interactivetool_rstudio_askor.xml

<tool id="interactive_tool_rstudio_askor" tool_type="interactive" name="RStudio AskoR" version="0.1">
    <requirements>
        <container type="docker">quay.io/genouest/docker-galaxy-rstudio-askor:latest</container>
    </requirements>
    <entry_points>
        <entry_point name="RStudio" requires_domain="True">
            <port>80</port>
            <url>rstudio/</url>
        </entry_point>
    </entry_points>
    <environment_variables>
        <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 -->
        <environment_variable name="REMOTE_HOST">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
        <environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
        <environment_variable name="DEBUG">true</environment_variable>
        <environment_variable name="DISABLE_AUTH">true</environment_variable>
        <environment_variable name="API_KEY" inject="api_key" />
    </environment_variables>
    <command detect_errors="aggressive"><![CDATA[
        #import re
        export GALAXY_WORKING_DIR=`pwd` &&
        mkdir -p ./rstudio/outputs/ &&
        mkdir -p ./rstudio/data &&

        ## change into the directory where the notebooks are located
        cd ./rstudio/ &&

        sed -i 's|/monitor.*||g' /etc/services.d/nginx/run &&

        /etc/init.d/syslog-ng start &&
        /init &
        ##rstudio-server start &&
        sleep 5 &&

        chmod 777 /tmp -R &&
        tail -f /var/log/rstudio-server/rserver.log

    ]]>
    </command>
    <inputs>
        <!--<param name="input" type="data" optional="true" label="Include data into the environment"/>-->
    </inputs>
    <outputs>
        <data name="jupyter_notebook" format="ipynb" label=""></data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="mode" value="previous" />
            <param name="ipynb" value="test.ipynb" />
            <param name="run_it" value="true" />
            <output name="jupyter_notebook" file="test.ipynb" ftype="ipynb"/>
        </test>
    </tests>
    <help>
    This familiar R analysis software suite will let you explore your
    datasets in depth. Comes with ggplot2, RODBC, maps, shinyapps, knitr,
    LaTeX, bioconductor, cummeRbund, and many more pre-installed packages.

    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
    do the heavy lifting and data reduction steps in Galaxy and the plotting and more `interactive` part on smaller datasets in RStudio.

    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().

    For example, gx_get(42) will fetch dataset 42 from your history and return the file location
    </help>
</tool>