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Add path to run script

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This commit is contained in:
Anup Kumar
2021-02-25 12:58:40 +01:00
parent 5d2bbb720a
commit c4a76dad32
1 changed files with 25 additions and 24 deletions
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tools/interactive/interactivetool_ml_jupyter_notebook.xml
+25 -24
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@@ -1,18 +1,19 @@
<tool id="interactive_ml_tool_jupyter_notebook" tool_type="interactive" name="Interactive Machine Learning Jupyter Notebook" version="0.1">
<tool id="interactive_ml_tool_jupyter_notebook" tool_type="interactive" name="Interactive Jupyter Notebook for Machine learning" version="0.1">
<requirements>
<container type="docker">docker.io/anupkumar/docker-ml-jupyter:latest</container>
<container type="docker">docker.io/anupkumar/sample-docker-ml-jupyter:latest</container>
</requirements>
<entry_points>
<entry_point name="Jupyter Interactive Tool" requires_domain="True">
<port>8888</port>
<url>ipython/lab</url>
<url>ipython/lab</url>
</entry_point>
</entry_points>
<environment_variables>
<environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
<environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
<environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
<environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
<environment_variable name="GALAXY_URL">$__galaxy_url__</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[
@@ -26,26 +27,26 @@
## change into the directory where the notebooks are located
cd ./jupyter/ &&
export PATH=/home/jovyan/.local/bin:\$PATH &&
#if $mode.mode_select == 'scratch':
## copy default machine learning notebook
cp '$__tool_directory__/default_notebook_ml.ipynb' ./tensorflow_notebook.ipynb &&
jupyter trust ./tensorflow_notebook.ipynb &&
jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
cp ./tensorflow_notebook.ipynb '$jupyter_notebook'
#else:
#set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
cp '$mode.ipynb' ./${cleaned_name}.ipynb &&
jupyter trust ./${cleaned_name}.ipynb &&
#if $mode.run_it:
jupyter nbconvert --to notebook --execute --output ./tensorflow_notebook.ipynb --allow-errors ./*.ipynb &&
#else:
jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
#end if
cp ./tensorflow_notebook.ipynb '$jupyter_notebook'
#end if
export PATH=/home/jovyan/.local/bin:/usr/local/bin:\$PATH &&
/usr/local/bin/start-notebook.sh
##if $mode.mode_select == 'scratch':
## copy default notebook
##cp '$__tool_directory__/default_notebook_ml.ipynb' ./ipython_galaxy_notebook_ml.ipynb &&
##jupyter trust ./ipython_galaxy_notebook_ml.ipynb &&
##jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
##cp ./ipython_galaxy_notebook_ml.ipynb '$jupyter_notebook'
##else:
##set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
##cp '$mode.ipynb' ./${cleaned_name}.ipynb &&
##jupyter trust ./${cleaned_name}.ipynb &&
##if $mode.run_it:
##jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook_ml.ipynb --allow-errors ./*.ipynb &&
##else:
##jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
##end if
##cp ./ipython_galaxy_notebook_ml.ipynb '$jupyter_notebook'
##end if
]]>
</command>
<inputs>