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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 81492a9c8b9e5649a3867bc30afe617a30fb47a1"
author gga
date Tue, 14 Apr 2020 10:42:05 -0400
parents dd63c6e11a95
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dc738069b5ac 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
dc738069b5ac 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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dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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4 Galaxy tools to interface with Apollo.
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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5 Uses `python-apollo <https://github.com/galaxy-genome-annotation/python-apollo>`__ for most of it.
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556c8296b73b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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556c8296b73b planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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7 Environment
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8 -----------
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10 The following environment variables can be set:
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dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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12 +--------------------------------+-----------------------------------------------------------+
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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13 | ENV | Use |
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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14 +================================+===========================================================+
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 | ``$GALAXY_WEBAPOLLO_URL`` | The URL at which Apollo is accessible, internal to Galaxy |
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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16 | | and where the tools run. Must be absolute, with FQDN and |
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17 | | protocol. |
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18 +--------------------------------+-----------------------------------------------------------+
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19 | ``$GALAXY_WEBAPOLLO_USER`` | The admin user which Galaxy should use to talk to Apollo. |
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20 | | |
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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21 +--------------------------------+-----------------------------------------------------------+
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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22 | ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user. |
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23 +--------------------------------+-----------------------------------------------------------+
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24 | ``$ARROW_GLOBAL_CONFIG_PATH`` | Path to a python-apollo/arrow conf file. Use in place of |
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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25 | | ``$GALAXY_WEBAPOLLO_URL``, ``$GALAXY_WEBAPOLLO_USER`` |
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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26 | | and ``$GALAXY_WEBAPOLLO_PASSWORD``. |
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27 +--------------------------------+-----------------------------------------------------------+
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28 | ``$GALAXY_WEBAPOLLO_EXT_URL`` | May be relative or absolute. |
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dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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29 | | The external URL at which Apollo is accessible to end |
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30 | | users. |
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dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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31 +--------------------------------+-----------------------------------------------------------+
dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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32 | ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to |
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33 | | exchange JBrowse instances. If not set, JBrowse data will |
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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34 | | be zipped and sent to the remote server. |
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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35 +--------------------------------+-----------------------------------------------------------+
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36 | ``$GALAXY_APOLLO_ORG_SUFFIX`` | Set to 'id' if you want organism names to be suffixed |
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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37 | | with user id to avoid name collisions. Set to 'email' to |
dd63c6e11a95 "planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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38 | | use user email as suffix. Leave empty for no suffix. |
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dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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41 License
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42 -------
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dc738069b5ac planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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44 All python scripts, wrappers, and the webapollo.py are licensed under
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45 MIT license.