Mercurial > repos > gga > chado_organism_add_organism

diff README.rst @ 0:51ac1ffb4f38 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
author gga
date Thu, 21 Jun 2018 08:44:11 -0400
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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.