+    [[ $source != /* ]] && source="$dir/$source"
  done
-  cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
+  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
 }
 # ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
 # usage   : ViashFindTargetDir 'ScriptPath'
 # $1      : The location from where to start the upward search
 # returns : The absolute path of the '.build.yaml' file
 function ViashFindTargetDir {
-  SOURCE="$1"
-  while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
-    SOURCE=${SOURCE%/*}
+  local source="$1"
+  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
+    source=${source%/*}
  done
-  echo $SOURCE
+  echo $source
 }
 # see https://en.wikipedia.org/wiki/Syslog#Severity_level
 VIASH_LOGCODE_EMERGENCY=0
@@ -215,9 +215,9 @@ function ViashDockerInstallationCheck {
  fi

  ViashDebug "Checking whether the Docker daemon is running"
-  save=$-; set +e
-  docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  out=$?
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
@@ -269,9 +269,9 @@ function ViashDockerPull {
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
-    save=$-; set +e
+    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
-    out=$?
+    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
@@ -291,7 +291,8 @@ function ViashDockerPull {
 #   echo $?                                     # returns '1'
 function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
-  save=$-; set +e
+  local save=$-; set +e
+  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
@@ -315,9 +316,9 @@ function ViashDockerPush {
 # examples:
 #   ViashDockerPullElseBuild mynewcomponent
 function ViashDockerPullElseBuild {
-  save=$-; set +e
+  local save=$-; set +e
  ViashDockerPull $1
-  out=$?
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
@@ -474,9 +475,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
-LABEL org.opencontainers.image.created="2024-08-21T11:35:59Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:02:47Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
+LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -503,6 +504,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -533,14 +537,17 @@ function ViashAbsolutePath {
  )
 }
 # 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
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
 # examples:
 #   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
 #   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
 function ViashDockerAutodetectMount {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -548,7 +555,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
@@ -556,7 +563,9 @@ function ViashDockerAutodetectMount {
  fi
 }
 function ViashDockerAutodetectMountArg {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -564,17 +573,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
 }
 function ViashDockerStripAutomount {
-  abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#/viash_automount}"
+  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)

@@ -647,6 +661,18 @@ while [[ $# -gt 0 ]]; do
            VIASH_MODE='dockerfile'
            shift 1
            ;;
+        ---docker_run_args)
+            VIASH_DOCKER_RUN_ARGS+=("$2")
+            shift 2
+            ;;
+        ---docker_run_args=*)
+            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -708,6 +734,10 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  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
--- a/target/executable/busco/busco_list_datasets/.config.vsh.yaml
+++ b/target/executable/busco/busco_list_datasets/.config.vsh.yaml
@@ -144,15 +144,15 @@ build_info:
  engine: "docker|native"
  output: "target/executable/busco/busco_list_datasets"
  executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
-  viash_version: "0.9.0-RC6"
-  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
+  viash_version: "0.9.0-RC7"
+  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
  version: "main"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0-RC7"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/busco/busco_list_datasets/busco_list_datasets
+++ b/target/executable/busco/busco_list_datasets/busco_list_datasets
@@ -2,7 +2,7 @@

 # busco_list_datasets main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
 # derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
 # Data Intuitive.
 # 
@@ -57,24 +57,24 @@ function ViashRemoveFlags {
 # $1      : Should always be set to ${BASH_SOURCE[0]}
 # returns : The absolute path of the bash file
 function ViashSourceDir {
-  SOURCE="$1"
-  while [ -h "$SOURCE" ]; do
-    DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  local source="$1"
+  while [ -h "$source" ]; do
+    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
+    source="$(readlink "$source")"
+    [[ $source != /* ]] && source="$dir/$source"
  done
-  cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
+  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
 }
 # ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
 # usage   : ViashFindTargetDir 'ScriptPath'
 # $1      : The location from where to start the upward search
 # returns : The absolute path of the '.build.yaml' file
 function ViashFindTargetDir {
-  SOURCE="$1"
-  while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
-    SOURCE=${SOURCE%/*}
+  local source="$1"
+  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
+    source=${source%/*}
  done
-  echo $SOURCE
+  echo $source
 }
 # see https://en.wikipedia.org/wiki/Syslog#Severity_level
 VIASH_LOGCODE_EMERGENCY=0
@@ -205,9 +205,9 @@ function ViashDockerInstallationCheck {
  fi

  ViashDebug "Checking whether the Docker daemon is running"
-  save=$-; set +e
-  docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  out=$?
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
@@ -259,9 +259,9 @@ function ViashDockerPull {
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
-    save=$-; set +e
+    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
-    out=$?
+    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
@@ -281,7 +281,8 @@ function ViashDockerPull {
 #   echo $?                                     # returns '1'
 function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
-  save=$-; set +e
+  local save=$-; set +e
+  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
@@ -305,9 +306,9 @@ function ViashDockerPush {
 # examples:
 #   ViashDockerPullElseBuild mynewcomponent
 function ViashDockerPullElseBuild {
-  save=$-; set +e
+  local save=$-; set +e
  ViashDockerPull $1
-  out=$?
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
@@ -464,9 +465,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
-LABEL org.opencontainers.image.created="2024-08-21T11:35:59Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:02:47Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
+LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -493,6 +494,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -523,14 +527,17 @@ function ViashAbsolutePath {
  )
 }
 # 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
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
 # examples:
 #   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
 #   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
 function ViashDockerAutodetectMount {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -538,7 +545,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
@@ -546,7 +553,9 @@ function ViashDockerAutodetectMount {
  fi
 }
 function ViashDockerAutodetectMountArg {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -554,17 +563,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
 }
 function ViashDockerStripAutomount {
-  abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#/viash_automount}"
+  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)

@@ -632,6 +646,18 @@ while [[ $# -gt 0 ]]; do
            VIASH_MODE='dockerfile'
            shift 1
            ;;
+        ---docker_run_args)
+            VIASH_DOCKER_RUN_ARGS+=("$2")
+            shift 2
+            ;;
+        ---docker_run_args=*)
+            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -693,6 +719,10 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  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
--- a/target/executable/busco/busco_run/.config.vsh.yaml
+++ b/target/executable/busco/busco_run/.config.vsh.yaml
@@ -422,15 +422,15 @@ build_info:
  engine: "docker|native"
  output: "target/executable/busco/busco_run"
  executable: "target/executable/busco/busco_run/busco_run"
-  viash_version: "0.9.0-RC6"
-  git_commit: "766ab6c9c3059004c7c3f205621909b2d8b0b26d"
+  viash_version: "0.9.0-RC7"
+  git_commit: "2b29a47575db9dbdff8448b287925c25d9a8b01d"
  git_remote: "https://github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
  version: "main"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0-RC7"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/busco/busco_run/busco_run
+++ b/target/executable/busco/busco_run/busco_run
@@ -2,7 +2,7 @@

 # busco_run main
 # 
-# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
+# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
 # derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
 # Data Intuitive.
 # 
@@ -57,24 +57,24 @@ function ViashRemoveFlags {
 # $1      : Should always be set to ${BASH_SOURCE[0]}
 # returns : The absolute path of the bash file
 function ViashSourceDir {
-  SOURCE="$1"
-  while [ -h "$SOURCE" ]; do
-    DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
-    SOURCE="$(readlink "$SOURCE")"
-    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
+  local source="$1"
+  while [ -h "$source" ]; do
+    local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
+    source="$(readlink "$source")"
+    [[ $source != /* ]] && source="$dir/$source"
  done
-  cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
+  cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
 }
 # ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
 # usage   : ViashFindTargetDir 'ScriptPath'
 # $1      : The location from where to start the upward search
 # returns : The absolute path of the '.build.yaml' file
 function ViashFindTargetDir {
-  SOURCE="$1"
-  while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
-    SOURCE=${SOURCE%/*}
+  local source="$1"
+  while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
+    source=${source%/*}
  done
-  echo $SOURCE
+  echo $source
 }
 # see https://en.wikipedia.org/wiki/Syslog#Severity_level
 VIASH_LOGCODE_EMERGENCY=0
@@ -372,9 +372,9 @@ function ViashDockerInstallationCheck {
  fi

  ViashDebug "Checking whether the Docker daemon is running"
-  save=$-; set +e
-  docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
-  out=$?
+  local save=$-; set +e
+  local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
@@ -426,9 +426,9 @@ function ViashDockerPull {
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker pull $1 && return 0 || return 1
  else
-    save=$-; set +e
+    local save=$-; set +e
    docker pull $1 2> /dev/null > /dev/null
-    out=$?
+    local out=$?
    [[ $save =~ e ]] && set -e
    if [ $out -ne 0 ]; then
      ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
@@ -448,7 +448,8 @@ function ViashDockerPull {
 #   echo $?                                     # returns '1'
 function ViashDockerPush {
  ViashNotice "Pushing image to '$1'"
-  save=$-; set +e
+  local save=$-; set +e
+  local out
  if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
    docker push $1
    out=$?
@@ -472,9 +473,9 @@ function ViashDockerPush {
 # examples:
 #   ViashDockerPullElseBuild mynewcomponent
 function ViashDockerPullElseBuild {
-  save=$-; set +e
+  local save=$-; set +e
  ViashDockerPull $1
-  out=$?
+  local out=$?
  [[ $save =~ e ]] && set -e
  if [ $out -ne 0 ]; then
    ViashDockerBuild $@
@@ -631,9 +632,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version

 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
-LABEL org.opencontainers.image.created="2024-08-21T11:35:59Z"
+LABEL org.opencontainers.image.created="2024-09-02T13:02:48Z"
 LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
-LABEL org.opencontainers.image.revision="766ab6c9c3059004c7c3f205621909b2d8b0b26d"
+LABEL org.opencontainers.image.revision="2b29a47575db9dbdff8448b287925c25d9a8b01d"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -660,6 +661,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -690,14 +694,17 @@ function ViashAbsolutePath {
  )
 }
 # 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
+# $1                             : The parameter value
+# returns                        : New parameter
+# $VIASH_DIRECTORY_MOUNTS        : Added another parameter to be passed to docker
+# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
 # examples:
 #   ViashDockerAutodetectMount /path/to/bar      # returns '/viash_automount/path/to/bar'
 #   ViashDockerAutodetectMountArg /path/to/bar   # returns '--volume="/path/to:/viash_automount/path/to"'
 function ViashDockerAutodetectMount {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -705,7 +712,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  if [ -z "$base_name" ]; then
    echo "$mount_target"
  else
@@ -713,7 +720,9 @@ function ViashDockerAutodetectMount {
  fi
 }
 function ViashDockerAutodetectMountArg {
-  abs_path=$(ViashAbsolutePath "$1")
+  local abs_path=$(ViashAbsolutePath "$1")
+  local mount_source
+  local base_name
  if [ -d "$abs_path" ]; then
    mount_source="$abs_path"
    base_name=""
@@ -721,17 +730,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$abs_path"`
    base_name=`basename "$abs_path"`
  fi
-  mount_target="/viash_automount$mount_source"
+  local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
  ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
  echo "--volume=\"$mount_source:$mount_target\""
 }
 function ViashDockerStripAutomount {
-  abs_path=$(ViashAbsolutePath "$1")
-  echo "${abs_path#/viash_automount}"
+  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)

@@ -1046,6 +1060,18 @@ while [[ $# -gt 0 ]]; do
            VIASH_MODE='dockerfile'
            shift 1
            ;;
+        ---docker_run_args)
+            VIASH_DOCKER_RUN_ARGS+=("$2")
+            shift 2
+            ;;
+        ---docker_run_args=*)
+            VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -1107,6 +1133,10 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  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