Mercurial > repos > gga > apollo_create_account
view README.rst @ 10:a46a509386d3 draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
| author | gga |
|---|---|
| date | Mon, 02 Dec 2019 05:50:13 -0500 |
| parents | 08f8e19005a8 |
| children |
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Galaxy-apollo ============= 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 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.