Mercurial > repos > gga > tripal_organism_add_organism

annotate README.rst @ 6:3ad5a94fb0d8 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/tripal commit 35c5eff77b573a66f3611b4906417df9a440c857
author gga
date Tue, 05 Mar 2019 05:22:03 -0500
parents e35aee4aa5df
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
1 Galaxy-tripal
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
2 =============
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
3
2
e35aee4aa5df planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents: 1
diff changeset
4 Galaxy tools to interface with Tripal using python-tripal
1
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
5
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
6 Dependencies
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
7 ------------
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
8
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
9 You will need to install some python modules in the Galaxy virtualenv for these
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
10 tools to be fully functional:
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
11
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
12 .. code:: bash
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
13
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
14 . /path/to/galaxy/.venv/bin/activate
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
15 pip install future tripal
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
16 deactivate
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
17
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
18 Environment
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
19 -----------
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
20
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
21 The following environment variables must be set:
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
22
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
23 +--------------------------------+-----------------------------------------------------------+
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
24 | ENV | Use |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
25 +================================+===========================================================+
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
26 | ``$GALAXY_TRIPAL_URL`` | The URL at which Tripal is accessible, internal to Galaxy |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
27 | | and where the tools run. Must be absolute, with FQDN and |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
28 | | protocol. |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
29 +--------------------------------+-----------------------------------------------------------+
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
30 | ``$GALAXY_TRIPAL_USER`` | The admin user which Galaxy should use to talk to Tripal. |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
31 | | |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
32 +--------------------------------+-----------------------------------------------------------+
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
33 | ``$GALAXY_TRIPAL_PASSWORD`` | The password for the admin user. |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
34 | | |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
35 | | |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
36 +--------------------------------+-----------------------------------------------------------+
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
37 | ``$GALAXY_TRIPAL_SHARED_DIR`` | Directory shared between Galaxy and Tripal, used to |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
38 | | exchange data files. |
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
39 +--------------------------------+-----------------------------------------------------------+
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
40
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
41
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
42 License
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
43 -------
c4607f65869c planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
44
2
e35aee4aa5df planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
gga
parents: 1
diff changeset
45 All python scripts and wrappers are licensed under MIT license.