Mercurial > repos > gga > apollo_list_organism

comparison README.rst @ 10:bc2b80fc7e30 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:49:03 -0500
parents b69804a685e2
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9:f26ac3b582e1 10:bc2b80fc7e30
1 Galaxy-apollo 1 Galaxy-apollo
2 ============= 2 =============
3 3
4 Galaxy tools to interface with Apollo The webapollo.py file is also 4 Galaxy tools to interface with Apollo.
5 `separately 5 Uses `python-apollo <https://github.com/galaxy-genome-annotation/python-apollo>`__ for most of it.
6 available <https://github.com/galaxy-genome-annotation/python-apollo>`__
7 as a pip-installable package.
8
9 Dependencies
10 ------------
11
12 You will need to install some python modules in the Galaxy virtualenv for these
13 tools to be fully functional:
14
15 .. code:: bash
16
17 . /path/to/galaxy/.venv/bin/activate
18 pip install six biopython bcbio-gff
19 deactivate
20 6
21 Environment 7 Environment
22 ----------- 8 -----------
23 9
24 The following environment variables must be set: 10 The following environment variables can be set:
25 11
26 +--------------------------------+-----------------------------------------------------------+ 12 +--------------------------------+-----------------------------------------------------------+
27 | ENV | Use | 13 | ENV | Use |
28 +================================+===========================================================+ 14 +================================+===========================================================+
29 | ``$GALAXY_WEBAPOLLO_URL`` | The URL at which Apollo is accessible, internal to Galaxy | 15 | ``$GALAXY_WEBAPOLLO_URL`` | The URL at which Apollo is accessible, internal to Galaxy |
32 +--------------------------------+-----------------------------------------------------------+ 18 +--------------------------------+-----------------------------------------------------------+
33 | ``$GALAXY_WEBAPOLLO_USER`` | The admin user which Galaxy should use to talk to Apollo. | 19 | ``$GALAXY_WEBAPOLLO_USER`` | The admin user which Galaxy should use to talk to Apollo. |
34 | | | 20 | | |
35 +--------------------------------+-----------------------------------------------------------+ 21 +--------------------------------+-----------------------------------------------------------+
36 | ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user. | 22 | ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user. |
37 | | | 23 +--------------------------------+-----------------------------------------------------------+
38 | | | 24 | ``$ARROW_GLOBAL_CONFIG_PATH`` | Path to a python-apollo/arrow conf file. Use in place of |
25 | | ``$GALAXY_WEBAPOLLO_URL``, ``$GALAXY_WEBAPOLLO_USER`` |
26 | | and ``$GALAXY_WEBAPOLLO_PASSWORD``. |
39 +--------------------------------+-----------------------------------------------------------+ 27 +--------------------------------+-----------------------------------------------------------+
40 | ``$GALAXY_WEBAPOLLO_EXT_URL`` | May be relative or absolute. | 28 | ``$GALAXY_WEBAPOLLO_EXT_URL`` | May be relative or absolute. |
41 | | The external URL at which Apollo is accessible to end | 29 | | The external URL at which Apollo is accessible to end |
42 | | users. | 30 | | users. |
43 +--------------------------------+-----------------------------------------------------------+ 31 +--------------------------------+-----------------------------------------------------------+
44 | ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to | 32 | ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to |
45 | | exchange JBrowse instances. | 33 | | exchange JBrowse instances. If not set, JBrowse data will |
34 | | be zipped and sent to the remote server. |
35 +--------------------------------+-----------------------------------------------------------+
36 | ``$GALAXY_APOLLO_ORG_SUFFIX`` | Set to 'id' if you want organism names to be suffixed |
37 | | with user id to avoid name collisions. Set to 'email' to |
38 | | use user email as suffix. Leave empty for no suffix. |
46 +--------------------------------+-----------------------------------------------------------+ 39 +--------------------------------+-----------------------------------------------------------+
47 40
48 License 41 License
49 ------- 42 -------
50 43