add 3 new ITs

2026-10-28 02:58:18 +08:00 · 2019-12-18 14:38:55 -05:00
parent 6f044b6a67
commit 278e25fc24
3 changed files with 197 additions and 0 deletions
@@ -0,0 +1,74 @@
+<tool id="interactive_tool_rstudio" tool_type="interactive" name="RStudio" version="0.1">
+    <requirements>
+        <container type="docker">quay.io/erasche/docker-rstudio-notebook:19.09</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">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
+        <environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
+        <environment_variable name="GALAXY_URL">${__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="DEBUG">true</environment_variable>
+        <environment_variable name="DISABLE_AUTH">true</environment_variable>
+        <environment_variable name="API_KEY" strip="True">
+            #if $__user__:
+                #for $api_key in $__user__.api_keys:
+                    ${api_key.key}
+                    #break
+                #end for
+            #end if
+        </environment_variable> <!-- FIXME: We should have a better way to get user's 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>