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1 # Hub Archive Creator
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2 This Galaxy tool permits to prepare your files to be ready for Assembly Hub visualization.
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3
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4 Into a publicly accessible Galaxy (Linux for maximum tools compatibility), you will be able to use UCSC Genome Browser fonctionality to see your tracks.
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5
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6 ## Features
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7 1. Create a structure for your tracks, and convert them to more efficient datatypes (e.g Bed => BigBed)
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8 2. Benefits from Galaxy strong features as well as UCSC Genome Browser's ones without the hassle to move your data from one to another
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9 3. Download and store, as a zip file, your tracks structured for UCSC TrackHub use
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10 4. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside UCSC Genome Browser...in a few clicks!
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11
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12 At the moment, Supported datatypes are:
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13 - Bam
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14 - Bed (Generic and Simple Repeats)
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15 - BigWig
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16 - Gff3
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17 - Gtf
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18 - Psl
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19
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20 ## Installation:
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21 1. You would need to add this tool into your Galaxy.
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22 1. (strongly preferred) **ToolShed Installation**: Tool is in [toolshed](https://toolshed.g2.bx.psu.edu/view/rmarenco/hubarchivecreator/fb5e60d4d18a)
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23 2. OR **Local Installation**: See https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial
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24 2. The tool can be used with or without Conda (activate it in your galaxy.ini)
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25 3. If installed without TS (by downloading on GitHub), you need to have all the binaries accessible within Galaxy.
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26 You can use the script [install_linux_binaries](util/install_linux_binaries) with a linux x86-64 (64bits)
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27 4. Install the UCSC Track Hub datatype:
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28 1. **Easy** => Use Galaxy 16.07 or latest to directly have Track Hub Datatype (See [this Galaxy Pull Request](https://github.com/galaxyproject/galaxy/pull/2348) for more information)
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29 2. OR Look into [trackHub README](trackHub/README.md) for more information or if you want to use Galaxy < 16.07
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30
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31 ### Binaries used by HAC:
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32 - bedToBigBed
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33 - faToTwoBit
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34 - genePredToBed
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35 - genePredToBigGenePred
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36 - gff3ToGenePred
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37 - gtfToGenePred
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38 - pslToBigPsl
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39 - samtools
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40 - sort
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41 - twoBitInfo
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42 See `<requirements` in [tool_dependencies.xml](tool_dependencies.xml) for an up-to-date used binaries list
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43
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44 ## Future
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45 See [TODO.md](todo.md) for more information
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46
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47 ## Contribute
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48
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49 - Issue Tracker: https://github.com/remimarenco/hub-archive-creator/issues
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50 - Source Code: https://github.com/remimarenco/hub-archive-creator
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51
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52 ## Support
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53
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54 If you are having issues, please let us know.
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55
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56 - For more information about how to use G-OnRamp:
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57 - [Wilson Leung](wleung@wustl.edu) - Product owner and developer
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58 - [Yating Liu](yliu41@wustl.edu) - Community manager and Developer
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59 - [Remi Marenco](remimarenco@gmail.com) - Main developer and Scrum Master
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60
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61 - For more information about the project vision, or for partneship:
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62 - [Elgin, Sarah](selgin@wustl.edu) - PI
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63 - [Jeremy Goecks](jgoecks@gwu.edu) - PI
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64
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65 ## License
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66
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67 The project is licensed under the Academic Free License 3.0. See [LICENSE.txt](LICENSE.txt).
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