Mercurial > repos > gga > chado_expression_delete_all_biomaterials

annotate README.rst @ 16:ded53bbfd8ab draft default tip

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 20d8d84d66eb27f870cadb94a02c97806090df24
author gga
date Wed, 11 May 2022 14:42:26 +0000
parents db7db54dd2d8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
1 Galaxy-chado
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
2 =============
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
3
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
4 Galaxy tools to interface with Tripal using python-chado
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
5
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
6 Dependencies
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
7 ------------
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
8
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
9 You will need to install some python modules in the Galaxy virtualenv for these
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
10 tools to be fully functional:
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
11
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
12 .. code:: bash
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
13
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
14 . /path/to/galaxy/.venv/bin/activate
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
15 pip install future chado
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
16 deactivate
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
17
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
18 Environment
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
19 -----------
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
20
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
21 The following environment variables must be set:
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
22
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
23 +--------------------------------+-----------------------------------------------------------+
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
24 | ENV | Use |
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
25 +================================+===========================================================+
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
26 | ``$GALAXY_CHADO_DBHOST`` | Host of the Chado database |
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
27 +--------------------------------+-----------------------------------------------------------+
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
28 | ``$GALAXY_CHADO_DBNAME`` | Name of the Chado database |
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
29 +--------------------------------+-----------------------------------------------------------+
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
30 | ``$GALAXY_CHADO_DBUSER`` | Username to connect to the database |
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
31 +--------------------------------+-----------------------------------------------------------+
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
32 | ``$GALAXY_CHADO_DBPASS`` | Password to connect to the database |
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
33 +--------------------------------+-----------------------------------------------------------+
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
34 | ``$GALAXY_CHADO_DBSCHEMA`` | Database schema. |
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
35 +--------------------------------+-----------------------------------------------------------+
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
36 | ``$GALAXY_CHADO_DBPORT`` | Port of the Chado database |
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
37 +--------------------------------+-----------------------------------------------------------+
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
38
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
39
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
40 License
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
41 -------
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
42
db7db54dd2d8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 3c4fb887c809face4fbe4602617d6dc094b15864
gga
parents:
diff changeset
43 All python scripts and wrappers are licensed under MIT license.