opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Update notebook

Browse Source
This commit is contained in:
anup kumar
2021-02-25 13:33:51 +01:00
parent 49d035dda9
commit a0fbe7c873
1 changed files with 14 additions and 15 deletions
Download Patch File Download Diff File Expand all files Collapse all files
tools/interactive/interactivetool_ml_jupyter_notebook.xml
+14 -15
View File
@@ -1,6 +1,6 @@
<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/sample-docker-ml-jupyter:latest</container>
<container type="docker">docker.io/anupkumar/docker-ml-jupyterlab:galaxy-integration</container>
</requirements>
<entry_points>
<entry_point name="Jupyter Interactive Tool" requires_domain="True">
@@ -18,7 +18,6 @@
</environment_variables>
<command detect_errors="aggressive"><![CDATA[
#import re
echo "Inside tool definition....================" &&
export GALAXY_WORKING_DIR=`pwd` &&
mkdir -p ./jupyter/outputs/ &&
mkdir -p ./jupyter/data &&
@@ -29,21 +28,21 @@
## change into the directory where the notebooks are located
cd ./jupyter/ &&
chown -R \$NB_USER:users `pwd` &&
##export PATH=/usr/local/bin:\$PATH &&
#if $mode.mode_select == 'scratch':
cp '$__tool_directory__/default_notebook_ml.ipynb' ./ipython_galaxy_notebook_ml.ipynb &&
jupyter trust ./ipython_galaxy_notebook_ml.ipynb &&
cp '$__tool_directory__/default_tensorflow_notebook.ipynb' ./default_tensorflow_notebook.ipynb &&
chown \$NB_USER ./default_tensorflow_notebook.ipynb &&
jupyter trust ./default_tensorflow_notebook.ipynb &&
/usr/local/bin/start-notebook.sh
#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'
##else:
##set $cleaned_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
##cp '$mode.ipynb' ./${cleaned_name}.ipynb &&
##jupyter trust ./${cleaned_name}.ipynb &&
##if $mode.run_it:
##jupyter nbconvert --to notebook --execute --output ./default_tensorflow_notebook.ipynb --allow-errors ./*.ipynb &&
##else:
##jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True &&
###end if
##cp ./default_tensorflow_notebook.ipynb '$jupyter_notebook'
#end if
##if $mode.mode_select == 'scratch':