Mercurial > repos > gga > apollo_iframe
annotate README.rst @ 12:3b6e8fd61dad draft
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 6d9302680b01ce11a8f2ee744942296243d5d004"
| author | gga |
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| date | Fri, 24 Apr 2020 08:51:21 -0400 |
| parents | c6172b538caf |
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| rev | line source |
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99b348a1d355
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 |
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99b348a1d355
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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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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c6172b538caf
"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. |
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c6172b538caf
"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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d9c47037fdc5
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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6 |
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d9c47037fdc5
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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d9c47037fdc5
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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8 ----------- |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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9 |
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c6172b538caf
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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10 The following environment variables can be set: |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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11 |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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12 +--------------------------------+-----------------------------------------------------------+ |
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99b348a1d355
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 | |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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14 +================================+===========================================================+ |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 | ``$GALAXY_WEBAPOLLO_URL`` | The URL at which Apollo is accessible, internal to Galaxy | |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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16 | | and where the tools run. Must be absolute, with FQDN and | |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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17 | | protocol. | |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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18 +--------------------------------+-----------------------------------------------------------+ |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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19 | ``$GALAXY_WEBAPOLLO_USER`` | The admin user which Galaxy should use to talk to Apollo. | |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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20 | | | |
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99b348a1d355
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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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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22 | ``$GALAXY_WEBAPOLLO_PASSWORD`` | The password for the admin user. | |
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c6172b538caf
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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23 +--------------------------------+-----------------------------------------------------------+ |
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c6172b538caf
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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24 | ``$ARROW_GLOBAL_CONFIG_PATH`` | Path to a python-apollo/arrow conf file. Use in place of | |
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c6172b538caf
"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`` | |
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c6172b538caf
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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26 | | and ``$GALAXY_WEBAPOLLO_PASSWORD``. | |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
gga
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27 +--------------------------------+-----------------------------------------------------------+ |
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d9c47037fdc5
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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28 | ``$GALAXY_WEBAPOLLO_EXT_URL`` | May be relative or absolute. | |
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99b348a1d355
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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d9c47037fdc5
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f55bad7dcf56bd9625874cd89f3894aee35d91ef
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30 | | users. | |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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31 +--------------------------------+-----------------------------------------------------------+ |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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32 | ``$GALAXY_SHARED_DIR`` | Directory shared between Galaxy and Apollo, used to | |
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c6172b538caf
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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33 | | exchange JBrowse instances. If not set, JBrowse data will | |
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c6172b538caf
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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34 | | be zipped and sent to the remote server. | |
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c6172b538caf
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
gga
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35 +--------------------------------+-----------------------------------------------------------+ |
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c6172b538caf
"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
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36 | ``$GALAXY_APOLLO_ORG_SUFFIX`` | Set to 'id' if you want organism names to be suffixed | |
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c6172b538caf
"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 | |
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c6172b538caf
"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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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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39 +--------------------------------+-----------------------------------------------------------+ |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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40 |
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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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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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42 ------- |
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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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43 |
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99b348a1d355
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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99b348a1d355
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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45 MIT license. |