[Cdd-commits] r1056 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Fri Sep  5 12:44:03 2008
New Revision: 1056

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
More BioLinux packages (revised, because BioLinux packaging seems to be dirty regarding assembling different projects with different licenses)


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 12:44:03 2008
@@ -1939,3 +1939,56 @@
  .
  This package is include into BioLinux distribution
  http://envgen.nox.ac.uk/biolinux.html
+
+Depends: caftools
+Homepage: http://www.sanger.ac.uk/Software/formats/CAF/userguide.shtml
+License: Free for non-commercial purposes
+Responsible: BioLinux <helpdesk at nebc.nox.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: Tools to maintain DNA sequence assemblies
+ This is V2 of the CAF (Common Assembly Format) C-tools.  It comprises
+ a set of libraries and programs for manipulating DNA sequence
+ assemblies using CAF files.
+ .
+ The CAF specification can be found at:
+ http://www.sanger.ac.uk/Software/formats/CAF/
+ .
+ The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
+ maintains a package called bio-linux-assembly-conversion-tools which
+ contains caftools and roche2gap in one package with the following
+ description:
+ .
+ Conversion tools for handling 454 assemblies.
+ .
+ This package contains code from different authors that allow sequence
+ assemblies to be converted into formats such as CAF (Common Assembly
+ Format) or GAP4. This package includes tools to convert assemblies
+ from Newbler's ace format for loading into a gap4 assembly.
+
+Depends: roche454ace2caf
+Homepage: http://genome.imb-jena.de/software/roche454ace2caf/
+License: not specified
+Responsible: BioLinux <helpdesk at nebc.nox.ac.uk>
+Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
+Pkg-Description: convert GS20 or FLX assemblies into CAF format
+ Some tools to convert GS20 or FLX assemblies (454Contigs.ace) into
+ CAF format so that these are correct viewable/editable/... whithin
+ the staden package (gap4).  You have then access to "hidden data",
+ exact aligned trace and there positions, base values etc and whith
+ staden-1-7-0 you have graphical access to the associated flowgramm
+ traces (SFF format).
+ .
+ Description, Goals - please take a look at
+ http://genome.imb-jena.de/software/roche454ace2caf/Poster_UserMeeting_GS20_Munich_070328.pdf
+ .
+ The BioLinux distribution http://envgen.nox.ac.uk/biolinux.html
+ maintains a package called bio-linux-assembly-conversion-tools which
+ contains caftools and roche2gap in one package with the following
+ description:
+ .
+ Conversion tools for handling 454 assemblies.
+ .
+ This package contains code from different authors that allow sequence
+ assemblies to be converted into formats such as CAF (Common Assembly
+ Format) or GAP4. This package includes tools to convert assemblies
+ from Newbler's ace format for loading into a gap4 assembly.