| Galaxy-apollo
=============
Galaxy tools to interface with Apollo.
Uses `python-apollo `__ for most of it.
Environment
-----------
The following environment variables can 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. |
| | |
+--------------------------------+-----------------------------------------------------------+
| ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user. |
+--------------------------------+-----------------------------------------------------------+
| ``$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. |
+--------------------------------+-----------------------------------------------------------+
| ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to |
| | exchange JBrowse instances. If not set, JBrowse data will |
| | be zipped and sent to the remote server. |
+--------------------------------+-----------------------------------------------------------+
| ``$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
-------
All python scripts, wrappers, and the webapollo.py are licensed under
MIT license.
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