[Blends-commit] r2838 - in /projects/med/trunk/debian-med/tasks: bio bio-ngs cloud

[plessy at users.alioth.debian.org]

Author: plessy
Date: Wed Jun  8 11:06:45 2011
New Revision: 2838

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2838
Log:
bedtools accepted, filo next ?

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=2838&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Wed Jun  8 11:06:45 2011
@@ -347,7 +347,7 @@
 
 Depends: staden-io-lib-utils
 
-Depends: samtools
+Depends: samtools, bedtools
 
 Depends: r-bioc-hilbertvis
 Published-Authors: Simon Anders
@@ -3756,19 +3756,6 @@
   * Translation of nucleotide sequences to amino acid sequences
   * Residue selections
 
-Depends: bedtools
-License: GPL-2+
-Homepage: http://code.google.com/p/bedtools/
-WNPP: 629597
-Vcs-Git: http://git.debian.org/?p=debian-med/bedtools.git
-Language: C++
-Pkg-Description: suite of utilities for comparing genomic features
- The BEDTools utilities allow one to address common genomics tasks such as
- finding feature overlaps and computing coverage. The utilities are largely
- based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using
- BEDTools, one can develop sophisticated pipelines that answer complicated
- research questions by streaming several BEDTools together.
-
 Depends: cinema
 License: LGPL
 Language: Java
@@ -3784,6 +3771,23 @@
  although its easy to add new ones. A large number of alignments in the
  appropriate format can be found as part of the align compendium at
 
+Depends: filo
+License: GPL-2
+Language: C++
+Homepage: https://github.com/arq5x/filo
+Vcs-Git: git://git.debian.org/git/debian-med/filo.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/filo.git
+Pkg-Description: FILe and stream Operations
+ The following tools are available as part of the filo package:
+ .
+ groupBy is a useful tool that mimics the "groupBy" clause in database
+ systems.
+ .
+ shuffle will randomize the order of lines in a file. In other words,
+ if you have a sorted file, shuffle will undo the sort.
+ .
+ stats is a small utility for computing descriptive statistic on a
+ given column of a tab-delimited file or stream.
 
 Comment: Several related R packages are listed at CRAN:
          http://cran.r-project.org/web/views/Genetics.html

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=2838&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-ngs (original)
+++ projects/med/trunk/debian-med/tasks/bio-ngs Wed Jun  8 11:06:45 2011
@@ -8,6 +8,7 @@
  packages is complete regarding NGS.
 
 Depends:
+	bedtools,
 	bwa,
 	bowtie,
 	fastx-toolkit,

Modified: projects/med/trunk/debian-med/tasks/cloud
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/cloud?rev=2838&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/cloud (original)
+++ projects/med/trunk/debian-med/tasks/cloud Wed Jun  8 11:06:45 2011
@@ -66,6 +66,7 @@
 
 X-Begin-Category: High throughput sequencing
 Depends:
+	bedtools,
 	bwa,
 	last-align,
 	maq,