--- a/README.rst	Mon Jul 29 10:10:09 2019 -0400
+++ b/README.rst	Mon Dec 02 05:48:12 2019 -0500
@@ -1,27 +1,13 @@
 Galaxy-apollo
 =============
 
-Galaxy tools to interface with Apollo The webapollo.py file is also
-`separately
-available <https://github.com/galaxy-genome-annotation/python-apollo>`__
-as a pip-installable package.
-
-Dependencies
-------------
-
-You will need to install some python modules in the Galaxy virtualenv for these
-tools to be fully functional:
-
-.. code:: bash
-
-    . /path/to/galaxy/.venv/bin/activate
-    pip install six biopython bcbio-gff
-    deactivate
+Galaxy tools to interface with Apollo.
+Uses `python-apollo <https://github.com/galaxy-genome-annotation/python-apollo>`__ for most of it.
 
 Environment
 -----------
 
-The following environment variables must be set:
+The following environment variables can be set:
 
 +--------------------------------+-----------------------------------------------------------+
 | ENV                            | Use                                                       |
@@ -34,15 +20,22 @@
 |                                |                                                           |
 +--------------------------------+-----------------------------------------------------------+
 | ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user.                          |
-|                                |                                                           |
-|                                |                                                           |
++--------------------------------+-----------------------------------------------------------+
+| ``$ARROW_GLOBAL_CONFIG_PATH``  | Path to a python-apollo/arrow conf file. Use in place of  |
+|                                | ``$GALAXY_WEBAPOLLO_URL``, ``$GALAXY_WEBAPOLLO_USER``     |
+|                                | and ``$GALAXY_WEBAPOLLO_PASSWORD``.                       |
 +--------------------------------+-----------------------------------------------------------+
 | ``$GALAXY_WEBAPOLLO_EXT_URL``  | May be relative or absolute.                              |
 |                                | The external URL at which Apollo is accessible to end     |
 |                                | users.                                                    |
 +--------------------------------+-----------------------------------------------------------+
 | ``$GALAXY_SHARED_DIR``         | Directory shared between Galaxy and Apollo, used to       |
-|                                | exchange JBrowse instances.                               |
+|                                | exchange JBrowse instances. If not set, JBrowse data will |
+|                                | be zipped and sent to the remote server.                  |
++--------------------------------+-----------------------------------------------------------+
+| ``$GALAXY_APOLLO_ORG_SUFFIX``  | Set to 'id' if you want organism names to be suffixed     |
+|                                | with user id to avoid name collisions. Set to 'email' to  |
+|                                | use user email as suffix. Leave empty for no suffix.      |
 +--------------------------------+-----------------------------------------------------------+
 
 License