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author yating-l
date Wed, 31 May 2017 15:45:47 -0400
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1 # JBrowse Hub Creator
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2 This Galaxy tool permits to prepare your files to be ready for JBrowse visualization.
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4 ## Features
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5 1. Similar interface to Hub Archive Creator.
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6 2. Convert tracks to GFF3 datatypes (e.g Blastxml => GFF3) in order to import feature data from the flat files
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7 3. Generate a zip file including all the tracks and configuration for JBrowse visualization
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8 4. Group the tracks
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9 5. Set the color for each track
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10 6. Set the label for each track
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11 7. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks!
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13 At the moment, Supported datatypes are:
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14 - Bam
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15 - Bed
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16 - Splice Junctions (BED 12+1)
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17 - Simple Repeats (BED 4+12)
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18 - BigWig
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19 - Gff3
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20 - Gtf
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21 - Blastxml
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23 ## Installation:
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24 1. You would need to add this tool into your Galaxy.
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25 1. (strongly preferred) **ToolShed Installation**: Tool is in [testtoolshed](https://testtoolshed.g2.bx.psu.edu/view/yating-l/jbrowse_hub/b7bf45272ab7)
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26 2. OR **Local Installation**: See https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial
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27 2. The tool can be used with or without Conda (activate it in your galaxy.ini)
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28 3. If installed without TS (by downloading on GitHub), you need to have all the binaries accessible within Galaxy.
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29 You can use the script [install_linux_binaries](util/install_linux_binaries) with a linux x86-64 (64bits)
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31 ## Future
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32 See [TODO.md](todo.md) for more information
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34 ## Contribute
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36 - Source Code: https://github.com/Yating-L/jbrowse_hub
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38 ## Support
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40 If you are having issues, please let us know.
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42 - For more information about how to use G-OnRamp:
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43 - [Wilson Leung](wleung@wustl.edu) - Product owner and developer
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44 - [Yating Liu](yliu41@wustl.edu) - Community manager and Developer
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46 - For more information about the project vision, or for partneship:
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47 - [Elgin, Sarah](selgin@wustl.edu) - PI
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48 - [Jeremy Goecks](jgoecks@gwu.edu) - PI
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50 ## License
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52 The project is licensed under the Academic Free License 3.0. See [LICENSE.txt](LICENSE.txt).