From bcd4e0e5891a738b2d9681762a601c88e915ea52 Mon Sep 17 00:00:00 2001
From: github-actions <github-actions@github.com>
Date: Sat, 20 Jul 2024 05:01:49 +0000
Subject: [PATCH] Push generated bioc2024bamSliceR

---
 generated/bioc2024bamSliceR.Dockerfile           |  4 ++--
 generated/workshop-toolconf-values.yaml          |  2 ++
 generated/workshop-values-bioc2024bamSliceR.yaml |  2 +-
 generated/workshop-values.yaml                   | 14 +++++++-------
 4 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/generated/bioc2024bamSliceR.Dockerfile b/generated/bioc2024bamSliceR.Dockerfile
index a95ce20..1c00381 100644
--- a/generated/bioc2024bamSliceR.Dockerfile
+++ b/generated/bioc2024bamSliceR.Dockerfile
@@ -1,2 +1,2 @@
-FROM ghcr.io/bioconductor/bioconductor:devel
-RUN sudo apt-get update && sudo apt-get -y install apt-file &&  echo trichelab/bamSliceR,BSgenome.Hsapiens.UCSC.hg38,BiocParallel,Homo.sapiens,TxDb.Hsapiens.UCSC.hg38.knownGene,VariantTools,biomaRt,data.table,ensemblVEP,gampR,httr,jsonlite,rtracklayer,stringr | tr ',' '\n' > /tmp/pkglist && cat /tmp/pkglist | xargs -i Rscript -e "if (!require('rspm')) { install.packages('rspm'); rspm::enable(); }; p = BiocManager::install(c('{}'), dependencies = c('Depends', 'Imports', 'LinkingTo', 'Suggests')); if(p %in% rownames(installed.packages())) q(status = 0) else if(strsplit(p, '/')[[1]][2] %in% rownames(installed.packages())) q(status = 0) else q(status = 1)"
+FROM ghcr.io/bioconductor/bioconductor:3.18
+RUN sudo apt-get update && sudo apt-get -y install apt-file &&  echo trichelab/bamSliceR | tr ',' '\n' > /tmp/pkglist && cat /tmp/pkglist | xargs -i Rscript -e "if (!require('rspm')) { install.packages('rspm'); rspm::enable(); }; p = BiocManager::install(c('{}'), dependencies = c('Depends', 'Imports', 'LinkingTo', 'Suggests')); if(p %in% rownames(installed.packages())) q(status = 0) else if(strsplit(p, '/')[[1]][2] %in% rownames(installed.packages())) q(status = 0) else q(status = 1)"
diff --git a/generated/workshop-toolconf-values.yaml b/generated/workshop-toolconf-values.yaml
index 8cb2d8f..afddd39 100644
--- 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-bioc2024bamSliceR.yaml b/generated/workshop-values-bioc2024bamSliceR.yaml
index 47c809f..2d07331 100644
--- a/generated/workshop-values-bioc2024bamSliceR.yaml
+++ b/generated/workshop-values-bioc2024bamSliceR.yaml
@@ -10,7 +10,7 @@
       <tool id="interactivetool_biocworkshop_bioc2024bamSliceR" 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>
           <requirements>
-              <container type="docker">ghcr.io/bioconductor/bioconductor:3.18</container>
+              <container type="docker">docker.io/bioconductor/workshop-contributions:devel-3431a869</container>
           </requirements>
           <entry_points>
               <entry_point name="bioc2024bamSliceR" requires_domain="True">
diff --git a/generated/workshop-values.yaml b/generated/workshop-values.yaml
index 085b763..3202270 100644
--- 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_bioc2024bamSliceR.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_bioc2024bamSliceR" 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>
           <requirements>
-              <container type="docker">ghcr.io/anthonychristidis/scdiagnosticsbioc2024demo:latest</container>
+              <container type="docker">docker.io/bioconductor/workshop-contributions:devel-3431a869</container>
           </requirements>
           <entry_points>
-              <entry_point name="scdiagnosticsbioc2024" requires_domain="True">
+              <entry_point name="bioc2024bamSliceR" 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/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>
           <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/trichelab/bamSliceR.</help>
       </tool>