Hi, I have a very basic notebook running in our local galaxy portal with interactive tools.
As you see, put() and get() functions are not recognized:
The tool-wrapper is the following taken from some official galaxy jupyterlab/jupyternotebook tutorial page.
What might I be missing to be able to have get() and put() working?
Tool wrapper:
<tool id="interactive_tool_jupyter_notebook" tool_type="interactive" name="General Jupyter Notebook" version="0.1">
<description>Default empty notebook, reuse a previous one, or upload a new</description>
<requirements>
<container type="docker">quay.io/bgruening/docker-jupyter-notebook:2021-03-05</container>
</requirements>
<entry_points>
<entry_point name="Jupyter Interactive Tool" requires_domain="True">
<port>8888</port>
<url>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="API_KEY" inject="api_key" />
</environment_variables>
<command detect_errors="aggressive"><![CDATA[
#import re
export GALAXY_WORKING_DIR=`pwd` &&
mkdir -p ./jupyter/outputs/ &&
mkdir -p ./jupyter/data &&
#set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
ln -sf '$input' './jupyter/data/${cleaned_name}' &&
## change into the directory where the notebooks are located
cd ./jupyter/ &&
export PATH=/home/jovyan/.local/bin:\$PATH &&
#if $mode.mode_select == 'scratch':
## copy default notebook
cp '$__tool_directory__/default_notebook.ipynb' ./ipython_galaxy_notebook.ipynb &&
jupyter trust ./ipython_galaxy_notebook.ipynb &&
jupyter lab --allow-root --no-browser --ServerApp.token='' &&
cp ./ipython_galaxy_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 $mode.run_it:
jupyter nbconvert --to notebook --execute --output ./ipython_galaxy_notebook.ipynb --allow-errors ./*.ipynb &&
#else:
jupyter lab --allow-root --no-browser --ServerApp.token='' &&
#end if
cp ./ipython_galaxy_notebook.ipynb '$jupyter_notebook'
#end if
]]>
</command>
<inputs>
<conditional name="mode">
<param name="mode_select" type="select" label="Do you already have a notebook?" help="If not, no problem we will provide you with a default one.">
<option value="scratch">Start with a fresh notebook</option>
<option value="previous">Load a previous notebook</option>
</param>
<when value="scratch"/>
<when value="previous">
<param name="ipynb" type="data" format="ipynb" label="IPython Notebook"/>
<param name="run_it" type="boolean" truevalue="true" falsevalue="false" label="Execute notebook and return a new one."
help="This option is useful in workflows when you just want to execute a notebook and not dive into the webfrontend."/>
</when>
</conditional>
<param name="input" type="data" optional="true" label="Include data into the environment"/>
</inputs>
<outputs>
<data name="jupyter_notebook" format="ipynb" label="Executed Notebook"></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>
The Jupyter Notebook is an open-source web applicati...
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