Push generated bamslicerbioc2024

Bioconductor · Jul 21, 2024 · 3722887 · 3722887
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diff --git a/generated/bamslicerbioc2024.Dockerfile b/generated/bamslicerbioc2024.Dockerfile
@@ -0,0 +1,2 @@
+FROM ghcr.io/bioconductor/bioconductor:3.18
+RUN sudo apt-get update && sudo apt-get -y install apt-file &&  echo trichelab/bamSliceR | 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)"
diff --git a/generated/workshop-values-bamslicerbioc2024.yaml b/generated/workshop-values-bamslicerbioc2024.yaml
@@ -0,0 +1,35 @@
+  /galaxy/server/tools/interactive/biocworkshop_bamslicerbioc2024.xml:
+    useSecret: false
+    applyToJob: true
+    applyToSetupJob: true
+    applyToWeb: true
+    applyToWorkflow: true
+    applyToNginx: true
+    tpl: false
+    content: |
+      <tool id="interactivetool_biocworkshop_bamslicerbioc2024" tool_type="interactive" name="Package Demo: bamSliceR" version="0.1">
+          <description>A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories</description>
+          <requirements>
+              <container type="docker">docker.io/bioconductor/workshop-contributions:devel-3431a869</container>
+          </requirements>
+          <entry_points>
+              <entry_point name="bamslicerbioc2024" requires_domain="True">
+                  <port>8787</port>
+              </entry_point>
+          </entry_points>
+          <environment_variables>
+              <environment_variable name="DISABLE_AUTH">true</environment_variable>
+              <environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
+              <environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
+              <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/bamSliceR/README.md' ]; then echo '/home/rstudio/bamSliceR/README.md' > /tmp/startfile; else echo '/home/rstudio/README.md' > /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/trichelab/bamSliceR.</help>
+      </tool>
diff --git a/generated/workshop-values.yaml b/generated/workshop-values.yaml
@@ -1,5 +1,5 @@
 extraFileMappings:
-  /galaxy/server/tools/interactive/biocworkshop_bioc2024bamSliceR.xml:
+  /galaxy/server/tools/interactive/biocworkshop_bamslicerbioc2024.xml:
     useSecret: false
     applyToJob: true
     applyToSetupJob: true
@@ -8,13 +8,13 @@ extraFileMappings:
     applyToNginx: true
     tpl: false
     content: |
-      <tool id="interactivetool_biocworkshop_bioc2024bamSliceR" tool_type="interactive" name="Package Demo: bamSliceR" version="0.1">
+      <tool id="interactivetool_biocworkshop_bamslicerbioc2024" tool_type="interactive" name="Package Demo: bamSliceR" version="0.1">
           <description>A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories</description>
           <requirements>
               <container type="docker">docker.io/bioconductor/workshop-contributions:devel-3431a869</container>
           </requirements>
           <entry_points>
-              <entry_point name="bioc2024bamSliceR" requires_domain="True">
+              <entry_point name="bamslicerbioc2024" requires_domain="True">
                   <port>8787</port>
               </entry_point>
           </entry_points>
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		@@ -0,0 +1,2 @@
		FROM ghcr.io/bioconductor/bioconductor:3.18
		RUN sudo apt-get update && sudo apt-get -y install apt-file && echo trichelab/bamSliceR \| 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)"