Mercurial > repos > gga > chado_load_blast

annotate README.rst @ 7:10629751e10b draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit fa25d58f87bfe8b12dc9a497c08855ee5d8ff641"
author gga
date Thu, 24 Jun 2021 09:09:32 +0000
parents 1daff3b60f39
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1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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1 Galaxy-chado
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2 =============
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4 Galaxy tools to interface with Tripal using python-chado
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6 Dependencies
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7 ------------
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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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12 .. code:: bash
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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14 . /path/to/galaxy/.venv/bin/activate
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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15 pip install future chado
1daff3b60f39 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit 1640878827bdc3870b6f34eded3a3f7571a1849f"
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16 deactivate
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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.