Mercurial > repos > gga > chado_organism_delete_organisms

annotate README.rst @ 12:80dc4a25db97 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
author gga
date Wed, 21 Aug 2019 05:08:18 -0400
parents 29ac3aedc97d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
29ac3aedc97d 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
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
2 =============
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
3
29ac3aedc97d 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
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
5
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
6 Dependencies
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
7 ------------
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
8
29ac3aedc97d 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
29ac3aedc97d 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:
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
11
29ac3aedc97d 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
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
13
29ac3aedc97d 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
29ac3aedc97d 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
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
16 deactivate
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
17
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
18 Environment
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
19 -----------
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
20
29ac3aedc97d 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:
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
22
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
23 +--------------------------------+-----------------------------------------------------------+
29ac3aedc97d 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 |
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
25 +================================+===========================================================+
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
26 | ``$GALAXY_CHADO_DBHOST`` | Host of the Chado database |
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
27 +--------------------------------+-----------------------------------------------------------+
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
28 | ``$GALAXY_CHADO_DBNAME`` | Name of the Chado database |
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
29 +--------------------------------+-----------------------------------------------------------+
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
30 | ``$GALAXY_CHADO_DBUSER`` | Username to connect to the database |
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
31 +--------------------------------+-----------------------------------------------------------+
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
32 | ``$GALAXY_CHADO_DBPASS`` | Password to connect to the database |
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
33 +--------------------------------+-----------------------------------------------------------+
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
34 | ``$GALAXY_CHADO_DBSCHEMA`` | Database schema. |
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
35 +--------------------------------+-----------------------------------------------------------+
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
36 | ``$GALAXY_CHADO_DBPORT`` | Port of the Chado database |
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
37 +--------------------------------+-----------------------------------------------------------+
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
38
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
39
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
40 License
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
41 -------
29ac3aedc97d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents:
diff changeset
42
29ac3aedc97d 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.