[Cdd-commits] r397 - in projects/med/trunk/debian-med: debian menu/bio menu/bio-dev tasks

CDD Subversion Commit noreply at alioth.debian.org
Mon Sep 26 11:25:10 UTC 2005 

Author: tille
Date: Mon Sep 26 11:25:09 2005
New Revision: 397

Added:
   projects/med/trunk/debian-med/menu/bio-dev/libbio-ruby.txt
   projects/med/trunk/debian-med/menu/bio/mipe.txt
   projects/med/trunk/debian-med/menu/bio/sim4.txt
Modified:
   projects/med/trunk/debian-med/debian/changelog
   projects/med/trunk/debian-med/debian/control.stub
   projects/med/trunk/debian-med/tasks/bio
   projects/med/trunk/debian-med/tasks/bio-dev
Log:
Added some more dependencies


Modified: projects/med/trunk/debian-med/debian/changelog
==============================================================================
--- projects/med/trunk/debian-med/debian/changelog	(original)
+++ projects/med/trunk/debian-med/debian/changelog	Mon Sep 26 11:25:09 2005
@@ -1,3 +1,15 @@
+debian-med (0.9.1) unstable; urgency=low
+
+  * Rebuilded with cdd-dev 0.3.11 (and increased versioned dependency
+    because 0.3.10 created broken *.dsc file)
+    Closes: #328428
+  * Standards-Version: 3.6.2 (no changes necessary)
+  * Added dependencies:
+    med-bio:     mipe, sim4, perlprimer
+    med-bio-dev: libbio-ruby
+
+ -- Andreas Tille <tille at debian.org>  Sun, 25 Sep 2005 21:14:47 +0200
+
 debian-med (0.9) unstable; urgency=low
 
   * Removed gnutrion from tools because it was removed from Debian at all

Modified: projects/med/trunk/debian-med/debian/control.stub
==============================================================================
--- projects/med/trunk/debian-med/debian/control.stub	(original)
+++ projects/med/trunk/debian-med/debian/control.stub	Mon Sep 26 11:25:09 2005
@@ -2,8 +2,8 @@
 Section: misc
 Priority: extra
 Maintainer: Andreas Tille <tille at debian.org>
-Build-Depends-Indep: debhelper (>= 4), cdd-dev (>= 0.3.9)
-Standards-Version: 3.6.1
+Build-Depends-Indep: debhelper (>= 4), cdd-dev (>= 0.3.11)
+Standards-Version: 3.6.2
 
 Package: med
 Architecture: all

Added: projects/med/trunk/debian-med/menu/bio-dev/libbio-ruby.txt
==============================================================================
--- (empty file)
+++ projects/med/trunk/debian-med/menu/bio-dev/libbio-ruby.txt	Mon Sep 26 11:25:09 2005
@@ -0,0 +1,12 @@
+BioRuby tools for computational molecular biology
+
+Some information about libbio-ruby from the Debian-Med project.
+
+ BioRuby project aims to implement an integrated environment for
+ Bioinformatics with Ruby language. Design philosophy of the BioRuby library
+ is KISS (keep it simple and stupid) to maximize the usability and the
+ efficiency for biologists as a daily tool. The project was started in Japan
+ and supported by University of Tokyo (Human Genome Center), Kyoto University
+ (Bioinformatics Center) and the Open Bio Foundation.
+
+Homepage: http://www.bioruby.org/

Added: projects/med/trunk/debian-med/menu/bio/mipe.txt
==============================================================================
--- (empty file)
+++ projects/med/trunk/debian-med/menu/bio/mipe.txt	Mon Sep 26 11:25:09 2005
@@ -0,0 +1,44 @@
+Tools to store PCR-derived data
+
+Some information about mipe from the Debian-Med project.
+
+ MIPE provides a standard format to exchange and/or storage of all
+ information associated with PCR experiments using a flat text file. This will:
+  * allow for exchange of PCR data between researchers/laboratories
+  * enable traceability of the data
+  * prevent problems when submitting data to dbSTS or dbSNP
+  * enable the writing of standard scripts to extract data (e.g. a
+    list of PCR primers, SNP positions or haplotypes for different animals)
+
+ Although this tool can be used for data storage, it's primary focus
+ should be data exchange. For larger reporisitories, relational databases
+ are more appropriate for storage of these data. The MIPE format could
+ then be used as a standard format to import into and/or export from
+ these databases.
+
+Homepage: http://mipe.sourceforge.net
+
+You should also read the relevant man pages:
+
+   man mipe06to07
+   man mipe08to09
+   man mipe0_9to1_0
+   man mipe2dbSTS
+   man mipe2fas
+   man mipe2html
+   man mipe2pcroverview
+   man mipe2pcrprimers
+   man mipe2putativesbeprimers
+   man mipe2sbeprimers
+   man mipe2snps
+   man mipeCheckSanity
+   man removePcrFromMipe
+   man removeSbeFromMipe
+   man sbe2mipe
+   man snp2mipe
+   man snpPosOnDesign
+   man snpPosOnSource
+   man csv2mipe
+   man genotype2mipe
+   man mipe2genotypes
+   man removeSnpFromMipe

Added: projects/med/trunk/debian-med/menu/bio/sim4.txt
==============================================================================
--- (empty file)
+++ projects/med/trunk/debian-med/menu/bio/sim4.txt	Mon Sep 26 11:25:09 2005
@@ -0,0 +1,25 @@
+Tool for aligning cDNA and genomic DNA
+
+Some information about sim4 from the Debian-Med project.
+
+ sim4 is a similarity-based tool for aligning an expressed DNA sequence
+ (EST, cDNA, mRNA) with a genomic sequence for the gene. It also detects end
+ matches when the two input sequences overlap at one end (i.e., the start of
+ one sequence overlaps the end of the other).
+
+ sim4 employs a blast-based technique to first determine the basic matching
+ blocks representing the "exon cores". In this first stage, it detects all
+ possible exact matches of W-mers (i.e., DNA words of size W) between the two
+ sequences and extends them to maximal scoring gap-free segments. In the
+ second stage, the exon cores are extended into the adjacent as-yet-unmatched
+ fragments using greedy alignment algorithms, and heuristics are used to favor
+ configurations that conform to the splice-site recognition signals (GT-AG,
+ CT-AC). If necessary, the process is repeated with less stringent parameters
+ on the unmatched fragments.
+
+
+Homepage: http://www.bx.psu.edu/miller_lab/
+
+Please read the man page of this project:
+
+     man sim4

Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Mon Sep 26 11:25:09 2005
@@ -21,5 +21,9 @@
 
 Depends: muscle, gff2aplot, t-coffee, gff2ps, gdpc
 
+Depends: mipe, perlprimer
+
+Depends: sim4
+
 Suggests: arb
 Why: non-free can only be suggested

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	Mon Sep 26 11:25:09 2005
@@ -10,3 +10,5 @@
 Why: libmotif-dev conflicts lesstif-dev, so if someone wants to install libmotif-dev it must be possible to deinstall libvibrant6-dev without beeing forced to deinstall med-bio-dev as well
 
 Depends: python-biopython
+
+Depends: libbio-ruby

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