Mercurial > repos > gga > chado_export_export_gbk

comparison README.rst @ 0:3ec83754aaef 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 08:43:54 -0400
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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.