Mercurial > repos > gga > chado_organism_add_organism
comparison README.rst @ 0:51ac1ffb4f38 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
| author | gga |
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| date | Thu, 21 Jun 2018 08:44:11 -0400 |
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| -1:000000000000 | 0:51ac1ffb4f38 |
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| 1 Galaxy-chado | |
| 2 ============= | |
| 3 | |
| 4 Galaxy tools to interface with Tripal using python-chado | |
| 5 | |
| 6 Dependencies | |
| 7 ------------ | |
| 8 | |
| 9 You will need to install some python modules in the Galaxy virtualenv for these | |
| 10 tools to be fully functional: | |
| 11 | |
| 12 .. code:: bash | |
| 13 | |
| 14 . /path/to/galaxy/.venv/bin/activate | |
| 15 pip install future chado | |
| 16 deactivate | |
| 17 | |
| 18 Environment | |
| 19 ----------- | |
| 20 | |
| 21 The following environment variables must be set: | |
| 22 | |
| 23 +--------------------------------+-----------------------------------------------------------+ | |
| 24 | ENV | Use | | |
| 25 +================================+===========================================================+ | |
| 26 | ``$GALAXY_CHADO_DBHOST`` | Host of the Chado database | | |
| 27 +--------------------------------+-----------------------------------------------------------+ | |
| 28 | ``$GALAXY_CHADO_DBNAME`` | Name of the Chado database | | |
| 29 +--------------------------------+-----------------------------------------------------------+ | |
| 30 | ``$GALAXY_CHADO_DBUSER`` | Username to connect to the database | | |
| 31 +--------------------------------+-----------------------------------------------------------+ | |
| 32 | ``$GALAXY_CHADO_DBPASS`` | Password to connect to the database | | |
| 33 +--------------------------------+-----------------------------------------------------------+ | |
| 34 | ``$GALAXY_CHADO_DBSCHEMA`` | Database schema. | | |
| 35 +--------------------------------+-----------------------------------------------------------+ | |
| 36 | ``$GALAXY_CHADO_DBPORT`` | Port of the Chado database | | |
| 37 +--------------------------------+-----------------------------------------------------------+ | |
| 38 | |
| 39 | |
| 40 License | |
| 41 ------- | |
| 42 | |
| 43 All python scripts and wrappers are licensed under MIT license. |