Mercurial > repos > gga > chado_analysis_get_analyses

annotate README.rst @ 13:73e61659cdac draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bfca9a8c38694bbf04d92a6668e4ea31cf658eb8"
author gga
date Thu, 14 Nov 2019 09:54:52 -0500
parents 693fd0ba9cf2
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693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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1 Galaxy-chado
693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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2 =============
693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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4 Galaxy tools to interface with Tripal using python-chado
693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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6 Dependencies
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7 ------------
693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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9 You will need to install some python modules in the Galaxy virtualenv for these
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10 tools to be fully functional:
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693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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12 .. code:: bash
693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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14 . /path/to/galaxy/.venv/bin/activate
693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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15 pip install future chado
693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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16 deactivate
693fd0ba9cf2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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18 Environment
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19 -----------
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21 The following environment variables must be set:
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23 +--------------------------------+-----------------------------------------------------------+
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24 | ENV | Use |
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25 +================================+===========================================================+
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26 | ``$GALAXY_CHADO_DBHOST`` | Host of the Chado database |
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27 +--------------------------------+-----------------------------------------------------------+
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28 | ``$GALAXY_CHADO_DBNAME`` | Name of the Chado database |
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29 +--------------------------------+-----------------------------------------------------------+
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30 | ``$GALAXY_CHADO_DBUSER`` | Username to connect to the database |
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31 +--------------------------------+-----------------------------------------------------------+
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32 | ``$GALAXY_CHADO_DBPASS`` | Password to connect to the database |
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33 +--------------------------------+-----------------------------------------------------------+
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34 | ``$GALAXY_CHADO_DBSCHEMA`` | Database schema. |
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35 +--------------------------------+-----------------------------------------------------------+
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36 | ``$GALAXY_CHADO_DBPORT`` | Port of the Chado database |
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37 +--------------------------------+-----------------------------------------------------------+
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40 License
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41 -------
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43 All python scripts and wrappers are licensed under MIT license.