deploy: d45aa5e

openpipelines-bio · May 30, 2024 · e56b8a4 · e56b8a4
1 parent 9ffc9b1
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diff --git a/target/docker/annotate/popv/.config.vsh.yaml b/target/docker/annotate/popv/.config.vsh.yaml
@@ -1,7 +1,7 @@
 functionality:
   name: "popv"
   namespace: "annotate"
-  version: "v1.0.0-rc5"
+  version: "1.0.0-rc5"
   authors:
   - name: "Matthias Beyens"
     roles:
@@ -253,7 +253,7 @@ platforms:
   image: "python:3.9-slim"
   target_organization: "openpipelines-bio"
   target_registry: "ghcr.io"
-  target_tag: "v1.0.0-rc5"
+  target_tag: "1.0.0-rc5"
   namespace_separator: "/"
   resolve_volume: "Automatic"
   chown: true
@@ -352,6 +352,6 @@ info:
   output: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv"
   executable: "/home/runner/work/openpipeline/openpipeline/target/docker/annotate/popv/popv"
   viash_version: "0.8.5"
-  git_commit: "f7f0e24a3e997b7403c5b81c96fb6a9441682846"
+  git_commit: "9ffc9b19ec3087ab67bd62f0b4bde61ce0648d58"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.0-rc4-3-gf7f0e24a3e"
+  git_tag: "1.0.0-rc4-4-g9ffc9b19ec"
diff --git a/target/docker/annotate/popv/popv b/target/docker/annotate/popv/popv
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# popv v1.0.0-rc5
+# popv 1.0.0-rc5
 # 
 # This wrapper script is auto-generated by viash 0.8.5 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "popv v1.0.0-rc5"
+  echo "popv 1.0.0-rc5"
   echo ""
   echo "Performs popular major vote cell typing on single cell sequence data using"
   echo "multiple algorithms. Note that this is a one-shot version of PopV."
@@ -503,10 +503,10 @@ RUN cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git && \
 
 LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component annotate popv"
-LABEL org.opencontainers.image.created="2024-05-29T14:52:41Z"
+LABEL org.opencontainers.image.created="2024-05-30T12:24:04Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="f7f0e24a3e997b7403c5b81c96fb6a9441682846"
-LABEL org.opencontainers.image.version="v1.0.0-rc5"
+LABEL org.opencontainers.image.revision="9ffc9b19ec3087ab67bd62f0b4bde61ce0648d58"
+LABEL org.opencontainers.image.version="1.0.0-rc5"
 
 VIASHDOCKER
 }
@@ -657,7 +657,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "popv v1.0.0-rc5"
+            echo "popv 1.0.0-rc5"
             exit
             ;;
         --input)
@@ -890,14 +890,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
 ViashDockerInstallationCheck
 
 if [ $VIASH_MODE == "docker_setup" ]; then
-  ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate/popv:v1.0.0-rc5' "$VIASH_DOCKER_SETUP_STRATEGY"
+  ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc5' "$VIASH_DOCKER_SETUP_STRATEGY"
   exit 0
 fi
-ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate/popv:v1.0.0-rc5' ifneedbepullelsecachedbuild
+ViashDockerSetup 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc5' ifneedbepullelsecachedbuild
 
 if [ $VIASH_MODE == "docker_debug" ]; then
-  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate/popv:v1.0.0-rc5'"
-  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate/popv:v1.0.0-rc5'
+  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc5'"
+  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc5'
   exit 0
 fi
 
@@ -1120,7 +1120,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
 function ViashPerformChown {
   if (( ${#VIASH_CHOWN_VARS[@]} )); then
     set +e
-    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/annotate/popv:v1.0.0-rc5 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
+    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc5 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
     set -e
   fi
 }
@@ -1139,8 +1139,8 @@ fi
 # set dependency paths
 
 
-ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate/popv:v1.0.0-rc5)"
-cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate/popv:v1.0.0-rc5
+ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc5)"
+cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/annotate/popv:1.0.0-rc5
 set -e
 tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-popv-XXXXXX").py
 function clean_up {

diff --git a/target/docker/cluster/leiden/.config.vsh.yaml b/target/docker/cluster/leiden/.config.vsh.yaml
@@ -1,7 +1,7 @@
 functionality:
   name: "leiden"
   namespace: "cluster"
-  version: "v1.0.0-rc5"
+  version: "1.0.0-rc5"
   authors:
   - name: "Dries De Maeyer"
     roles:
@@ -147,7 +147,7 @@ platforms:
   image: "python:3.11-slim"
   target_organization: "openpipelines-bio"
   target_registry: "ghcr.io"
-  target_tag: "v1.0.0-rc5"
+  target_tag: "1.0.0-rc5"
   namespace_separator: "/"
   resolve_volume: "Automatic"
   chown: true
@@ -230,6 +230,6 @@ info:
   output: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden"
   executable: "/home/runner/work/openpipeline/openpipeline/target/docker/cluster/leiden/leiden"
   viash_version: "0.8.5"
-  git_commit: "f7f0e24a3e997b7403c5b81c96fb6a9441682846"
+  git_commit: "9ffc9b19ec3087ab67bd62f0b4bde61ce0648d58"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.0-rc4-3-gf7f0e24a3e"
+  git_tag: "1.0.0-rc4-4-g9ffc9b19ec"
diff --git a/target/docker/cluster/leiden/leiden b/target/docker/cluster/leiden/leiden
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# leiden v1.0.0-rc5
+# leiden 1.0.0-rc5
 # 
 # This wrapper script is auto-generated by viash 0.8.5 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "leiden v1.0.0-rc5"
+  echo "leiden 1.0.0-rc5"
   echo ""
   echo "Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy"
   echo "framework] [Wolf18]."
@@ -460,10 +460,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer"
 LABEL org.opencontainers.image.description="Companion container for running component cluster leiden"
-LABEL org.opencontainers.image.created="2024-05-29T14:52:42Z"
+LABEL org.opencontainers.image.created="2024-05-30T12:24:04Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="f7f0e24a3e997b7403c5b81c96fb6a9441682846"
-LABEL org.opencontainers.image.version="v1.0.0-rc5"
+LABEL org.opencontainers.image.revision="9ffc9b19ec3087ab67bd62f0b4bde61ce0648d58"
+LABEL org.opencontainers.image.version="1.0.0-rc5"
 
 VIASHDOCKER
 }
@@ -614,7 +614,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "leiden v1.0.0-rc5"
+            echo "leiden 1.0.0-rc5"
             exit
             ;;
         --input)
@@ -776,14 +776,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
 ViashDockerInstallationCheck
 
 if [ $VIASH_MODE == "docker_setup" ]; then
-  ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster/leiden:v1.0.0-rc5' "$VIASH_DOCKER_SETUP_STRATEGY"
+  ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc5' "$VIASH_DOCKER_SETUP_STRATEGY"
   exit 0
 fi
-ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster/leiden:v1.0.0-rc5' ifneedbepullelsecachedbuild
+ViashDockerSetup 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc5' ifneedbepullelsecachedbuild
 
 if [ $VIASH_MODE == "docker_debug" ]; then
-  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster/leiden:v1.0.0-rc5'"
-  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster/leiden:v1.0.0-rc5'
+  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc5'"
+  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc5'
   exit 0
 fi
 
@@ -990,7 +990,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
 function ViashPerformChown {
   if (( ${#VIASH_CHOWN_VARS[@]} )); then
     set +e
-    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/cluster/leiden:v1.0.0-rc5 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
+    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc5 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
     set -e
   fi
 }
@@ -1009,8 +1009,8 @@ fi
 # set dependency paths
 
 
-ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster/leiden:v1.0.0-rc5)"
-cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster/leiden:v1.0.0-rc5
+ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc5)"
+cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/cluster/leiden:1.0.0-rc5
 set -e
 tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-leiden-XXXXXX").py
 function clean_up {

diff --git a/target/docker/compression/compress_h5mu/.config.vsh.yaml b/target/docker/compression/compress_h5mu/.config.vsh.yaml
@@ -1,7 +1,7 @@
 functionality:
   name: "compress_h5mu"
   namespace: "compression"
-  version: "v1.0.0-rc5"
+  version: "1.0.0-rc5"
   authors:
   - name: "Dries Schaumont"
     roles:
@@ -89,7 +89,7 @@ platforms:
   image: "python:3.10-slim"
   target_organization: "openpipelines-bio"
   target_registry: "ghcr.io"
-  target_tag: "v1.0.0-rc5"
+  target_tag: "1.0.0-rc5"
   namespace_separator: "/"
   resolve_volume: "Automatic"
   chown: true
@@ -171,6 +171,6 @@ info:
   output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu"
   executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/compress_h5mu/compress_h5mu"
   viash_version: "0.8.5"
-  git_commit: "f7f0e24a3e997b7403c5b81c96fb6a9441682846"
+  git_commit: "9ffc9b19ec3087ab67bd62f0b4bde61ce0648d58"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.0-rc4-3-gf7f0e24a3e"
+  git_tag: "1.0.0-rc4-4-g9ffc9b19ec"
diff --git a/target/docker/compression/compress_h5mu/compress_h5mu b/target/docker/compression/compress_h5mu/compress_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# compress_h5mu v1.0.0-rc5
+# compress_h5mu 1.0.0-rc5
 # 
 # This wrapper script is auto-generated by viash 0.8.5 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -173,7 +173,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "compress_h5mu v1.0.0-rc5"
+  echo "compress_h5mu 1.0.0-rc5"
   echo ""
   echo "Compress a MuData file."
   echo ""
@@ -423,10 +423,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component compression compress_h5mu"
-LABEL org.opencontainers.image.created="2024-05-29T14:52:43Z"
+LABEL org.opencontainers.image.created="2024-05-30T12:24:06Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="f7f0e24a3e997b7403c5b81c96fb6a9441682846"
-LABEL org.opencontainers.image.version="v1.0.0-rc5"
+LABEL org.opencontainers.image.revision="9ffc9b19ec3087ab67bd62f0b4bde61ce0648d58"
+LABEL org.opencontainers.image.version="1.0.0-rc5"
 
 VIASHDOCKER
 }
@@ -577,7 +577,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "compress_h5mu v1.0.0-rc5"
+            echo "compress_h5mu 1.0.0-rc5"
             exit
             ;;
         --input)
@@ -683,14 +683,14 @@ eval set -- $VIASH_POSITIONAL_ARGS
 ViashDockerInstallationCheck
 
 if [ $VIASH_MODE == "docker_setup" ]; then
-  ViashDockerSetup 'ghcr.io/openpipelines-bio/compression/compress_h5mu:v1.0.0-rc5' "$VIASH_DOCKER_SETUP_STRATEGY"
+  ViashDockerSetup 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc5' "$VIASH_DOCKER_SETUP_STRATEGY"
   exit 0
 fi
-ViashDockerSetup 'ghcr.io/openpipelines-bio/compression/compress_h5mu:v1.0.0-rc5' ifneedbepullelsecachedbuild
+ViashDockerSetup 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc5' ifneedbepullelsecachedbuild
 
 if [ $VIASH_MODE == "docker_debug" ]; then
-  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression/compress_h5mu:v1.0.0-rc5'"
-  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression/compress_h5mu:v1.0.0-rc5'
+  ViashNotice "+ docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc5'"
+  docker run --entrypoint=bash -i --rm -v "$(pwd)":/pwd --workdir /pwd -t 'ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc5'
   exit 0
 fi
 
@@ -874,7 +874,7 @@ VIASH_UNIQUE_MOUNTS=($(for val in "${VIASH_EXTRA_MOUNTS[@]}"; do echo "$val"; do
 function ViashPerformChown {
   if (( ${#VIASH_CHOWN_VARS[@]} )); then
     set +e
-    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/compression/compress_h5mu:v1.0.0-rc5 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
+    eval docker run --entrypoint=chown -i --rm ${VIASH_UNIQUE_MOUNTS[@]} ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc5 "$(id -u):$(id -g)" --silent --recursive ${VIASH_CHOWN_VARS[@]}
     set -e
   fi
 }
@@ -893,8 +893,8 @@ fi
 # set dependency paths
 
 
-ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression/compress_h5mu:v1.0.0-rc5)"
-cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression/compress_h5mu:v1.0.0-rc5
+ViashDebug "Running command: $(echo docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc5)"
+cat << VIASHEOF | eval docker run --entrypoint=bash -i --rm ${VIASH_UNIQUE_MOUNTS[@]} $VIASH_EXTRA_DOCKER_ARGS ghcr.io/openpipelines-bio/compression/compress_h5mu:1.0.0-rc5
 set -e
 tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-compress_h5mu-XXXXXX").py
 function clean_up {

diff --git a/target/docker/compression/tar_extract/.config.vsh.yaml b/target/docker/compression/tar_extract/.config.vsh.yaml
@@ -1,7 +1,7 @@
 functionality:
   name: "tar_extract"
   namespace: "compression"
-  version: "v1.0.0-rc5"
+  version: "1.0.0-rc5"
   arguments:
   - type: "file"
     name: "--input"
@@ -93,7 +93,7 @@ platforms:
   image: "ubuntu:latest"
   target_organization: "openpipelines-bio"
   target_registry: "ghcr.io"
-  target_tag: "v1.0.0-rc5"
+  target_tag: "1.0.0-rc5"
   namespace_separator: "/"
   resolve_volume: "Automatic"
   chown: true
@@ -107,6 +107,6 @@ info:
   output: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract"
   executable: "/home/runner/work/openpipeline/openpipeline/target/docker/compression/tar_extract/tar_extract"
   viash_version: "0.8.5"
-  git_commit: "f7f0e24a3e997b7403c5b81c96fb6a9441682846"
+  git_commit: "9ffc9b19ec3087ab67bd62f0b4bde61ce0648d58"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
-  git_tag: "1.0.0-rc4-3-gf7f0e24a3e"
+  git_tag: "1.0.0-rc4-4-g9ffc9b19ec"