Push generated sfebioc2024

Bioconductor · Jul 22, 2024 · e183654 · e183654
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commit e183654
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Showing 4 changed files with 47 additions and 9 deletions.
diff --git a/generated/sfebioc2024.container b/generated/sfebioc2024.container
@@ -0,0 +1 @@
+ghcr.io/lambdamoses/sfeworkshop2024:latest
diff --git a/generated/workshop-toolconf-values.yaml b/generated/workshop-toolconf-values.yaml
@@ -11,7 +11,7 @@ configs:
         <label text="CBRC 2024" id="cbrc2024" />
           <tool file="interactive/biocworkshop_cbrcvoyagermar2024.xml" />
         <label text="Archived Events" id="archived" />
-        <section name="CDNMWS" id="cdnmws" >
+        <section name="cdnmws" id="cdnmws" >
           <tool file="interactive/biocworkshop_cdnmws1.xml" />
         </section>
         <section name="ABACBS 2023" id="abacbs2023" >
@@ -84,6 +84,7 @@ configs:
           <tool file="interactive/biocshiny_iseehub.xml" />
         </section>
         <label text="BioC2024" id="bioc2024" />
+          <tool file="interactive/biocworkshop_sfebioc2024.xml" />
           <tool file="interactive/biocworkshop_bioc2024diffmeth.xml" />
           <tool file="interactive/biocworkshop_scdiagnosticsbioc2024.xml" />
           <tool file="interactive/biocworkshop_flamesbioc2024.xml" />
@@ -120,7 +121,7 @@ configs:
         <label text="CBRC 2024" id="cbrc2024" />
           <tool id="interactivetool_biocworkshop_cbrcvoyagermar2024" />
         <label text="Archived Events" id="archived" />
-        <section name="CDNMWS" id="cdnmws" >
+        <section name="cdnmws" id="cdnmws" >
           <tool id="interactivetool_biocworkshop_cdnmws1" />
         </section>
         <section name="ABACBS 2023" id="abacbs2023" >
@@ -193,6 +194,7 @@ configs:
           <tool id="interactivetool_biocshiny_iseehub" />
         </section>
         <label text="BioC2024" id="bioc2024" />
+          <tool id="interactivetool_biocworkshop_sfebioc2024" />
           <tool id="interactivetool_biocworkshop_bioc2024diffmeth" />
           <tool id="interactivetool_biocworkshop_scdiagnosticsbioc2024" />
           <tool id="interactivetool_biocworkshop_flamesbioc2024" />

diff --git a/generated/workshop-values-sfebioc2024.yaml b/generated/workshop-values-sfebioc2024.yaml
@@ -0,0 +1,35 @@
+  /galaxy/server/tools/interactive/biocworkshop_sfebioc2024.xml:
+    useSecret: false
+    applyToJob: true
+    applyToSetupJob: true
+    applyToWeb: true
+    applyToWorkflow: true
+    applyToNginx: true
+    tpl: false
+    content: |
+      <tool id="interactivetool_biocworkshop_sfebioc2024" tool_type="interactive" name="Exploratory spatial data analysis from single molecules to multiple samples" version="0.1">
+          <description>Using SpatialFeatureExperiment and Voyager with support for transcript spot geometries in rowGeometries, plotting transcript spots, aggregating transcript spots with a spatial grid or any geometry, aggregating cell level data with a spatial grid or any geometry, splitting SFE objects with geometries, and improved support for images and affine transformations</description>
+          <requirements>
+              <container type="docker">ghcr.io/lambdamoses/sfeworkshop2024:latest</container>
+          </requirements>
+          <entry_points>
+              <entry_point name="sfebioc2024" 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/SFEWorkshop2024/vignettes/workshop.Rmd' ]; then echo '/home/rstudio/SFEWorkshop2024/vignettes/workshop.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/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; 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/lambdamoses/SFEWorkshop2024.</help>
+      </tool>
diff --git a/generated/workshop-values.yaml b/generated/workshop-values.yaml
@@ -1,5 +1,5 @@
 extraFileMappings:
-  /galaxy/server/tools/interactive/biocworkshop_bamslicerbioc2024.xml:
+  /galaxy/server/tools/interactive/biocworkshop_sfebioc2024.xml:
     useSecret: false
     applyToJob: true
     applyToSetupJob: true
@@ -8,13 +8,13 @@ extraFileMappings:
     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>
+      <tool id="interactivetool_biocworkshop_sfebioc2024" tool_type="interactive" name="Exploratory spatial data analysis from single molecules to multiple samples" version="0.1">
+          <description>Using SpatialFeatureExperiment and Voyager with support for transcript spot geometries in rowGeometries, plotting transcript spots, aggregating transcript spots with a spatial grid or any geometry, aggregating cell level data with a spatial grid or any geometry, splitting SFE objects with geometries, and improved support for images and affine transformations</description>
           <requirements>
-              <container type="docker">docker.io/bioconductor/workshop-contributions:devel-3431a869</container>
+              <container type="docker">ghcr.io/lambdamoses/sfeworkshop2024:latest</container>
           </requirements>
           <entry_points>
-              <entry_point name="bamslicerbioc2024" requires_domain="True">
+              <entry_point name="sfebioc2024" 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/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>
+          <command detect_errors="aggressive">export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/SFEWorkshop2024/vignettes/workshop.Rmd' ]; then echo '/home/rstudio/SFEWorkshop2024/vignettes/workshop.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/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; 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>
+          <help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/lambdamoses/SFEWorkshop2024.</help>
       </tool>