Mercurial > repos > gga > apollo_list_organism

annotate README.rst @ 2:c570db69288b draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 33ce5bd0cce35a12725b9ef9aed0683f3c41fbf9
author gga
date Wed, 20 Sep 2017 09:09:58 -0400
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1 Galaxy-apollo
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2 =============
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4 Galaxy tools to interface with Apollo The webapollo.py file is also
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5 `separately
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6 available <https://github.com/galaxy-genome-annotation/python-apollo>`__
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7 as a pip-installable package.
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9 Dependencies
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10 ------------
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12 You will need to install some python modules in the Galaxy virtualenv for these
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13 tools to be fully functional:
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15 .. code:: bash
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17 . /path/to/galaxy/.venv/bin/activate
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18 pip install future biopython bcbio-gff
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19 deactivate
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21 Environment
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22 -----------
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24 The following environment variables must be set:
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26 +--------------------------------+-----------------------------------------------------------+
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27 | ENV | Use |
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28 +================================+===========================================================+
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29 | ``$GALAXY_WEBAPOLLO_URL`` | The URL at which Apollo is accessible, internal to Galaxy |
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30 | | and where the tools run. Must be absolute, with FQDN and |
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31 | | protocol. |
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32 +--------------------------------+-----------------------------------------------------------+
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33 | ``$GALAXY_WEBAPOLLO_USER`` | The admin user which Galaxy should use to talk to Apollo. |
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34 | | |
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35 +--------------------------------+-----------------------------------------------------------+
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36 | ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user. |
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37 | | |
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38 | | |
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39 +--------------------------------+-----------------------------------------------------------+
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40 | ``$GALAXY_WEBAPOLLO_EXT_URL`` | May be relative or absolute. |
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41 | | The external URL at which Apollo is accessible to end |
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42 | | users. |
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43 +--------------------------------+-----------------------------------------------------------+
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44 | ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to |
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45 | | exchange JBrowse instances. |
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46 +--------------------------------+-----------------------------------------------------------+
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48 License
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49 -------
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50
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51 All python scripts, wrappers, and the webapollo.py are licensed under
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52 MIT license.