Push generated mig2025spatial

Author: github-actions

generated/mig2025spatial.Dockerfile

@@ -1,2 +1,3 @@
 FROM ghcr.io/bioconductor/bioconductor:devel
 RUN sudo apt-get update && sudo apt-get -y install apt-file &&  echo bhuvad/CosMxSpatialAnalysisWorkshop | tr ',' '\n' > /tmp/pkglist && cat /tmp/pkglist | xargs -i Rscript -e "if (!require('rspm')) { install.packages('rspm'); rspm::enable(); }; p = BiocManager::install(c('{}'), dependencies = c('Depends', 'Imports', 'LinkingTo', 'Suggests')); if(p %in% rownames(installed.packages())) q(status = 0) else if(strsplit(p, '/')[[1]][2] %in% rownames(installed.packages())) q(status = 0) else q(status = 1)"
+RUN sudo apt-get update && sudo apt-get -y install apt-file &&  cd /home/rstudio && echo "vignettes/workflow_spatial_cosmx.Rmd" | tr ',' '\n' > vignlist && echo "https://github.com/bhuvad/CosMxSpatialAnalysisWorkshop" | tr ',' '\n' > sourcelist && cat sourcelist | xargs -i bash -c 'git clone {} && cp -r $(basename {}) tmpsource/' && cd tmpsource && curl -o install.sh https://raw.githubusercontent.com/Bioconductor/workshop-contributions/main/.github/scripts/install_missing.sh && cat ../vignlist | xargs -i bash install.sh {} && cd .. && rm -rf vignlist tmpsource/ 

generated/mig2025spatial.container

@@ -1 +1 @@
-ghcr.io/bioconductor/workshop-contributions:devel-e132dfd9
+ghcr.io/bioconductor/workshop-contributions:devel-8fceb82f

generated/workshop-values-mig2025spatial.yaml

@@ -10,7 +10,7 @@
       <tool id="interactivetool_biocworkshop_mig2025spatial" tool_type="interactive" name="Introduction to imaging-based spatial transcriptomics analysis" version="0.1">
           <description>This workflow package shows how a basic analysis of spatial transcriptomics datasets is performed to gain biological insight.</description>
           <requirements>
-              <container type="docker">ghcr.io/bioconductor/workshop-contributions:devel-e132dfd9</container>
+              <container type="docker">ghcr.io/bioconductor/workshop-contributions:devel-8fceb82f</container>
           </requirements>
           <entry_points>
               <entry_point name="mig2025spatial" requires_domain="True">

generated/workshop-values.yaml

@@ -11,7 +11,7 @@ extraFileMappings:
       <tool id="interactivetool_biocworkshop_mig2025spatial" tool_type="interactive" name="Introduction to imaging-based spatial transcriptomics analysis" version="0.1">
           <description>This workflow package shows how a basic analysis of spatial transcriptomics datasets is performed to gain biological insight.</description>
           <requirements>
-              <container type="docker">ghcr.io/bioconductor/workshop-contributions:devel-e132dfd9</container>
+              <container type="docker">ghcr.io/bioconductor/workshop-contributions:devel-8fceb82f</container>
           </requirements>
           <entry_points>
               <entry_point name="mig2025spatial" requires_domain="True">