From c4a76dad327958f17a019cabb36954a751e4f582 Mon Sep 17 00:00:00 2001
From: Anup Kumar <anup.rulez@gmail.com>
Date: Wed, 24 Feb 2021 09:30:26 +0000
Subject: [PATCH] Add path to run script

---
 .../interactivetool_ml_jupyter_notebook.xml   | 49 ++++++++++---------
 1 file changed, 25 insertions(+), 24 deletions(-)

diff --git a/tools/interactive/interactivetool_ml_jupyter_notebook.xml b/tools/interactive/interactivetool_ml_jupyter_notebook.xml
index b442b25f0a1..e56329cdee9 100644
--- a/tools/interactive/interactivetool_ml_jupyter_notebook.xml
+++ b/tools/interactive/interactivetool_ml_jupyter_notebook.xml
@@ -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>