Mercurial > repos > gga > apollo_fetch_jbrowse
diff README.rst @ 10:dca2fb399ee6 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 05:45:36 -0500 |
| parents | 9968eec7430e |
| children |
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--- a/README.rst Mon Jul 29 10:09:38 2019 -0400 +++ b/README.rst Mon Dec 02 05:45:36 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