<commit_before>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.

Environ

The following environment variables must be set:

+----------------+-----------------------------------------------------------+
| ENV            | Use                                                       |
+================+===========================================================+
| ``$GALAXY_WEBA | The URL at which Apollo is accessible, internal to Galaxy |
| POLLO_URL``    | and where the tools run. Must be absolute, with FQDN and  |
|                | protocol.                                                 |
+----------------+-----------------------------------------------------------+
| ``$GALAXY_WEBA | The admin user which Galaxy should use to talk to Apollo. |
| POLLO_USER``   |                                                           |
+----------------+-----------------------------------------------------------+
| ``$GALAXY_WEBA | The password for the admin user.                          |
| POLLO_PASSWORD |                                                           |
| ``             |                                                           |
+----------------+-----------------------------------------------------------+
| ``$GALAXY_WEBA | The external URL at which Apollo is accessible to end     |
| POLLO_EXT_URL` | users. May be relative or absolute.                       |
| `              |                                                           |
+----------------+-----------------------------------------------------------+
| ``$GALAXY_SHAR | Directory shared between Galaxy and Apollo, used to       |
| ED_DIR``       | exchange JBrowse instances.                               |
+----------------+-----------------------------------------------------------+

License
-------

All python scripts, wrappers, and the webapollo.py are licensed under
MIT license.<commit_msg>rst lint<commit_after>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.

Environ

The following environment variables must be set:

+--------------------------------+-----------------------------------------------------------+
| ENV                            | Use                                                       |
+================================+===========================================================+
| ``$GALAXY_WEBAPOLLO_URL``      | The URL at which Apollo is accessible, internal to Galaxy |
|                                | and where the tools run. Must be absolute, with FQDN and  |
|                                | protocol.                                                 |
+--------------------------------+-----------------------------------------------------------+
| ``$GALAXY_WEBAPOLLO_USER``     | The admin user which Galaxy should use to talk to Apollo. |
|                                |                                                           |
+--------------------------------+-----------------------------------------------------------+
| ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user.                          |
|                                |                                                           |
|                                |                                                           |
+--------------------------------+-----------------------------------------------------------+
| ``$GALAXY_WEBAPOLLO_EXT_URL``  | users. May be relative or absolute.                       |
|                                | The external URL at which Apollo is accessible to end     |
|                                |                                                           |
+--------------------------------+-----------------------------------------------------------+
| ``$GALAXY_SHARED_DIR``         | Directory shared between Galaxy and Apollo, used to       |
|                                | exchange JBrowse instances.                               |
+--------------------------------+-----------------------------------------------------------+

License
-------

All python scripts, wrappers, and the webapollo.py are licensed under
MIT license.
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