[Cdd-commits] r1055 - projects/med/trunk/debian-med/tasks
CDD Subversion Commit
noreply at alioth.debian.org
Fri Sep 5 11:51:45 UTC 2008
Author: tille
Date: Fri Sep 5 11:51:45 2008
New Revision: 1055
Modified:
projects/med/trunk/debian-med/tasks/bio
projects/med/trunk/debian-med/tasks/bio-dev
Log:
Removed additional information from resolved WNPPs. Thanks to the people who worked on the packages.
Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Fri Sep 5 11:51:45 2008
@@ -43,6 +43,8 @@
work under Mac OSX only and it is not really maintained (Debian QA group).
We want to keep track of it anyway.
+Depends: maq
+
Depends: meme
Homepage: http://meme.nbcr.net/meme/
Responsible: Steffen Moeller <moeller at debian.org>
@@ -1615,42 +1617,6 @@
This package is include into BioLinux distribution
http://envgen.nox.ac.uk/biolinux.html
-Depends: maq
-Homepage: http://maq.sourceforge.net/
-License: GPL
-WNPP: 489836
-Responsible: Charles Plessy <plessy at debian.org>
-Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/?rev=0&sc=0
-Pkg-Description: maps short fixed-legth polymporphic DNA sequence reads to reference sequences
- Maq (short for Mapping and Assembly with Quality) builds mapping assemblies
- from short reads generated by the next-generation sequencing machines. It is
- particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has a
- preliminary functionality to handle ABI SOLiD data. Maq is previously known as
- mapass2.
- .
- With Maq you can:
- - Fast align Illumina/SOLiD reads to the reference genome. With the
- default options, one million pairs of reads can be mapped to the
- human genome in about 10 CPU hours with less than 1G memory.
- - Accurately measure the error probability of the alignment of each
- individual read.
- - Call the consensus genotypes, including homozygous and heterozygous
- polymorphisms, with a Phred probabilistic quality assigned to each base.
- - Find short indels with paired end reads.
- - Accurately find large scale genomic deletions and translocations with
- paired end reads.
- - Discover potential CNVs by checking read depth.
- - Evaluate the accuracy of raw base qualities from sequencers and help
- to check the systematic errors.
- .
- However, Maq can NOT:
- - Do de novo assembly. (Maq can only call the consensus by mapping reads
- to a known reference.)
- - Map shorts reads against themselves. (Maq can only find complete overlap
- between reads.)
- - Align capillary reads or 454 reads to the reference. (Maq cannot align
- reads longer than 63bp.)
-
Depends: srf
Homepage: http://srf.sourceforge.net/
License: Apache License V2.0
Modified: projects/med/trunk/debian-med/tasks/bio-dev
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-dev (original)
+++ projects/med/trunk/debian-med/tasks/bio-dev Fri Sep 5 11:51:45 2008
@@ -22,6 +22,12 @@
Depends: libajax5-dev, libnucleus5-dev
+Depends: libtfbs-perl
+
+Depends: libgo-perl
+
+Depends: r-cran-genetics, r-cran-haplo.stats
+
Depends: bioconductor
Homepage: http://www.bioconductor.org/
Responsible: Debian CRAN/BioConductor/Omegahat packaging team <pkg-bioc-devel at lists.alioth.debian.org>
@@ -149,53 +155,6 @@
investigate gene expression data from microarrays with the
statistical package R.
-Depends: libtfbs-perl
-Homepage: http://forkhead.cgb.ki.se/TFBS/
-Responsible: Steffen Moeller <moeller at debian.org>
-WNPP: 320777
-License: artistic
-Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/tfbs/trunk/?rev=0&sc=0
-Pkg-Description: Perl extension for scanning a DNA sequences for TFBS
- TFBS Perl OO modules implement classes for the representation of objects
- encountered in analysis of protein-binding sites in DNA sequences.The
- objects defined by TFBS classes include:
- * pattern definition objects, currently position specific score matrices
- (raw frequency, information content and position weight matrices)with
- methods for interconversion between matrix types, sequence searching
- with a matrix profile, sequence 'logo' drawing and matrix manipulation;
- * a composite object representing a set of position specific score
- matrices, with methods for the identification of motifs within DNA
- sequences with the set of profiles from its member matrices;
- * methods for searching pairwise alignments for patterns conserved
- in both sequences (phylogenetic footprinting) defined for both matrix
- profile and composite (matrix set) objects;
- * an object representing DNA binding site sequence, and an object
- representing sets of DNA binding sequences, with methods and helper
- classes to facilitate scanning, filtering and statistical analyses;
- * an object representing a pair of DNA binding site sequences, and an
- object representing a set of such pairs, for storage, manipulation and
- analysis of phylogenetic footprinting searches;
- * database interfaces to relational, flat file and WWW database of
- position-specifc score matrices, with methods for searching existing
- databases, as well as creating new ones containing user-defined matrices.
- * interfaces to matrix pattern generating programs
- .
- The modules within the TFBS set are fully integrated and compatible with
- Bioperl.
-
-Depends: libgo-perl
-Homepage: http://geneontology.sourceforge.net/
-Responsible: Charles Plessy <plessy at debian.org>
-WNPP: 452923
-Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/libgo-perl/trunk/?rev=0&sc=0
-License: artistic
-Pkg-Description: parses all Gene Ontology files formats and types
- This is a collection of perl code for dealing with Gene Ontologies (GO)
- and OBO style ontologies. It is part of the `go-dev' distribution, but
- this Debian package is made from the CPAN archive. This package
- contains both scripts (which can be used with no knowledge of perl),
- and libraries which will be of use to perl programmers using GO or OBO.
-
Depends: libbio-mage-utils-perl
Homepage: http://mged.sourceforge.net/
License: MIT/X
@@ -248,34 +207,3 @@
.
The LibSBML code is very portable and is supported on Linux, Windows
(native), and Mac OS X.
-
-Depends: r-cran-genetics
-Homepage: http://cran.r-project.org/web/packages/genetics
-License: GPL
-WNPP: 492114
-Responsible: Steffen Moeller <moeller at debian.org>
-Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-genetics/trunk/?rev=0&sc=0
-Pkg-Description: GNU R package for population genetics
- Classes and methods for handling genetic data. Includes The package
- provides a library for the statistics environment R that contains
- classes to represent genotypes and haplotypes at single markers up
- to multiple markers on multiple chromosomes. Function include allele
- frequencies, flagging homo/heterozygotes, flagging carriers of certain
- alleles, estimating and testing for Hardy-Weinberg disequilibrium,
- estimating and testing for linkage disequilibrium, and more.
-
-Depends: r-cran-haplo.stats
-Homepage: http://cran.r-project.org/web/packages/haplo.stats/index.html
-License: GPL
-WNPP: 492122
-Responsible: Steffen Moeller <moeller at debian.org>
-Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-haplo.stats/trunk/?rev=0&sc=0
-Pkg-Description: GNU R package for haplotype analysis
- haplo.stats: Statistical Analysis of Haplotypes with Traits and
- Covariates when Linkage Phase is Ambiguous
- A suite of S-PLUS/R routines for the analysis of indirectly measured
- haplotypes. The statistical methods assume that all subjects are
- unrelated and that haplotypes are ambiguous (due to unknown linkage
- phase of the genetic markers). The main functions are: haplo.em,
- haplo.glm, haplo.score, haplo.power, and seqhap. Copyright: 2003 Mayo
- Foundation for Medical Education and Research.
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