Mercurial > repos > gga > tripal_analysis_add_analysis

annotate README.rst @ 2:ab0942a9ae18 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 81a83f06b49db32928ba0cd44e5b6d0431868d27
author gga
date Thu, 21 Jun 2018 08:49:47 -0400
parents 41b30b63dc62
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
41b30b63dc62 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
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
2 =============
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
3
2
ab0942a9ae18 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
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
5
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
6 Dependencies
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
7 ------------
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
8
41b30b63dc62 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
41b30b63dc62 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:
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
11
41b30b63dc62 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
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
13
41b30b63dc62 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
41b30b63dc62 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
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
16 deactivate
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
17
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
18 Environment
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
19 -----------
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
20
41b30b63dc62 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:
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
22
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
23 +--------------------------------+-----------------------------------------------------------+
41b30b63dc62 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 |
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
25 +================================+===========================================================+
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
26 | ``$GALAXY_TRIPAL_URL`` | The URL at which Tripal is accessible, internal to Galaxy |
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
27 | | and where the tools run. Must be absolute, with FQDN and |
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
28 | | protocol. |
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
29 +--------------------------------+-----------------------------------------------------------+
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
30 | ``$GALAXY_TRIPAL_USER`` | The admin user which Galaxy should use to talk to Tripal. |
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
31 | | |
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
32 +--------------------------------+-----------------------------------------------------------+
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
33 | ``$GALAXY_TRIPAL_PASSWORD`` | The password for the admin user. |
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
34 | | |
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
35 | | |
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
36 +--------------------------------+-----------------------------------------------------------+
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
37 | ``$GALAXY_TRIPAL_SHARED_DIR`` | Directory shared between Galaxy and Tripal, used to |
41b30b63dc62 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. |
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
39 +--------------------------------+-----------------------------------------------------------+
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
40
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
41
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
42 License
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
43 -------
41b30b63dc62 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
gga
parents:
diff changeset
44
2
ab0942a9ae18 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.