[Blends-commit] r3157 - in /projects/med/trunk/debian-med/tasks: bio bio-ngs cloud

[plessy at users.alioth.debian.org]

Author: plessy
Date: Sun Feb 19 05:09:10 2012
New Revision: 3157

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3157
Log:
TopHat is now available in Debian.

Modified:
    projects/med/trunk/debian-med/tasks/bio
    projects/med/trunk/debian-med/tasks/bio-ngs
    projects/med/trunk/debian-med/tasks/cloud

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=3157&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sun Feb 19 05:09:10 2012
@@ -52,7 +52,7 @@
  old unmaintained version remained at code.google.com.  Please drop the
  maintainer a note if you have any news of this project.
 
-Depends:     boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, wise
+Depends:     boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, tophat, wise
 
 Depends:     maqview
 
@@ -3768,20 +3768,6 @@
  nice features, from displaying through animation to analysing.
  It can be scripted, clustered, and runs on all common OS.
 
-Depends: tophat
-License: Artistic
-Homepage: http://tophat.cbcb.umd.edu/
-Vcs-Git: git://git.debian.org/debian-med/tophat.git
-Vcs-Browser: http://git.debian.org/?p=debian-med/tophat.git;a=summary
-Pkg-Description: TopHat is a fast splice junction mapper for RNA-Seq reads
- It aligns RNA-Seq reads to mammalian-sized genomes using the ultra
- high-throughput short read aligner Bowtie, and then analyzes the
- mapping results to identify splice junctions between exons.
- TopHat is a collaborative effort between the University of Maryland
- Center for Bioinformatics and Computational Biology and the
- University of California, Berkeley Departments of Mathematics and
- Molecular and Cell Biology.
-
 Depends: hhsuite
 Homepage: http://toolkit.genzentrum.lmu.de/sections/search
 License: GPL-3.0+

Modified: projects/med/trunk/debian-med/tasks/bio-ngs
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-ngs?rev=3157&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-ngs (original)
+++ projects/med/trunk/debian-med/tasks/bio-ngs Sun Feb 19 05:09:10 2012
@@ -22,6 +22,7 @@
 	sra-toolkit,
 	ssake,
 	tabix,
+	tophat,
 	vcftools,
 	velvet
 

Modified: projects/med/trunk/debian-med/tasks/cloud
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/cloud?rev=3157&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/cloud (original)
+++ projects/med/trunk/debian-med/tasks/cloud Sun Feb 19 05:09:10 2012
@@ -90,6 +90,7 @@
 	r-bioc-hilbertvis,
 	samtools,
 	ssake,
+	tophat,
 	velvet
 X-End-Category: High throughput sequencing