[med-svn] r15048 - trunk/packages/staden/trunk/debian

Tue Oct 29 19:29:33 UTC 2013

Author: tille
Date: 2013-10-29 19:29:33 +0000 (Tue, 29 Oct 2013)
New Revision: 15048

Modified:
   trunk/packages/staden/trunk/debian/changelog
   trunk/packages/staden/trunk/debian/control
   trunk/packages/staden/trunk/debian/copyright
   trunk/packages/staden/trunk/debian/watch
Log:
Merge code available from competing packaging from git://anonscm.debian.org/git/collab-maint/staden.git into this place where we should continue the work on staden


Modified: trunk/packages/staden/trunk/debian/changelog
===================================================================

--- trunk/packages/staden/trunk/debian/changelog	2013-10-29 18:54:39 UTC (rev 15047)
+++ trunk/packages/staden/trunk/debian/changelog	2013-10-29 19:29:33 UTC (rev 15048)
@@ -1,5 +1,7 @@
 staden (2.0.0b9-1) UNRELEASED; urgency=low
 
+  * Initial release to Debian (Closes: #710324)
+
   * Fix dependency for Debian after realising io-lib was already packaged
     as libstaden-read
 

Modified: trunk/packages/staden/trunk/debian/control
===================================================================
--- trunk/packages/staden/trunk/debian/control	2013-10-29 18:54:39 UTC (rev 15047)
+++ trunk/packages/staden/trunk/debian/control	2013-10-29 19:29:33 UTC (rev 15048)
@@ -7,6 +7,8 @@
  tcl8.5-dev, tk8.5-dev, tklib, libpng12-dev, libncurses5-dev, iwidgets4,
  libcurl4-openssl-dev
 Standards-Version: 3.9.3
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/staden/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/staden/trunk/
 Homepage: https://staden.sf.net
 
 Package: staden
@@ -14,13 +16,84 @@
 Depends: ${misc:Depends}, ${shlibs:Depends}, staden-common (= ${source:Version}), staden-io-lib-utils
 Recommends: staden-doc
 Description: DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin)
- A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and 
- analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
+ Staden is a fully developed set of DNA sequence assembly (Gap4 and
+ Gap5), editing and analysis tools (Spin).
+ .
+ Gap4 performs sequence assembly, contig ordering based on read pair
+ data, contig joining based on sequence comparisons, assembly checking,
+ repeat searching, experiment suggestion, read pair analysis and contig
+ editing. It has graphical views of contigs, templates, readings and
+ traces which all scroll in register. Contig editor searches and
+ experiment suggestion routines use confidence values to calculate the
+ confidence of the consensus sequence and hence identify only places
+ requiring visual trace inspection or extra data. The result is
+ extremely rapid finishing and a consensus of known accuracy.
+ .
+ Pregap4 provides a graphical user interface to set up the processing
+ required to prepare trace data for assembly or analysis, and automates
+ these processes.
+ .
+ Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and
+ ZTR trace files.
+ .
+ Prefinish analyses partially completed sequence assemblies and suggests
+ the most efficient set of experiments to help finish the project.
+ .
+ Tracediff and hetscan automatically locate mutations by comparing trace
+ data against reference traces. They annotate the mutations found ready
+ for viewing in gap4.
+ .
+ Spin analyses nucleotide sequences to find genes, restriction sites,
+ motifs, etc. It can perform translations, find open reading frames,
+ count codons, etc. Many results are presented graphically and a sliding
+ sequence window is linked to the graphics cursor. Spin also compares
+ pairs of sequences in many ways. It has very rapid dot matrix analysis,
+ global and local alignment algorithms, plus a sliding sequence window
+ linked to the graphical plots. It can compare nucleic acid against
+ nucleic acid, protein against protein, and protein against nucleic
+ acid.
 
 Package: staden-common
 Architecture: all
 Depends: ${misc:Depends}
 Recommends: ksh | zsh
 Description: Architecture independent files for Staden
- This package contains the architecture independent data files and scripts that
- come with the Staden package.
+ Staden is a fully developed set of DNA sequence assembly (Gap4 and
+ Gap5), editing and analysis tools (Spin).
+ .
+ Gap4 performs sequence assembly, contig ordering based on read pair
+ data, contig joining based on sequence comparisons, assembly checking,
+ repeat searching, experiment suggestion, read pair analysis and contig
+ editing. It has graphical views of contigs, templates, readings and
+ traces which all scroll in register. Contig editor searches and
+ experiment suggestion routines use confidence values to calculate the
+ confidence of the consensus sequence and hence identify only places
+ requiring visual trace inspection or extra data. The result is
+ extremely rapid finishing and a consensus of known accuracy.
+ .
+ Pregap4 provides a graphical user interface to set up the processing
+ required to prepare trace data for assembly or analysis, and automates
+ these processes.
+ .
+ Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and
+ ZTR trace files.
+ .
+ Prefinish analyses partially completed sequence assemblies and suggests
+ the most efficient set of experiments to help finish the project.
+ .
+ Tracediff and hetscan automatically locate mutations by comparing trace
+ data against reference traces. They annotate the mutations found ready
+ for viewing in gap4.
+ .
+ Spin analyses nucleotide sequences to find genes, restriction sites,
+ motifs, etc. It can perform translations, find open reading frames,
+ count codons, etc. Many results are presented graphically and a sliding
+ sequence window is linked to the graphics cursor. Spin also compares
+ pairs of sequences in many ways. It has very rapid dot matrix analysis,
+ global and local alignment algorithms, plus a sliding sequence window
+ linked to the graphical plots. It can compare nucleic acid against
+ nucleic acid, protein against protein, and protein against nucleic
+ acid.
+ .
+ This package contains the architecture independent data files and
+ scripts that come with the Staden package.

Modified: trunk/packages/staden/trunk/debian/copyright
===================================================================
--- trunk/packages/staden/trunk/debian/copyright	2013-10-29 18:54:39 UTC (rev 15047)
+++ trunk/packages/staden/trunk/debian/copyright	2013-10-29 19:29:33 UTC (rev 15048)
@@ -1,7 +1,7 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: Staden
-Upstream-Contact: James Bonfield
-Source: https://sourceforge.net/p/staden/code/HEAD/tree/
+Upstream-Name: the Staden Package
+Upstream-Contact: http://sourceforge.net/p/staden/bugs/
+Source: http://sourceforge.net/projects/staden/files/
 
 Files: *
 Copyright: 2005-2013, James Bonfield

Modified: trunk/packages/staden/trunk/debian/watch
===================================================================
--- trunk/packages/staden/trunk/debian/watch	2013-10-29 18:54:39 UTC (rev 15047)
+++ trunk/packages/staden/trunk/debian/watch	2013-10-29 19:29:33 UTC (rev 15048)
@@ -1,2 +1,5 @@
+# Run the "uscan" command to check for upstream updates and more.
 version=3
-http://sf.net/staden/staden-([0-9ab.]*).tar.(?:bz2|gz)
+# use qa.debian.org redirector; see man uscan
+opts=dversionmangle=s/~b/b/ \
+http://sf.net/staden/staden-(\d.*)-src\.tar\.gz


