[Blends-commit] r2757 - in /projects/med/trunk/debian-med/tasks: bio bio-ngs cloud

[plessy at users.alioth.debian.org]

Author: plessy
Date: Tue Apr 19 01:27:42 2011
New Revision: 2757

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2757
Log:
fastx-toolkit accepted 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=2757&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Tue Apr 19 01:27:42 2011
@@ -47,7 +47,7 @@
  old unmaintained version remained at code.google.com.  Please drop the
  maintainer a note if you have any news of this project.
 
-Depends:     boxshade, gff2aplot, muscle, sim4, sibsim4, tabix, wise
+Depends:     boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, wise
 
 Depends: bwa
 Published-Title: Fast and accurate short read alignment with Burrows-Wheeler transform
@@ -2897,29 +2897,6 @@
  .
  They provide two programs: kemp for the frequentist test and basu for
  the Bayesian test, and some auxiliary scripts.
-
-Depends: fastx-toolkit
-Homepage: http://hannonlab.cshl.edu/fastx_toolkit
-License: AGPL / MIT
-WNPP: 622700
-Responsible: Charles Plessy <plessy at debian.org>
-Vcs-Browser: http://git.debian.org/?p=debian-med/fastx-toolkit.git
-Vcs-Git: git://git.debian.org/git/debian-med/fastx-toolkit.git
-Pkg-Description: collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
- Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple
- short-reads sequences (possibly with quality information).  The main processing of such
- FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other
- databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP,
- LastZ, MAQ and many many others.
- .
- However, It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the
- sequences to the genome - manipulating the sequences to produce better mapping results.
- .
- The FASTX-Toolkit tools perform some of these preprocessing tasks.
-Remark: See also
- http://hannonlab.cshl.edu/column_normalizer/
- .
- http://hannonlab.cshl.edu/crosstab/
 
 Depends: grogui
 Homepage: http://www.kde-apps.org/content/show.php?content=47665

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=2757&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-ngs (original)
+++ projects/med/trunk/debian-med/tasks/bio-ngs Tue Apr 19 01:27:42 2011
@@ -6,6 +6,7 @@
 Depends:
 	bwa,
 	bowtie,
+	fastx-toolkit,
 	last-align,
 	maq,
 	picard-tools,

Modified: projects/med/trunk/debian-med/tasks/cloud
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/cloud?rev=2757&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/cloud (original)
+++ projects/med/trunk/debian-med/tasks/cloud Tue Apr 19 01:27:42 2011
@@ -33,6 +33,7 @@
 	dialign,
 	dialign-tx,
 	exonerate,
+	fastx-toolkit,
 	gff2aplot,
 	glam2,
 	gmap,