mirror of
https://github.com/galaxyproject/galaxy.git
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68 lines
3.2 KiB
XML
68 lines
3.2 KiB
XML
<tool id="interactive_tool_rstudio" tool_type="interactive" name="RStudio" version="0.1">
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<requirements>
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<container type="docker">quay.io/erasche/docker-rstudio-notebook:19.09</container>
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</requirements>
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<entry_points>
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<entry_point name="RStudio" requires_domain="True">
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<port>80</port>
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<url>rstudio/</url>
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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="HISTORY_ID" strip="True">${__app__.security.encode_id($jupyter_notebook.history_id)}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
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<environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
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<environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
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<environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
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<environment_variable name="DEBUG">true</environment_variable>
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<environment_variable name="DISABLE_AUTH">true</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"><![CDATA[
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#import re
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export GALAXY_WORKING_DIR=`pwd` &&
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mkdir -p ./rstudio/outputs/ &&
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mkdir -p ./rstudio/data &&
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## change into the directory where the notebooks are located
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cd ./rstudio/ &&
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sed -i 's|/monitor.*||g' /etc/services.d/nginx/run &&
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/etc/init.d/syslog-ng start &&
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/init &
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##rstudio-server start &&
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sleep 5 &&
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chmod 777 /tmp -R &&
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tail -f /var/log/rstudio-server/rserver.log
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]]>
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</command>
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<inputs>
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<!--<param name="input" type="data" optional="true" label="Include data into the environment"/>-->
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</inputs>
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<outputs>
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<data name="jupyter_notebook" format="ipynb" label=""></data>
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</outputs>
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<tests>
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<test expect_num_outputs="1">
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<param name="mode" value="previous" />
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<param name="ipynb" value="test.ipynb" />
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<param name="run_it" value="true" />
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<output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
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</test>
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</tests>
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<help>
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This familiar R analysis software suite will let you explore your
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datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr,
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LaTeX, bioconductor, cummeRbund, and many more pre-installed packages.
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Galaxy offers you to use RStudio directly in Galaxy accessing and interacting with Galaxy datasets as you like. A very common use-case is to
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do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in RStudio.
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The convenience functions gx_put() and gx_get() are available to you to interact with your current Galaxy history. You can save your workspace with gx_save().
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For example, gx_get(42) will fetch dataset 42 from your history and return the file location
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</help>
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</tool>
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