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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Mon, 06 Nov 2017 13:13:01 -0500
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1 # HubArchiveCreator's TODO
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3 *TODO file inspired from: http://lifehacker.com/why-a-github-gist-is-my-favorite-to-do-list-1493063613*
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5 ### TO COMPLETE
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3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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8 - [ ] Parse the [JSON received from Galaxy inputs](hubArchiveCreator.xml#L47-L137) in a class instead of doing [this spaghetti code](hubArchiveCreator.py#L137-L149)
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9 - [ ] 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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10 - [ ] Move the class and others program related files, into separated folders
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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11 - [ ] Take into account the name of the reference genome / the change:
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12 - [ ] Somebody could want to launch two visualisations of two different genomes. Repeats of Genome with extensions associated
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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13 - [ ] Replace Gff3/GTF by an abstract class GeneralFormat, with two sub-classes GFF3Format and GTFFormat
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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14 - [ ] 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
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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15 - [ ] Remove the non-explicit parameters for the communication between Galaxy Wrapper and the entry point
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16 - [ ] Rename all occurences of `extension` with `datatype`
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17 - [ ] Follow https://google.github.io/styleguide/pyguide.html
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18 - [ ] Migrate to Python 3
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19 - [ ] Remove the repetition of the extension file if it already exists
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20 - [ ] Better thinking about the tool_directory management / Classes path refactoring
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22 ### DONE
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25 - [x] Add TDD => First add the test. It should not pass. Implement. It should now pass :)
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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26 - [x] TrackHub should check if the 2bit already exists instead of recreating it (which is the case atm)
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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27 - [x] Add a debug mode to have more outputs
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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28 - [x] Improve the standard output of HAC
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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29 - [x] Each time a file is added => Print it in the output with the full path (or relative path to root)
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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30 - [x] Find why a $ (newline) is added when installing dependencies from tool_dependencies.xml
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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31 - [x] Sort the order of the HTML directories/files
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32 - [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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33 - [x] Add sorting BED if not sorted (Use the output of bedToBigBed)
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34 - [x] Add a script to install the huba datatype
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35 - [x] Add the possibility to add a new item in TrackDb.txt through a public function from TrackHub.py => addTrack() in TrackHub.py
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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36 - [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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37 - [x] Add a class named ~~TrfBigProcess~~ BedSimpleRepeats
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38 - [x] Add a class named TrackHub: Create the base TrackHub hierarchy
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39 - [x] Change the Name of the classes
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40 - [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)
3f7c40fb51e8 planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c778f8ee85e9acc924c5c0a30042ac90c8e7a70d-dirty
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41 - [x] Add a class named AugustusProcess
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42 - [x] Process the Augustus output to BigBed
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43 - [x] create folders + add the files into the right location
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44 - [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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45 - [x] Refactoring of the AugustusProcess class to behave like a class and not like a procedural masked into a class
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46 - [x] Rename AugustusProcess into something more generic if the process is shared (gtf to BigBed) => Gff3.py
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47 - [x] Use gffToBed for Gtf instead of GtfToGenePred => Cancelled
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48 - [x] Clean the mess with the File handling (sometimes File, sometimes String, sometimes open File)
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49 - [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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50 - [x] Refactor the creation of the structure to TrackHub: Access to paths via this Class, and creation of file through it