Mercurial > repos > gga > tripal_organism_get_organisms

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit ea279e5b47cf3d5767328d17b0e40e57b0238ea1"
author gga
date Wed, 14 Aug 2019 10:04:40 -0400
parents 49d35a38bd85
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8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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1 Galaxy-tripal
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2 =============
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49d35a38bd85 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit 81a83f06b49db32928ba0cd44e5b6d0431868d27
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4 Galaxy tools to interface with Tripal using python-tripal
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8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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6 Dependencies
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7 ------------
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8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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9 You will need to install some python modules in the Galaxy virtualenv for these
8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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10 tools to be fully functional:
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8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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12 .. code:: bash
8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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14 . /path/to/galaxy/.venv/bin/activate
8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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15 pip install future tripal
8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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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 | ``$GALAXY_TRIPAL_URL`` | The URL at which Tripal is accessible, internal to Galaxy |
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27 | | and where the tools run. Must be absolute, with FQDN and |
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28 | | protocol. |
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29 +--------------------------------+-----------------------------------------------------------+
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30 | ``$GALAXY_TRIPAL_USER`` | The admin user which Galaxy should use to talk to Tripal. |
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31 | | |
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32 +--------------------------------+-----------------------------------------------------------+
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33 | ``$GALAXY_TRIPAL_PASSWORD`` | The password for the admin user. |
8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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34 | | |
8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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35 | | |
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36 +--------------------------------+-----------------------------------------------------------+
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37 | ``$GALAXY_TRIPAL_SHARED_DIR`` | Directory shared between Galaxy and Tripal, used to |
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38 | | exchange data files. |
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39 +--------------------------------+-----------------------------------------------------------+
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8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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8c9e0534386d planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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42 License
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43 -------
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44
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45 All python scripts and wrappers are licensed under MIT license.