Push generated phantasusbioc2024

generated/phantasusbioc2024.container

@@ -0,0 +1 @@
+ghcr.io/assaron/phantasuspkgdemo:latest

generated/workshop-toolconf-values.yaml

@@ -82,6 +82,8 @@ configs:
         </section>
         <label text="cdnmws" id="cdnmws" />
           <tool file="interactive/biocworkshop_cdnmws1.xml" />
+        <label text="BioC2024" id="bioc2024" />
+          <tool file="interactive/biocworkshop_phantasusbioc2024.xml" />
       </toolbox>
   integrated_tool_panel.xml: |
     <?xml version='1.0'?>
@@ -179,4 +181,6 @@ configs:
         </section>
         <label text="cdnmws" id="cdnmws" />
           <tool id="interactivetool_biocworkshop_cdnmws1" />
+        <label text="BioC2024" id="bioc2024" />
+          <tool id="interactivetool_biocworkshop_phantasusbioc2024" />
     </toolbox>

generated/workshop-values-phantasusbioc2024.yaml

@@ -0,0 +1,35 @@
+  /galaxy/server/tools/interactive/biocworkshop_phantasusbioc2024.xml:
+    useSecret: false
+    applyToJob: true
+    applyToSetupJob: true
+    applyToWeb: true
+    applyToWorkflow: true
+    applyToNginx: true
+    tpl: false
+    content: |
+      <tool id="interactivetool_biocworkshop_phantasusbioc2024" tool_type="interactive" name="Package demo: phantasus" version="0.1">
+          <description>visual and interactive gene expression analysis with phantasus package</description>
+          <requirements>
+              <container type="docker">ghcr.io/assaron/phantasuspkgdemo:latest</container>
+          </requirements>
+          <entry_points>
+              <entry_point name="phantasusbioc2024" 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">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(getwd()) }, 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/assaron/phantasusPkgDemo.</help>
+      </tool>

generated/workshop-values.yaml

@@ -1,5 +1,5 @@
 extraFileMappings:
-  /galaxy/server/tools/interactive/biocworkshop_biocrstudio319.xml:
+  /galaxy/server/tools/interactive/biocworkshop_phantasusbioc2024.xml:
     useSecret: false
     applyToJob: true
     applyToSetupJob: true
@@ -8,13 +8,13 @@ extraFileMappings:
     applyToNginx: true
     tpl: false
     content: |
-      <tool id="interactivetool_biocworkshop_biocrstudio319" tool_type="interactive" name="RStudio Bioc 3.19" version="0.1">
-          <description>Bioconductor 3.19 with R 4.4.1</description>
+      <tool id="interactivetool_biocworkshop_phantasusbioc2024" tool_type="interactive" name="Package demo: phantasus" version="0.1">
+          <description>visual and interactive gene expression analysis with phantasus package</description>
           <requirements>
-              <container type="docker">ghcr.io/bioconductor/bioconductor:3.19</container>
+              <container type="docker">ghcr.io/assaron/phantasuspkgdemo:latest</container>
           </requirements>
           <entry_points>
-              <entry_point name="biocrstudio319" requires_domain="True">
+              <entry_point name="phantasusbioc2024" requires_domain="True">
                   <port>8787</port>
               </entry_point>
           </entry_points>
@@ -32,5 +32,5 @@ extraFileMappings:
           </outputs>
           <tests>
           </tests>
-          <help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/Bioconductor/workshop-contributions/issues/78.</help>
+          <help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/assaron/phantasusPkgDemo.</help>
       </tool>