diff README.md @ 13:43a700afd457 draft

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
parents 237707a6b74d
children
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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