Mercurial > repos > gga > chado_organism_get_organisms
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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit a2ffd6de889096d5326410800d7f972e16347bc4
author | gga |
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date | Thu, 02 Aug 2018 04:52:39 -0400 |
parents | 1ce80eabf7eb |
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Galaxy-chado ============= Galaxy tools to interface with Tripal using python-chado 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 future chado deactivate Environment ----------- The following environment variables must be set: +--------------------------------+-----------------------------------------------------------+ | ENV | Use | +================================+===========================================================+ | ``$GALAXY_CHADO_DBHOST`` | Host of the Chado database | +--------------------------------+-----------------------------------------------------------+ | ``$GALAXY_CHADO_DBNAME`` | Name of the Chado database | +--------------------------------+-----------------------------------------------------------+ | ``$GALAXY_CHADO_DBUSER`` | Username to connect to the database | +--------------------------------+-----------------------------------------------------------+ | ``$GALAXY_CHADO_DBPASS`` | Password to connect to the database | +--------------------------------+-----------------------------------------------------------+ | ``$GALAXY_CHADO_DBSCHEMA`` | Database schema. | +--------------------------------+-----------------------------------------------------------+ | ``$GALAXY_CHADO_DBPORT`` | Port of the Chado database | +--------------------------------+-----------------------------------------------------------+ License ------- All python scripts and wrappers are licensed under MIT license.