From f384154e20bafeb97b0b92de9e396bd65a863ccf Mon Sep 17 00:00:00 2001 From: Anup Kumar Date: Thu, 24 Jun 2021 15:08:56 +0200 Subject: [PATCH] Update tools --- .../interactivetool_ml_jupyter_notebook.xml | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/tools/interactive/interactivetool_ml_jupyter_notebook.xml b/tools/interactive/interactivetool_ml_jupyter_notebook.xml index 04800297d9b..905c8ea5ee4 100644 --- a/tools/interactive/interactivetool_ml_jupyter_notebook.xml +++ b/tools/interactive/interactivetool_ml_jupyter_notebook.xml @@ -21,18 +21,24 @@ export GALAXY_WORKING_DIR=`pwd` && mkdir -p ./jupyter/outputs/ && mkdir -p ./jupyter/data && + mkdir -p ./jupyter/notebooks && #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/ && - chown -R \$NB_USER:users `pwd` && + cp /home/\$NB_USER/notebooks/*.ipynb ./jupyter/notebooks/ && + cd ./jupyter/ && + export HOME=/home/\$NB_USER/ && + export PATH=/home/\$NB_USER/.local/bin:\$PATH && + chown -R \$NB_USER:users `pwd` && #if $mode.mode_select == 'scratch': - cp '$__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 + cp '$__tool_directory__/home_page.ipynb' ./home_page.ipynb && + chown \$NB_USER ./home_page.ipynb && + jupyter trust ./home_page.ipynb && + + jupyter lab --allow-root --no-browser --NotebookApp.shutdown_button=True + ##/usr/local/bin/start-notebook.sh #end if ]]>