Mercurial > repos > yating-l > jbrowsearchivecreator

annotate README.md @ 4:7e471cdd9e71 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 8d93b27353190eb23490c9480e560d84cb60c973
author yating-l
date Fri, 07 Jul 2017 16:17:57 -0400
parents ac83821b0e06
children 237707a6b74d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
1 # JBrowse Hub Creator
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
2 This Galaxy tool permits to prepare your files to be ready for JBrowse visualization.
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
3
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
4 ## Features
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
5 1. Similar interface to Hub Archive Creator.
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
6 2. Convert tracks to GFF3 datatypes (e.g Blastxml => GFF3) in order to import feature data from the flat files
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
7 3. Generate a zip file including all the tracks and configuration for JBrowse visualization
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
8 4. Group the tracks
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
9 5. Set the color for each track
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
10 6. Set the label for each track
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
11 7. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks!
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
12
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
13 At the moment, Supported datatypes are:
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
14 - Bam
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
15 - Bed
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
16 - Splice Junctions (BED 12+1)
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
17 - Simple Repeats (BED 4+12)
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
18 - BigWig
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
19 - Gff3
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
20 - Gtf
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
21 - Blastxml
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
22
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
23 ## Installation:
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
24 1. You would need to add this tool into your Galaxy.
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
25 1. (strongly preferred) **ToolShed Installation**: Tool is in [testtoolshed](https://testtoolshed.g2.bx.psu.edu/view/yating-l/jbrowse_hub/b7bf45272ab7)
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
26 2. OR **Local Installation**: See https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
27 2. The tool can be used with or without Conda (activate it in your galaxy.ini)
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
28 3. If installed without TS (by downloading on GitHub), you need to have all the binaries accessible within Galaxy.
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
29 You can use the script [install_linux_binaries](util/install_linux_binaries) with a linux x86-64 (64bits)
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
30
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
31 ## Future
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
32 See [TODO.md](todo.md) for more information
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
33
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
34 ## Contribute
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
35
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
36 - Source Code: https://github.com/Yating-L/jbrowse_hub
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
37
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
38 ## Support
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
39
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
40 If you are having issues, please let us know.
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
41
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
42 - For more information about how to use G-OnRamp:
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
43 - [Wilson Leung](wleung@wustl.edu) - Product owner and developer
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
44 - [Yating Liu](yliu41@wustl.edu) - Community manager and Developer
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
45
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
46 - For more information about the project vision, or for partneship:
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
47 - [Elgin, Sarah](selgin@wustl.edu) - PI
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
48 - [Jeremy Goecks](jgoecks@gwu.edu) - PI
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
49
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
50 ## License
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
51
ac83821b0e06 planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit bd7c7df707bfbcfa317c30caed48734d027dd889-dirty
yating-l
parents:
diff changeset
52 The project is licensed under the Academic Free License 3.0. See [LICENSE.txt](LICENSE.txt).