Push generated bioc2024bamSliceR

generated/bioc2024bamSliceR.Dockerfile

@@ -0,0 +1,2 @@
+FROM ghcr.io/bioconductor/bioconductor:devel
+RUN sudo apt-get update && sudo apt-get -y install apt-file &&  echo trichelab/bamSliceR,BSgenome.Hsapiens.UCSC.hg38,BiocParallel,Homo.sapiens,TxDb.Hsapiens.UCSC.hg38.knownGene,VariantTools,biomaRt,data.table,ensemblVEP,gampR,httr,jsonlite,rtracklayer,stringr | 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)"

generated/bioc2024bamSliceR.container

@@ -0,0 +1 @@
+ghcr.io/bioconductor/workshop-contributions:devel-dabb9c4e

generated/workshop-values.yaml

@@ -1,5 +1,5 @@
 extraFileMappings:
-  /galaxy/server/tools/interactive/biocworkshop_vjcontobioc2024.xml:
+  /galaxy/server/tools/interactive/biocworkshop_eurobioc2024isee.xml:
     useSecret: false
     applyToJob: true
     applyToSetupJob: true
@@ -8,13 +8,13 @@ extraFileMappings:
     applyToNginx: true
     tpl: false
     content: |
-      <tool id="interactivetool_biocworkshop_vjcontobioc2024" tool_type="interactive" name="Package Demo: ontoProc" version="0.1">
-          <description>Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN</description>
+      <tool id="interactivetool_biocworkshop_eurobioc2024isee" tool_type="interactive" name="Package demo: iSEE" version="0.1">
+          <description>Interactive SummarizedExperiment Explorer</description>
           <requirements>
-              <container type="docker">ghcr.io/vjcitn/ontoprocws:latest</container>
+              <container type="docker">ghcr.io/isee/iseedemoeurobioc2024:latest</container>
           </requirements>
           <entry_points>
-              <entry_point name="vjcontobioc2024" requires_domain="True">
+              <entry_point name="eurobioc2024isee" requires_domain="True">
                   <port>8787</port>
               </entry_point>
           </entry_points>
@@ -25,12 +25,12 @@ extraFileMappings:
               <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
               <environment_variable name="API_KEY" inject="api_key" />
           </environment_variables>
-          <command detect_errors="aggressive">export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/ontoProcWS/vignettes/owlents.Rmd' ]; then echo '/home/rstudio/ontoProcWS/vignettes/owlents.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/owlents.Rmd' > /tmp/startfile; fi ; echo "{ 'visual_markdown_editing_is_default': true }" > /etc/rstudio/rstudio-prefs.json ; echo "setwd('/home/rstudio'); setHook('rstudio.sessionInit', function(newSession) { if (newSession) rstudioapi::filesPaneNavigate('\$(dirname \$(cat /tmp/startfile))'); rstudioapi::navigateToFile('\$(cat /tmp/startfile)') }, action = 'append')" > /home/rstudio/.Rprofile; export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; chown -R rstudio /home/rstudio/*; rm /tmp/startfile; chown -R rstudio /home/rstudio/.*; /init</command>
+          <command detect_errors="aggressive">export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/iSEEDemoEuroBioC2024/vignettes/workshop_isee_extension.Rmd' ]; then echo '/home/rstudio/iSEEDemoEuroBioC2024/vignettes/workshop_isee_extension.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/workshop_isee_extension.Rmd' > /tmp/startfile; fi ; echo "{ 'visual_markdown_editing_is_default': true }" > /etc/rstudio/rstudio-prefs.json ; echo "setwd('/home/rstudio'); setHook('rstudio.sessionInit', function(newSession) { if (newSession) rstudioapi::filesPaneNavigate('\$(dirname \$(cat /tmp/startfile))'); rstudioapi::navigateToFile('\$(cat /tmp/startfile)') }, action = 'append')" > /home/rstudio/.Rprofile; export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; chown -R rstudio /home/rstudio/*; rm /tmp/startfile; chown -R rstudio /home/rstudio/.*; /init</command>
           <inputs>
           </inputs>
           <outputs>
           </outputs>
           <tests>
           </tests>
-          <help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/vjcitn/ontoProcWS.</help>
+          <help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/iSEE/iSEEDemoEuroBioC2024.</help>
       </tool>