Mercurial > repos > yating-l > jbrowsearchivecreator
diff README.md @ 13:43a700afd457 draft
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit bcb239c4045d2c47a8acad5fbd29eea03663e187
author | yating-l |
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date | Tue, 19 Jun 2018 17:59:51 -0400 |
parents | 237707a6b74d |
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--- a/README.md Sat Jun 02 13:08:46 2018 -0400 +++ b/README.md Tue Jun 19 17:59:51 2018 -0400 @@ -1,5 +1,5 @@ # JBrowse Hub Creator -This Galaxy tool permits to prepare your files to be ready for JBrowse visualization. +This Galaxy tool is used to prepare your files to be ready for JBrowse visualization. ## Features 1. Similar interface to Hub Archive Creator. @@ -7,33 +7,36 @@ 3. Group the tracks 4. Set the color for each track 5. Set the label for each track -6. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks! +6. Support generating Tabix Indexed CanVasFeatures tracks +7. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks! At the moment, Supported datatypes are: -- Bam -- Bed +- BAM +- BED + - Generic BED - Splice Junctions (BED 12+1) - Simple Repeats (BED 4+12) + - BLAT alignment (BigPsl) + - BLAST alignment (BED 12+12) - BigWig -- Gff3 -- Gtf -- Blastxml -- BigPsl +- GFF3 +- GTF +- Blast XML output ## Installation: -1. You would need to add this tool into your Galaxy. - 1. (strongly preferred) **ToolShed Installation**: Tool is in [testtoolshed](https://testtoolshed.g2.bx.psu.edu/view/yating-l/jbrowse_hub/b7bf45272ab7) - 2. OR **Local Installation**: See https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial -2. The tool can be used with or without Conda (activate it in your galaxy.ini) -3. If installed without TS (by downloading on GitHub), you need to have all the binaries accessible within Galaxy. - You can use the script [install_linux_binaries](util/install_linux_binaries) with a linux x86-64 (64bits) + +**ToolShed Installation**: +- The JBrowse Archive Creator tool is published at [ToolShed Repository](https://toolshed.g2.bx.psu.edu/view/yating-l/jbrowsearchivecreator) + +- 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. + ## Future See [TODO.md](todo.md) for more information ## Contribute -- Source Code: https://github.com/Yating-L/jbrowse_hub +- Source Code: https://github.com/goeckslab/jbrowse-archive-creator.git ## Support @@ -41,7 +44,7 @@ - For more information about how to use G-OnRamp: - [Wilson Leung](wleung@wustl.edu) - Product owner and developer - - [Yating Liu](yliu41@wustl.edu) - Community manager and Developer + - [Yating Liu](yliu41@wustl.edu) - Community manager and developer - For more information about the project vision, or for partneship: - [Elgin, Sarah](selgin@wustl.edu) - PI