Unverified Commit 2b25e81a authored by Dannon's avatar Dannon Committed by GitHub
Browse files

Merge pull request #14309 from blankenberg/jupytool 

[22.05] Fixes for JupyTool, and overlapping versions with jupyter.
parents 103c39f1 689a91d8

lib/galaxy/config/sample/tool_conf.xml.sample

+1 −1
Original line number Diff line number Diff line
@@ -136,7 +136,7 @@ 
    <tool file="interactive/interactivetool_cellxgene.xml" />

    <tool file="interactive/interactivetool_ethercalc.xml" />

    <tool file="interactive/interactivetool_hicbrowser.xml" />

    <tool file="interactive/interactivetool_jupyter_notebook_0.3.xml" />

    <tool file="interactive/interactivetool_jupyter_notebook_1.0.0.xml" />

    <tool file="interactive/interactivetool_jupyter_notebook.xml" />

    <tool file="interactive/interactivetool_neo4j.xml" />

    <tool file="interactive/interactivetool_phinch.xml" />

tools/interactive/interactivetool_jupyter_notebook_0.3.xml→tools/interactive/interactivetool_jupyter_notebook_1.0.0.xml

+14 −10
Original line number Diff line number Diff line 
<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive JupyTool and notebook" version="0.3" profile="22.01">

<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="Interactive JupyTool and notebook" version="1.0.0" profile="22.01">

    <requirements>

        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:ie2</container>

        <container type="docker">quay.io/bgruening/docker-jupyter-notebook:2021-03-05</container>

    </requirements>

    <entry_points>

        <entry_point name="JupyTool interactive tool" requires_domain="True">
@@ -75,7 +75,7 @@ except FileNotFoundError: 
        ]]>

    </configfile>

    </configfiles>

    <command detect_errors="aggressive"><![CDATA[

    <command><![CDATA[

        python staging_script.py &&

        export GALAXY_WORKING_DIR=`pwd` &&

        mkdir -p ./jupyter/outputs/collection &&
@@ -87,25 +87,29 @@ except FileNotFoundError: 
        export PATH=/home/jovyan/.local/bin:\$PATH &&

        cp '${galaxy_input_startup_script}' /home/jovyan/.ipython/profile_default/startup/00-load.py &&



        #set $output_notebook_name = 'ipython_galaxy_notebook.ipynb'

        #if $mode.mode_select == 'scratch':

            ## copy default notebook

            cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&

            jupyter trust ./ipython_galaxy_notebook.ipynb &&

            cp '$__tool_directory__/default_notebook.ipynb' ${output_notebook_name} &&

            jupyter trust ${output_notebook_name} &&

            jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&

            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'

        #else:

            #import re

            #set $cleaned_name = re.sub('[^\w\-\.]', '_', str($mode.ipynb.element_identifier))

            cp '$mode.ipynb' ./${cleaned_name}.ipynb &&

            jupyter trust ./${cleaned_name}.ipynb &&

            #if not $cleaned_name.endswith(".ipynb"):

                #set $cleaned_name = "%s.ipynb" % $cleaned_name

            #end if

            cp '$mode.ipynb' '${cleaned_name}' &&

            jupyter trust '${cleaned_name}' &&



            #if $mode.run_it:

                jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors  ./*.ipynb &&

                jupyter nbconvert --to notebook --execute --output '${output_notebook_name}' --allow-errors '${cleaned_name}' &&

            #else:

                #set $output_notebook_name = $cleaned_name

                jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&

            #end if

            cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'

        #end if

        cp '${output_notebook_name}' '$jupyter_notebook'

    ]]>

    </command>

    <inputs>