Mercurial > repos > gga > tripal_expression_add_expression

annotate README.rst @ 0:4c2abb21c608 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 690532f4a8e36a334b2d4e15b832532fc1bb8d39
author gga
date Mon, 25 Feb 2019 05:53:16 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
1 Galaxy-tripal
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
2 =============
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
3
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
4 Galaxy tools to interface with Tripal using python-tripal
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
5
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
6 Dependencies
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
7 ------------
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
8
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
9 You will need to install some python modules in the Galaxy virtualenv for these
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
10 tools to be fully functional:
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
11
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
12 .. code:: bash
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
13
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
14 . /path/to/galaxy/.venv/bin/activate
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
15 pip install future tripal
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
16 deactivate
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
17
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
18 Environment
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
19 -----------
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
20
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
21 The following environment variables must be set:
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
22
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
23 +--------------------------------+-----------------------------------------------------------+
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
24 | ENV | Use |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
25 +================================+===========================================================+
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
26 | ``$GALAXY_TRIPAL_URL`` | The URL at which Tripal is accessible, internal to Galaxy |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
27 | | and where the tools run. Must be absolute, with FQDN and |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
28 | | protocol. |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
29 +--------------------------------+-----------------------------------------------------------+
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
30 | ``$GALAXY_TRIPAL_USER`` | The admin user which Galaxy should use to talk to Tripal. |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
31 | | |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
32 +--------------------------------+-----------------------------------------------------------+
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
33 | ``$GALAXY_TRIPAL_PASSWORD`` | The password for the admin user. |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
34 | | |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
35 | | |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
36 +--------------------------------+-----------------------------------------------------------+
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
37 | ``$GALAXY_TRIPAL_SHARED_DIR`` | Directory shared between Galaxy and Tripal, used to |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
38 | | exchange data files. |
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
39 +--------------------------------+-----------------------------------------------------------+
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
40
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
41
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
42 License
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
43 -------
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
44
4c2abb21c608 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 690532f4a8e36a334b2d4e15b832532fc1bb8d39
gga
parents:
diff changeset
45 All python scripts and wrappers are licensed under MIT license.