Merge pull request #61 from bgruening/dev-1510

New release for Galaxy 15.10

Dockerfile

@@ -16,14 +16,11 @@ RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 && \
     libfreetype6-dev libpng-dev net-tools procps r-base libreadline-dev && \
     pip install distribute --upgrade && \
     pip install pyzmq ipython==2.4 jinja2 tornado pygments numpy biopython scikit-learn pandas \
-        scipy sklearn-pandas bioblend matplotlib patsy pysam khmer ggplot mpld3 sympy rpy2 && \
+        scipy sklearn-pandas bioblend matplotlib patsy pysam khmer ggplot mpld3 sympy rpy2 dask pyvcf && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 ADD ./startup.sh /startup.sh
-RUN chmod +x /startup.sh
-
 ADD ./monitor_traffic.sh /monitor_traffic.sh
-RUN chmod +x /monitor_traffic.sh
 
 # /import will be the universal mount-point for IPython
 # The Galaxy instance can copy in data that needs to be present to the IPython webserver

README.md

@@ -39,15 +39,14 @@ Some environment variables are made available to the user which will allow for c
 
 Variable            | Use
 ------------------- | ---
-`GALAXY_WEB_PORT`   | Port on which Galaxy is running, if applicable
-`NOTEBOOK_PASSWORD` | Password with which to secure the notebook
-`CORS_ORIGIN`       | If the notebook is proxied, this is the URL the end-user will see when trying to access a notebook
-`DOCKER_PORT`       | Used in Galaxy Interactive Environments to ensure that proxy routes are unique and accessible
 `API_KEY`           | Galaxy API Key with which to interface with Galaxy
-`HISTORY_ID`        | ID of current Galaxy History, used in easing the dataset upload/download process
-`REMOTE_HOST`       | Unused
-`GALAXY_URL`        | URL at which Galaxy is accessible
+`CORS_ORIGIN`       | If the notebook is proxied, this is the URL the end-user will see when trying to access a notebook
 `DEBUG`             | Enable debugging mode, mostly for developers
+`GALAXY_URL`        | URL at which Galaxy is accessible
+`GALAXY_WEB_PORT`   | Port on which Galaxy is running, if applicable
+`HISTORY_ID`        | ID of current Galaxy History, used in easing the dataset upload/download process
+`NOTEBOOK_PASSWORD` | Password with which to secure the notebook
+`PROXY_PREFIX`      | Prefix to URL which allows Galaxy proxy to share cookies with Galaxy itself.
 
 
 Authors

ipython_notebook_config.py

@@ -17,12 +17,10 @@
 
 # In case this Notebook was launched from Galaxy a config file exists in /import/
 # For standalone usage we fall back to a port-less URL
-if os.environ.get('DOCKER_PORT', 'none') == 'none':
-    c.NotebookApp.base_url = '/ipython/'
-    c.NotebookApp.webapp_settings = {'static_url_prefix': '/ipython/static/'}
-else:
-    c.NotebookApp.base_url = '/ipython/%s/' % os.environ['DOCKER_PORT']
-    c.NotebookApp.webapp_settings = {'static_url_prefix': '/ipython/%s/static/' % os.environ['DOCKER_PORT']}
+c.NotebookApp.base_url = '%s/ipython/' % os.environ.get('PROXY_PREFIX', '')
+c.NotebookApp.webapp_settings = {
+    'static_url_prefix': '%s/ipython/static/' % os.environ.get('PROXY_PREFIX', '')
+}
 
 if os.environ.get('NOTEBOOK_PASSWORD', 'none') != 'none':
     c.NotebookApp.password = os.environ['NOTEBOOK_PASSWORD']