Push generated scdiagnosticsbioc2024

Bioconductor · Jul 19, 2024 · 7fe934e · 7fe934e
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Showing 4 changed files with 49 additions and 7 deletions.
diff --git a/generated/scdiagnosticsbioc2024.container b/generated/scdiagnosticsbioc2024.container
@@ -0,0 +1 @@
+ghcr.io/anthonychristidis/scdiagnosticsbioc2024demo:latest
diff --git a/generated/workshop-toolconf-values.yaml b/generated/workshop-toolconf-values.yaml
@@ -83,10 +83,13 @@ configs:
         <label text="cdnmws" id="cdnmws" />
           <tool file="interactive/biocworkshop_cdnmws1.xml" />
         <label text="BioC2024" id="bioc2024" />
+          <tool file="interactive/biocworkshop_scdiagnosticsbioc2024.xml" />
           <tool file="interactive/biocworkshop_flamesbioc2024.xml" />
+          <tool file="interactive/biocworkshop_vjcontobioc2024.xml" />
           <tool file="interactive/biocworkshop_scigdbioc2024.xml" />
           <tool file="interactive/biocworkshop_bioc2024tidyworkshop.xml" />
           <tool file="interactive/biocworkshop_phantasusbioc2024.xml" />
+          <tool file="interactive/biocworkshop_jupyterbioc2024.xml" />
         <label text="EuroBioC2024" id="eurobioc2024" />
           <tool file="interactive/biocworkshop_eurobioc2024isee.xml" />
       </toolbox>
@@ -187,10 +190,13 @@ configs:
         <label text="cdnmws" id="cdnmws" />
           <tool id="interactivetool_biocworkshop_cdnmws1" />
         <label text="BioC2024" id="bioc2024" />
+          <tool id="interactivetool_biocworkshop_scdiagnosticsbioc2024" />
           <tool id="interactivetool_biocworkshop_flamesbioc2024" />
+          <tool id="interactivetool_biocworkshop_vjcontobioc2024" />
           <tool id="interactivetool_biocworkshop_scigdbioc2024" />
           <tool id="interactivetool_biocworkshop_bioc2024tidyworkshop" />
           <tool id="interactivetool_biocworkshop_phantasusbioc2024" />
+          <tool id="interactivetool_biocworkshop_jupyterbioc2024" />
         <label text="EuroBioC2024" id="eurobioc2024" />
           <tool id="interactivetool_biocworkshop_eurobioc2024isee" />
     </toolbox>
diff --git a/generated/workshop-values-scdiagnosticsbioc2024.yaml b/generated/workshop-values-scdiagnosticsbioc2024.yaml
@@ -0,0 +1,35 @@
+  /galaxy/server/tools/interactive/biocworkshop_scdiagnosticsbioc2024.xml:
+    useSecret: false
+    applyToJob: true
+    applyToSetupJob: true
+    applyToWeb: true
+    applyToWorkflow: true
+    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>
+          <requirements>
+              <container type="docker">ghcr.io/anthonychristidis/scdiagnosticsbioc2024demo:latest</container>
+          </requirements>
+          <entry_points>
+              <entry_point name="scdiagnosticsbioc2024" 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/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>
+          <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>
+      </tool>
diff --git a/generated/workshop-values.yaml b/generated/workshop-values.yaml
@@ -1,5 +1,5 @@
 extraFileMappings:
-  /galaxy/server/tools/interactive/biocworkshop_eurobioc2024isee.xml:
+  /galaxy/server/tools/interactive/biocworkshop_scdiagnosticsbioc2024.xml:
     useSecret: false
     applyToJob: true
     applyToSetupJob: true
@@ -8,13 +8,13 @@ extraFileMappings:
     applyToNginx: true
     tpl: false
     content: |
-      <tool id="interactivetool_biocworkshop_eurobioc2024isee" tool_type="interactive" name="Package demo: iSEE" version="0.1">
-          <description>Interactive SummarizedExperiment Explorer</description>
+      <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>
           <requirements>
-              <container type="docker">ghcr.io/isee/iseedemoeurobioc2024:latest</container>
+              <container type="docker">ghcr.io/anthonychristidis/scdiagnosticsbioc2024demo:latest</container>
           </requirements>
           <entry_points>
-              <entry_point name="eurobioc2024isee" requires_domain="True">
+              <entry_point name="scdiagnosticsbioc2024" 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/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>
+          <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>
           <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/iSEE/iSEEDemoEuroBioC2024.</help>
+          <help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/AnthonyChristidis/scDiagnosticsBioc2024Demo.</help>
       </tool>