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comparison README.rst @ 1:0a91d74fff9e draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
author gga
date Tue, 19 Sep 2017 12:23:22 -0400
parents b4a85d0c85b8
children 5559e41721c3
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0:b4a85d0c85b8 1:0a91d74fff9e
4 Galaxy tools to interface with Apollo The webapollo.py file is also 4 Galaxy tools to interface with Apollo The webapollo.py file is also
5 `separately 5 `separately
6 available <https://github.com/galaxy-genome-annotation/python-apollo>`__ 6 available <https://github.com/galaxy-genome-annotation/python-apollo>`__
7 as a pip-installable package. 7 as a pip-installable package.
8 8
9 Environ 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 future biopython bcbio-gff
19 deactivate
20
21 Environment
22 -----------
10 23
11 The following environment variables must be set: 24 The following environment variables must be set:
12 25
13 +--------------------------------+-----------------------------------------------------------+ 26 +--------------------------------+-----------------------------------------------------------+
14 | ENV | Use | 27 | ENV | Use |
22 +--------------------------------+-----------------------------------------------------------+ 35 +--------------------------------+-----------------------------------------------------------+
23 | ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user. | 36 | ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user. |
24 | | | 37 | | |
25 | | | 38 | | |
26 +--------------------------------+-----------------------------------------------------------+ 39 +--------------------------------+-----------------------------------------------------------+
27 | ``$GALAXY_WEBAPOLLO_EXT_URL`` | users. May be relative or absolute. | 40 | ``$GALAXY_WEBAPOLLO_EXT_URL`` | May be relative or absolute. |
28 | | The external URL at which Apollo is accessible to end | 41 | | The external URL at which Apollo is accessible to end |
29 | | | 42 | | users. |
30 +--------------------------------+-----------------------------------------------------------+ 43 +--------------------------------+-----------------------------------------------------------+
31 | ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to | 44 | ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to |
32 | | exchange JBrowse instances. | 45 | | exchange JBrowse instances. |
33 +--------------------------------+-----------------------------------------------------------+ 46 +--------------------------------+-----------------------------------------------------------+
34 47