Push generated bioc2023rcwl

Bioconductor · Aug 1, 2023 · 42e298e · 42e298e
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commit 42e298e
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Showing 4 changed files with 45 additions and 7 deletions.
diff --git a/generated/bioc2023rcwl.container b/generated/bioc2023rcwl.container
@@ -0,0 +1 @@
+ghcr.io/rworkflow/rcwlworkshop:latest
diff --git a/generated/workshop-toolconf-values.yaml b/generated/workshop-toolconf-values.yaml
@@ -3,6 +3,7 @@ configs:
     <?xml version='1.0' encoding='utf-8'?>
       <toolbox monitor="true">
         <label text="BioC 2023" id="bioc2023" />
+          <tool file="interactive/biocworkshop_bioc2023rcwl.xml" />
           <tool file="interactive/biocworkshop_bioc2023statial.xml" />
           <tool file="interactive/biocworkshop_bioc2023qsvar.xml" />
           <tool file="interactive/biocworkshop_bioc2023tidysce.xml" />
@@ -66,6 +67,7 @@ configs:
         its section) modify that file and restart Galaxy.
         -->
         <label text="BioC 2023" id="bioc2023" />
+          <tool file="interactive/biocworkshop_bioc2023rcwl.xml" />
           <tool file="interactive/biocworkshop_bioc2023statial.xml" />
           <tool id="interactivetool_biocworkshop_bioc2023qsvar" />
           <tool id="interactivetool_biocworkshop_bioc2023tidysce" />

diff --git a/generated/workshop-values-bioc2023rcwl.yaml b/generated/workshop-values-bioc2023rcwl.yaml
@@ -0,0 +1,35 @@
+  /galaxy/server/tools/interactive/biocworkshop_bioc2023rcwl.xml:
+    useSecret: false
+    applyToJob: true
+    applyToSetupJob: true
+    applyToWeb: true
+    applyToWorkflow: true
+    applyToNginx: true
+    tpl: false
+    content: |
+      <tool id="interactivetool_biocworkshop_bioc2023rcwl" tool_type="interactive" name="Package Demo: RcwlPipelines" version="0.1">
+          <description>Use R to Create and Execute Reproducible CWL Workflows for Genomic Research</description>
+          <requirements>
+              <container type="docker">ghcr.io/rworkflow/rcwlworkshop:latest</container>
+          </requirements>
+          <entry_points>
+              <entry_point name="bioc2023rcwl" 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/RcwlWorkshop/vignettes/ReUseData_Rcwl_Workshop.Rmd' ]; then echo '/home/rstudio/RcwlWorkshop/vignettes/ReUseData_Rcwl_Workshop.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/ReUseData_Rcwl_Workshop.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; 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/rworkflow/RcwlWorkshop.</help>
+      </tool>
diff --git a/generated/workshop-values.yaml b/generated/workshop-values.yaml
@@ -1,5 +1,5 @@
 extraFileMappings:
-  /galaxy/server/tools/interactive/biocworkshop_bioc2023demuxsnp.xml:
+  /galaxy/server/tools/interactive/biocworkshop_bioc2023rcwl.xml:
     useSecret: false
     applyToJob: true
     applyToSetupJob: true
@@ -8,13 +8,13 @@ extraFileMappings:
     applyToNginx: true
     tpl: false
     content: |
-      <tool id="interactivetool_biocworkshop_bioc2023demuxsnp" tool_type="interactive" name="Package Demo: demuxSNP" version="0.1">
-          <description>demonstrate different methods for visualising the data, carry out some benchmarking, and demonstrate the application of demuxSNP in scenarios where hashing quality is poor</description>
+      <tool id="interactivetool_biocworkshop_bioc2023rcwl" tool_type="interactive" name="Package Demo: RcwlPipelines" version="0.1">
+          <description>Use R to Create and Execute Reproducible CWL Workflows for Genomic Research</description>
           <requirements>
-              <container type="docker">ghcr.io/michaelplynch/demultiplexing-bioc23:latest</container>
+              <container type="docker">ghcr.io/rworkflow/rcwlworkshop:latest</container>
           </requirements>
           <entry_points>
-              <entry_point name="bioc2023demuxsnp" requires_domain="True">
+              <entry_point name="bioc2023rcwl" 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/demultiplexing-bioc23/vignettes/a-intro-to-demultiplexing.Rmd' ]; then echo '/home/rstudio/demultiplexing-bioc23/vignettes/a-intro-to-demultiplexing.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/a-intro-to-demultiplexing.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; 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/RcwlWorkshop/vignettes/ReUseData_Rcwl_Workshop.Rmd' ]; then echo '/home/rstudio/RcwlWorkshop/vignettes/ReUseData_Rcwl_Workshop.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/ReUseData_Rcwl_Workshop.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; 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/michaelplynch/demultiplexing-bioc23.</help>
+          <help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/rworkflow/RcwlWorkshop.</help>
       </tool>