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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
author yating-l
date Thu, 13 Apr 2017 10:36:12 -0400
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1 # JBrowse Hub Creator
2 This Galaxy tool permits to prepare your files to be ready for JBrowse visualization.
3
4 ## Features
5 1. Similar interface to Hub Archive Creator.
6 2. Convert tracks to GFF3 datatypes (e.g Blastxml => GFF3) in order to import feature data from the flat files
7 3. Generate a zip file including all the tracks and configuration for JBrowse visualization
8 4. Group the tracks
9 5. Set the color for each track
10 6. Set the label for each track
11 7. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks!
12
13 At the moment, Supported datatypes are:
14 - Bam
15 - Bed
16 - Splice Junctions (BED 12+1)
17 - Simple Repeats (BED 4+12)
18 - BigWig
19 - Gff3
20 - Gtf
21 - Blastxml
22
23 ## Installation:
24 1. You would need to add this tool into your Galaxy.
25 1. (strongly preferred) **ToolShed Installation**: Tool is in [testtoolshed](https://testtoolshed.g2.bx.psu.edu/view/yating-l/jbrowse_hub/b7bf45272ab7)
26 2. OR **Local Installation**: See https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial
27 2. The tool can be used with or without Conda (activate it in your galaxy.ini)
28 3. If installed without TS (by downloading on GitHub), you need to have all the binaries accessible within Galaxy.
29 You can use the script [install_linux_binaries](util/install_linux_binaries) with a linux x86-64 (64bits)
30
31 ## Future
32 See [TODO.md](todo.md) for more information
33
34 ## Contribute
35
36 - Source Code: https://github.com/Yating-L/jbrowse_hub
37
38 ## Support
39
40 If you are having issues, please let us know.
41
42 - For more information about how to use G-OnRamp:
43 - [Wilson Leung](wleung@wustl.edu) - Product owner and developer
44 - [Yating Liu](yliu41@wustl.edu) - Community manager and Developer
45
46 - For more information about the project vision, or for partneship:
47 - [Elgin, Sarah](selgin@wustl.edu) - PI
48 - [Jeremy Goecks](jgoecks@gwu.edu) - PI
49
50 ## License
51
52 The project is licensed under the Academic Free License 3.0. See [LICENSE.txt](LICENSE.txt).