Push generated bioc2024diffmeth

Bioconductor · Jul 19, 2024 · 2aafe85 · 2aafe85
1 parent 7fe934e
commit 2aafe85
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/generated/workshop-toolconf-values.yaml b/generated/workshop-toolconf-values.yaml
@@ -83,6 +83,7 @@ configs:
         <label text="cdnmws" id="cdnmws" />
           <tool file="interactive/biocworkshop_cdnmws1.xml" />
         <label text="BioC2024" id="bioc2024" />
+          <tool file="interactive/biocworkshop_bioc2024diffmeth.xml" />
           <tool file="interactive/biocworkshop_scdiagnosticsbioc2024.xml" />
           <tool file="interactive/biocworkshop_flamesbioc2024.xml" />
           <tool file="interactive/biocworkshop_vjcontobioc2024.xml" />
@@ -190,6 +191,7 @@ configs:
         <label text="cdnmws" id="cdnmws" />
           <tool id="interactivetool_biocworkshop_cdnmws1" />
         <label text="BioC2024" id="bioc2024" />
+          <tool id="interactivetool_biocworkshop_bioc2024diffmeth" />
           <tool id="interactivetool_biocworkshop_scdiagnosticsbioc2024" />
           <tool id="interactivetool_biocworkshop_flamesbioc2024" />
           <tool id="interactivetool_biocworkshop_vjcontobioc2024" />

diff --git a/generated/workshop-values.yaml b/generated/workshop-values.yaml
@@ -1,5 +1,5 @@
 extraFileMappings:
-  /galaxy/server/tools/interactive/biocworkshop_scdiagnosticsbioc2024.xml:
+  /galaxy/server/tools/interactive/biocworkshop_bioc2024diffmeth.xml:
     useSecret: false
     applyToJob: true
     applyToSetupJob: true
@@ -8,13 +8,13 @@ extraFileMappings:
     applyToNginx: true
     tpl: false
     content: |
-      <tool id="interactivetool_biocworkshop_scdiagnosticsbioc2024" tool_type="interactive" name="Package Demo: scDiagnostics" version="0.1">
-          <description>The package provides diagnostic plots to assess the quality of cell type assignments from single cell gene expression profiles</description>
+      <tool id="interactivetool_biocworkshop_bioc2024diffmeth" tool_type="interactive" name="Package Demo: NanoMethViz" version="0.1">
+          <description></description>
           <requirements>
-              <container type="docker">ghcr.io/anthonychristidis/scdiagnosticsbioc2024demo:latest</container>
+              <container type="docker">ghcr.io/shians/differential_methylation_workshop:latest</container>
           </requirements>
           <entry_points>
-              <entry_point name="scdiagnosticsbioc2024" requires_domain="True">
+              <entry_point name="bioc2024diffmeth" 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/scDiagnosticsBioc2024Demo/README.md' ]; then echo '/home/rstudio/scDiagnosticsBioc2024Demo/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>
+          <command detect_errors="aggressive">export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/differential_methylation_workshop/vignettes/workflow.rmd' ]; then echo '/home/rstudio/differential_methylation_workshop/vignettes/workflow.rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/workflow.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/AnthonyChristidis/scDiagnosticsBioc2024Demo.</help>
+          <help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/Shians/differential_methylation_workshop.</help>
       </tool>