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Fixes for JupyTool, and overlapping versions with jupyter.

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This commit is contained in:
Daniel Blankenberg
2022-07-11 18:06:35 -04:00
parent c811c17c0a
commit 4a83e6f04d
2 changed files with 15 additions and 11 deletions
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lib/galaxy/config/sample/tool_conf.xml.sample
+1 -1
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@@ -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.x.x.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.x.x.xml
+14 -10
View File
@@ -1,6 +1,6 @@
<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>