annotate README.rst @ 7:bece12dfcf6b draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit c5b949de324bf86c88c680767e56ac77685cd14c
author gga
date Mon, 05 Nov 2018 12:15:55 -0500
parents b5d8e6e26d01
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
1 Galaxy-chado
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
2 =============
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
3
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
4 Galaxy tools to interface with Tripal using python-chado
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
5
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
6 Dependencies
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
7 ------------
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
8
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
9 You will need to install some python modules in the Galaxy virtualenv for these
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
10 tools to be fully functional:
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
11
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
12 .. code:: bash
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
13
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
14 . /path/to/galaxy/.venv/bin/activate
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
15 pip install future chado
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
16 deactivate
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
17
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
18 Environment
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
19 -----------
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
20
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
21 The following environment variables must be set:
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
22
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
23 +--------------------------------+-----------------------------------------------------------+
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
24 | ENV | Use |
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
25 +================================+===========================================================+
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
26 | ``$GALAXY_CHADO_DBHOST`` | Host of the Chado database |
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
27 +--------------------------------+-----------------------------------------------------------+
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
28 | ``$GALAXY_CHADO_DBNAME`` | Name of the Chado database |
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
29 +--------------------------------+-----------------------------------------------------------+
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
30 | ``$GALAXY_CHADO_DBUSER`` | Username to connect to the database |
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
31 +--------------------------------+-----------------------------------------------------------+
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
32 | ``$GALAXY_CHADO_DBPASS`` | Password to connect to the database |
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
33 +--------------------------------+-----------------------------------------------------------+
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
34 | ``$GALAXY_CHADO_DBSCHEMA`` | Database schema. |
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
35 +--------------------------------+-----------------------------------------------------------+
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
36 | ``$GALAXY_CHADO_DBPORT`` | Port of the Chado database |
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
37 +--------------------------------+-----------------------------------------------------------+
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
38
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
39
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
40 License
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
41 -------
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
42
b5d8e6e26d01 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
43 All python scripts and wrappers are licensed under MIT license.