Mercurial > repos > yating-l > hubarchivecreator
annotate todo.md @ 0:3e0c61b52a06 draft
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
| author | yating-l |
|---|---|
| date | Mon, 31 Oct 2016 16:36:25 -0400 |
| parents | |
| children | 44577d6784b7 |
| rev | line source |
|---|---|
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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1 ### TEMP St Louis ### |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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2 - How to manage messages to user and debugging: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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3 - User should receive INFO / WARN / ERROR / CRITICAL: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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4 - User summary informations in stdout |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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5 - Full error in stderr |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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6 - Developer should receive all Logging stack: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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7 - Not the user summary in stdout |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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8 - Full stack in stdout and stderr directly |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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9 |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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10 - HOWTO: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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11 - Manage (at least) two type of Logging types: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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12 - The user one => When Debug mode is not set or disabled |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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13 - The dev one => When Debug mode is enabled |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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14 - User: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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15 - Two Handlers: stdout and stderr |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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16 - STDOUT: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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17 - Filter stdout: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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18 - NO ERROR and CRITICAL here |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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19 - (Warn) |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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20 - Formatter: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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21 - Only show %(message) for clarity |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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22 - STDERR: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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23 - Filter stderr => WARN / ERRROR / CRITICAL |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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24 - Formatter: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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25 - Show message |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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26 - Show traceback |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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27 - Dev: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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28 - One Handler: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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29 - To both stdout and stderr |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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30 - Filter: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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31 - Nope? |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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32 - Formatter: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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33 - Show traceback in both |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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34 |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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35 # HubArchiveCreator's TODO |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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36 |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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37 *TODO file inspired from: http://lifehacker.com/why-a-github-gist-is-my-favorite-to-do-list-1493063613* |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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38 |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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39 ### TO COMPLETE |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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40 |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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41 |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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42 - [ ] Don't let the Tool Classes manage the archive (add or remove files / folders) => Everything should pass through TrackHub or another class dedicated to that |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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43 - [ ] Move the class and others program related files, into separated folders |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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changeset
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44 - [ ] Take into account the name of the reference genome / the change: |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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45 - [ ] Somebody could want to launch two visualisations of two different genomes. Repeats of Genome with extensions associated |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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46 - [ ] Add TDD => First add the test. It should not pass. Implement. It should now pass :) |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
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47 - [ ] Replace Gff3 by an abstract class GeneralFormat, with two sub-classes GFF3Format and GTFFormat |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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48 - [ ] TrackHub should check if the 2bit already exists instead of recreating it (which is the case atm) |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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49 - [ ] Manage the error when a user is selecting Generic Bed instead of Bed Simple Repeats. Two options: a. Output a better error message ("Check with the other Bed options") b. Identify internally this is not a regular BED but a specific one |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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50 - [ ] Remove the non-explicit parameters for the communication between Galaxy Wrapper and the entry point |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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51 - [ ] Rename all occurences of `extension` which `datatype` |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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52 - [ ] Follow https://google.github.io/styleguide/pyguide.html |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
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53 - [ ] Move to Python 3 |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
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54 - [ ] Remove the repetition of the extension if it already exists |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
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55 - [ ] Better thinking about the tool_directory management / Classes path refactoring |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
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56 - [ ] Add a debug mode to have more outputs |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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57 - [ ] Improve the standard output of HAC |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
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58 - [ ] Find why a $ (newline) is added when installing dependencies from tool_dependencies.xml |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
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59 - [ ] Sort the order of the HTML directories/files |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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60 |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
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61 ### DONE |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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62 |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
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63 |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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64 - [x] Each time a file is added => Print it in the output with the full path (or relative path to root) |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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65 - [x] Add a script for Linux.x86_64 to download and and chmod +x the dependencies for local testing => util/install_linux_binaries.py |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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66 - [x] Add sorting BED if not sorted (Use the output of bedToBigBed) |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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67 - [x] Add a script to install the huba datatype |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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68 - [x] Add the possibility to add a new item in TrackDb.txt through a public function from TrackHub.py => addTrack() in TrackHub.py |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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69 - [x] Fix the errors for the stdio regexp not properly processed in error case (always green) => Used `detect_errors` in galaxy wrapper and raise Exception in Python |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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70 - [x] Add a class named ~~TrfBigProcess~~ BedSimpleRepeats |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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parents:
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71 - [x] Add a class named TrackHub: Create the base TrackHub hierarchy |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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72 - [x] Change the Name of the classes |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
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73 - [x] Add a class named AugustusProcess: Process the Augustus output to BigBed (and others needed in TrackHub) and (create folders + add the files into the right location => Process can be ported in a class responsible for that) |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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74 - [x] Add a class named AugustusProcess |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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75 - [x] Process the Augustus output to BigBed |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
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76 - [x] create folders + add the files into the right location |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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77 - [x] Creation of folders to be ported into a separated class => In Datatype.py but should be into a dedicated to file manipulation class |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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78 - [x] Refactoring of the AugustusProcess class to behave like a class and not like a procedural masked into a class |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
|
79 - [x] Rename AugustusProcess into something more generic if the process is shared (gtf to BigBed) => Gff3.py |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
|
80 - [x] Use gffToBed for Gtf instead of GtfToGenePred => Cancelled |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
|
81 - [x] Clean the mess with the File handling (sometimes File, sometimes String, sometimes open File) |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
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82 - [x] Find a way to avoid repetitions in TrackDb and Track (I repeat myself atm) => Track instance has a TrackDb instance as attribute |
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3e0c61b52a06
planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty
yating-l
parents:
diff
changeset
|
83 - [x] Refactor the creation of the structure to TrackHub: Access to paths via this Class, and creation of file through it |