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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit bcb239c4045d2c47a8acad5fbd29eea03663e187
author yating-l
date Tue, 19 Jun 2018 17:59:51 -0400
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12:9161beae834f 13:43a700afd457
1 # JBrowse Hub Creator 1 # JBrowse Hub Creator
2 This Galaxy tool permits to prepare your files to be ready for JBrowse visualization. 2 This Galaxy tool is used to prepare your files to be ready for JBrowse visualization.
3 3
4 ## Features 4 ## Features
5 1. Similar interface to Hub Archive Creator. 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 6 2. Convert tracks to GFF3 datatypes (e.g Blastxml => GFF3) in order to import feature data from the flat files
7 3. Group the tracks 7 3. Group the tracks
8 4. Set the color for each track 8 4. Set the color for each track
9 5. Set the label for each track 9 5. Set the label for each track
10 6. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks! 10 6. Support generating Tabix Indexed CanVasFeatures tracks
11 7. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks!
11 12
12 At the moment, Supported datatypes are: 13 At the moment, Supported datatypes are:
13 - Bam 14 - BAM
14 - Bed 15 - BED
16 - Generic BED
15 - Splice Junctions (BED 12+1) 17 - Splice Junctions (BED 12+1)
16 - Simple Repeats (BED 4+12) 18 - Simple Repeats (BED 4+12)
19 - BLAT alignment (BigPsl)
20 - BLAST alignment (BED 12+12)
17 - BigWig 21 - BigWig
18 - Gff3 22 - GFF3
19 - Gtf 23 - GTF
20 - Blastxml 24 - Blast XML output
21 - BigPsl
22 25
23 ## Installation: 26 ## 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 27
28 **ToolShed Installation**:
29
30 - The JBrowse Archive Creator tool is published at [ToolShed Repository](https://toolshed.g2.bx.psu.edu/view/yating-l/jbrowsearchivecreator)
31
32 - Refer to [Installing Tools into Galaxy](https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial) tutorial if you want to learn how to install a tool from ToolShed.
33
31 ## Future 34 ## Future
32 See [TODO.md](todo.md) for more information 35 See [TODO.md](todo.md) for more information
33 36
34 ## Contribute 37 ## Contribute
35 38
36 - Source Code: https://github.com/Yating-L/jbrowse_hub 39 - Source Code: https://github.com/goeckslab/jbrowse-archive-creator.git
37 40
38 ## Support 41 ## Support
39 42
40 If you are having issues, please let us know. 43 If you are having issues, please let us know.
41 44
42 - For more information about how to use G-OnRamp: 45 - For more information about how to use G-OnRamp:
43 - [Wilson Leung](wleung@wustl.edu) - Product owner and developer 46 - [Wilson Leung](wleung@wustl.edu) - Product owner and developer
44 - [Yating Liu](yliu41@wustl.edu) - Community manager and Developer 47 - [Yating Liu](yliu41@wustl.edu) - Community manager and developer
45 48
46 - For more information about the project vision, or for partneship: 49 - For more information about the project vision, or for partneship:
47 - [Elgin, Sarah](selgin@wustl.edu) - PI 50 - [Elgin, Sarah](selgin@wustl.edu) - PI
48 - [Jeremy Goecks](jgoecks@gwu.edu) - PI 51 - [Jeremy Goecks](jgoecks@gwu.edu) - PI
49 52