Mercurial > repos > iuc > ena_upload
annotate README.rst @ 12:70900c25b43b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit b9c33a82f739ebd40651bb7acfc1264208cea83c
| author | iuc |
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| date | Mon, 26 May 2025 10:03:21 +0000 |
| parents | e7995727674f |
| children |
| rev | line source |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
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1 ENA-upload-cli wrapper |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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2 ====================== |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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3 |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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4 Galaxy wrapper of the |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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5 `ena-upload-cli <https://github.com/usegalaxy-eu/ena-upload-cli>`__. |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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6 Templates that can be used in as input for the metadata can be found |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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7 `here <https://github.com/ELIXIR-Belgium/ENA-metadata-templates>`__ |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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8 |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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9 This tool is shipped in a ready to use Galaxy container found |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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10 `here <https://github.com/ELIXIR-Belgium/ena-upload-container>`__. |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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11 |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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12 Setting up credentials on Galaxy |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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13 -------------------------------- |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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14 |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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15 The admin of the server can set up global credentials through a file |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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16 with the format: |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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17 |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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18 .. code-block:: yaml |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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19 |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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20 username: webin_id |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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21 password: webin_password |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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22 |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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23 The path to this file must be exported as an environment variable called |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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24 $GALAXY_ENA_SECRETS |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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25 |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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26 Alternatively, the admin can enable users to set their own credentials |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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27 for this tool. To enable it, make sure the file |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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28 ``config/user_preferences_extra_conf.yml`` has the following section: |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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29 |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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30 .. code-block:: yaml |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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31 |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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32 ena_webin_account: |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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33 description: Your ENA Webin account details |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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34 inputs: |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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35 - name: webin_id |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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36 label: ENA Webin ID |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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37 type: text |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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38 required: False |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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39 - name: password |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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40 label: Password |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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41 type: password |
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e7995727674f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6428c6a64979e4a1f745066a62280e38ad98d249
iuc
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42 required: False |