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Push generated eurobioc2025omatutorial
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‎generated/eurobioc2025omatutorial.container‎

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ghcr.io/microbiome/omatutorials:latest

‎generated/workshop-toolconf-values.yaml‎

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<section name="CDNMWS" id="cdnmws" >
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<tool file="interactive/biocworkshop_cdnmws1.xml" />
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</section>
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<label text="EuroBioc2025" id="eurobioc2025" />
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<tool file="interactive/biocworkshop_eurobioc2025omatutorial.xml" />
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</toolbox>
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integrated_tool_panel.xml: |
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<?xml version='1.0'?>
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<section name="CDNMWS" id="cdnmws" >
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<tool id="interactivetool_biocworkshop_cdnmws1" />
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</section>
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<label text="EuroBioc2025" id="eurobioc2025" />
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<tool id="interactivetool_biocworkshop_eurobioc2025omatutorial" />
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</toolbox>

‎generated/workshop-values-eurobioc2025omatutorial.yaml‎

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/galaxy/server/tools/interactive/biocworkshop_eurobioc2025omatutorial.xml:
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useSecret: false
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applyToJob: true
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applyToSetupJob: true
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applyToWeb: true
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applyToWorkflow: true
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applyToNginx: true
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tpl: false
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content: |
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<tool id="interactivetool_biocworkshop_eurobioc2025omatutorial" tool_type="interactive" name="Orchestrating Microbiome Analysis with Bioconductor" version="0.1">
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<description>Introducing Bioconductor tools for microbiome data science through a practical case study</description>
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<requirements>
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<container type="docker">ghcr.io/microbiome/omatutorials:latest</container>
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</requirements>
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<entry_points>
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<entry_point name="eurobioc2025omatutorial" requires_domain="True">
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<port>8787</port>
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</entry_point>
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</entry_points>
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<environment_variables>
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<environment_variable name="DISABLE_AUTH">true</environment_variable>
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<environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
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<environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
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<environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
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<environment_variable name="API_KEY" inject="api_key" />
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</environment_variables>
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<command detect_errors="aggressive">export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/OMATutorials/vignettes/eurobioc2025.Rmd' ]; then echo '/home/rstudio/OMATutorials/vignettes/eurobioc2025.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/eurobioc2025.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>
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<inputs>
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</inputs>
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<outputs>
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</outputs>
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<tests>
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</tests>
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<help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/microbiome/OMATutorials.</help>
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</tool>

‎generated/workshop-values.yaml‎

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extraFileMappings:
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/galaxy/server/tools/interactive/biocworkshop_mig2025spatial.xml:
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/galaxy/server/tools/interactive/biocworkshop_eurobioc2025omatutorial.xml:
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useSecret: false
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applyToJob: true
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applyToSetupJob: true
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applyToNginx: true
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tpl: false
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content: |
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<tool id="interactivetool_biocworkshop_mig2025spatial" tool_type="interactive" name="Introduction to imaging-based spatial transcriptomics analysis" version="0.1">
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<description>This workflow package shows how a basic analysis of spatial transcriptomics datasets is performed to gain biological insight.</description>
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<tool id="interactivetool_biocworkshop_eurobioc2025omatutorial" tool_type="interactive" name="Orchestrating Microbiome Analysis with Bioconductor" version="0.1">
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<description>Introducing Bioconductor tools for microbiome data science through a practical case study</description>
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<requirements>
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<container type="docker">ghcr.io/bioconductor/workshop-contributions:devel-8fceb82f</container>
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<container type="docker">ghcr.io/microbiome/omatutorials:latest</container>
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</requirements>
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<entry_points>
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<entry_point name="mig2025spatial" requires_domain="True">
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<entry_point name="eurobioc2025omatutorial" requires_domain="True">
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<port>8787</port>
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</entry_point>
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</entry_points>
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<environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
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<environment_variable name="API_KEY" inject="api_key" />
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</environment_variables>
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<command detect_errors="aggressive">export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/CosMxSpatialAnalysisWorkshop/vignettes/workflow_spatial_cosmx.Rmd' ]; then echo '/home/rstudio/CosMxSpatialAnalysisWorkshop/vignettes/workflow_spatial_cosmx.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/workflow_spatial_cosmx.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>
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<command detect_errors="aggressive">export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/OMATutorials/vignettes/eurobioc2025.Rmd' ]; then echo '/home/rstudio/OMATutorials/vignettes/eurobioc2025.Rmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/eurobioc2025.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>
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<inputs>
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</inputs>
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<outputs>
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</outputs>
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<tests>
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</tests>
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<help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/bhuvad/CosMxSpatialAnalysisWorkshop.</help>
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<help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/microbiome/OMATutorials.</help>
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</tool>

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