[Blends-commit] r2634 - in /projects/med/trunk/debian-med/tasks: bio bio-ngs

[tille at users.alioth.debian.org]

Author: tille
Date: Sat Jan 29 15:04:02 2011
New Revision: 2634

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2634
Log:
Moved bowtie and mira prospective package description to bio-ngs

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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2634&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sat Jan 29 15:04:02 2011
@@ -1020,31 +1020,6 @@
   * Customizable plug-in architecture (e.g. run BLAST, dump & import many formats,
     find oligonucleotides, design primers, create restriction maps, edit features)
 
-Depends: mira
-Homepage: http://chevreux.org/projects_mira.html
-Responsible: Charles Plessy <plessy at debian.org>
-WNPP: 435915
-License: GPL
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mira/trunk/
-Pkg-Description: Whole Genome Shotgun and EST Sequence Assembler
- The mira genome fragment assembler is a specialised assembler for
- sequencing projects classified as 'hard' due to high number of similar
- repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
- specialised on reconstructing pristine mRNA transcripts while
- detecting and classifying single nucleotide polymorphisms (SNP)
- occuring in different variations thereof.
- .
- The assembler is routinely used for such various tasks as mutation
- detection in different cell types, similarity analysis of transcripts
- between organisms, and pristine assembly of sequences from various
- sources for oligo design in clinical microarray experiments.
-Published-Title: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
-Published-Authors: Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S.
-Published-In: Genome Res. Jun;14(6):1147-59.
-Published-Year: 2004
-Published-doi: 10.1101/gr.1917404
-Published-URL: http://pubmed.org/15140833
-
 Depends: phylographer
 Homepage: http://www.atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html
 Responsible: Charles Plessy <plessy at debian.org>
@@ -3173,19 +3148,6 @@
  seems to be no download option for TIGR Assembler at the J. Craig Venter Institute
  (formerly TIGR) any more.
 
-Depends: bowtie
-Homepage: http://bowtie-bio.sourceforge.net/
-WNPP: 604940
-License: Artistic
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/bowtie/trunk
-X-Category: Sequencing
-Pkg-Description: An ultrafast memory-efficient short read aligner
- Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
- DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
- reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep
- its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB
- for paired-end).
-
 Depends: crossbow
 Homepage: http://bowtie-bio.sourceforge.net/crossbow
 License: Artistic

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=2634&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-ngs (original)
+++ projects/med/trunk/debian-med/tasks/bio-ngs Sat Jan 29 15:04:02 2011
@@ -13,9 +13,45 @@
 	samtools,
 	ssake,
 	velvet,
-	bowtie,
-	mira,
 	saha2,
 	mosaik
 X-End-Category: High throughput sequencing
 
+Depends: bowtie
+Homepage: http://bowtie-bio.sourceforge.net/
+WNPP: 604940
+License: Artistic
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/bowtie/trunk
+X-Category: Sequencing
+Pkg-Description: An ultrafast memory-efficient short read aligner
+ Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
+ DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
+ reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep
+ its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB
+ for paired-end).
+
+Depends: mira
+Homepage: http://chevreux.org/projects_mira.html
+Responsible: Charles Plessy <plessy at debian.org>
+WNPP: 435915
+License: GPL
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mira/trunk/
+Pkg-Description: Whole Genome Shotgun and EST Sequence Assembler
+ The mira genome fragment assembler is a specialised assembler for
+ sequencing projects classified as 'hard' due to high number of similar
+ repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
+ specialised on reconstructing pristine mRNA transcripts while
+ detecting and classifying single nucleotide polymorphisms (SNP)
+ occuring in different variations thereof.
+ .
+ The assembler is routinely used for such various tasks as mutation
+ detection in different cell types, similarity analysis of transcripts
+ between organisms, and pristine assembly of sequences from various
+ sources for oligo design in clinical microarray experiments.
+Published-Title: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
+Published-Authors: Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WE, Wetter T, Suhai S.
+Published-In: Genome Res. Jun;14(6):1147-59.
+Published-Year: 2004
+Published-doi: 10.1101/gr.1917404
+Published-URL: http://pubmed.org/15140833
+