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annotate README.rst @ 0:f889e757ca93 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:45:08 -0400
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f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 Galaxy-apollo
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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2 =============
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f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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4 Galaxy tools to interface with Apollo The webapollo.py file is also
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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5 `separately
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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6 available <https://github.com/galaxy-genome-annotation/python-apollo>`__
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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7 as a pip-installable package.
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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9 Environ
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f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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11 The following environment variables must be set:
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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13 +--------------------------------+-----------------------------------------------------------+
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14 | ENV | Use |
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 +================================+===========================================================+
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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16 | ``$GALAXY_WEBAPOLLO_URL`` | The URL at which Apollo is accessible, internal to Galaxy |
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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17 | | and where the tools run. Must be absolute, with FQDN and |
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18 | | protocol. |
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19 +--------------------------------+-----------------------------------------------------------+
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20 | ``$GALAXY_WEBAPOLLO_USER`` | The admin user which Galaxy should use to talk to Apollo. |
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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21 | | |
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22 +--------------------------------+-----------------------------------------------------------+
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23 | ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user. |
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24 | | |
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25 | | |
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26 +--------------------------------+-----------------------------------------------------------+
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27 | ``$GALAXY_WEBAPOLLO_EXT_URL`` | users. May be relative or absolute. |
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28 | | The external URL at which Apollo is accessible to end |
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29 | | |
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30 +--------------------------------+-----------------------------------------------------------+
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31 | ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to |
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32 | | exchange JBrowse instances. |
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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33 +--------------------------------+-----------------------------------------------------------+
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35 License
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36 -------
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38 All python scripts, wrappers, and the webapollo.py are licensed under
f889e757ca93 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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39 MIT license.