[med-svn] r11020 - in trunk/packages: . pcma pcma/trunk pcma/trunk/debian

[Andreas Tille]

Author: tille
Date: 2012-05-27 07:58:59 +0000 (Sun, 27 May 2012)
New Revision: 11020

Added:
   trunk/packages/pcma/
   trunk/packages/pcma/trunk/
   trunk/packages/pcma/trunk/debian/
   trunk/packages/pcma/trunk/debian/changelog
   trunk/packages/pcma/trunk/debian/compat
   trunk/packages/pcma/trunk/debian/control
   trunk/packages/pcma/trunk/debian/copyright
   trunk/packages/pcma/trunk/debian/rules
   trunk/packages/pcma/trunk/debian/upstream
Log:
Take over information from task file


Added: trunk/packages/pcma/trunk/debian/changelog
===================================================================
--- trunk/packages/pcma/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/pcma/trunk/debian/changelog	2012-05-27 07:58:59 UTC (rev 11020)
@@ -0,0 +1,5 @@
+pcma (2-1) unstable; urgency=low
+
+  * Initial release
+
+ -- DMPT <debian-med-packaging at lists.alioth.debian.org>  Thu, 24 May 2012 14:30:13 +0200

Added: trunk/packages/pcma/trunk/debian/compat
===================================================================
--- trunk/packages/pcma/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/pcma/trunk/debian/compat	2012-05-27 07:58:59 UTC (rev 11020)
@@ -0,0 +1 @@
+9

Added: trunk/packages/pcma/trunk/debian/control
===================================================================
--- trunk/packages/pcma/trunk/debian/control	                        (rev 0)
+++ trunk/packages/pcma/trunk/debian/control	2012-05-27 07:58:59 UTC (rev 11020)
@@ -0,0 +1,28 @@
+Source: pcma
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.3
+Homepage: ftp://iole.swmed.edu/pub/PCMA/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pcma/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/pcma/trunk/
+
+Package: pcma
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Enhances: t-coffee
+Description: fast and accurate multiple sequence alignment based on profile consistency
+ PCMA (profile consistency multiple sequence alignment) is a progressive
+ multiple sequence alignment program that combines two different
+ alignment strategies. Highly similar sequences are aligned in a fast way
+ as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is
+ applied to align the relatively divergent groups based on
+ profile–profile comparison and consistency. The scoring function for
+ local alignments of pre-aligned groups is based on a novel
+ profile–profile comparison method that is a generalization of the
+ PSI-BLAST approach to profile–sequence comparison. PCMA balances speed
+ and accuracy in a flexible way and is suitable for aligning large
+ numbers of sequences.

Added: trunk/packages/pcma/trunk/debian/copyright
===================================================================
--- trunk/packages/pcma/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/pcma/trunk/debian/copyright	2012-05-27 07:58:59 UTC (rev 11020)
@@ -0,0 +1,14 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: ftp://iole.swmed.edu/pub/PCMA/
+
+Files: *
+Copyright: © 2003-2004 Jimin Pei, Ruslan Sadreyev and Nick V. Grishin
+License: non-free for commercial
+Comment:  Check with authors about licensing, they adopted code from clustalw which is now
+ free.  Thus a change might be possible
+
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: LGPL-3+
+Comment: Take over license of recent ClustalW for the packaging

Added: trunk/packages/pcma/trunk/debian/rules
===================================================================
--- trunk/packages/pcma/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/pcma/trunk/debian/rules	2012-05-27 07:58:59 UTC (rev 11020)
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@


Property changes on: trunk/packages/pcma/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/pcma/trunk/debian/upstream
===================================================================
--- trunk/packages/pcma/trunk/debian/upstream	                        (rev 0)
+++ trunk/packages/pcma/trunk/debian/upstream	2012-05-27 07:58:59 UTC (rev 11020)
@@ -0,0 +1,12 @@
+Reference:
+  Author: Jimin Pei and Ruslan Sadreyev and Nick V. Grishin
+  Title: "PCMA: fast and accurate multiple sequence alignment based on profile consistency"
+  Journal: Bioinformatics
+  Year: 2003
+  Volume: 19
+  Number: 3
+  Pages: 427-428
+  DOI: 10.1093/bioinformatics/btg008
+  PMID: 12584134
+  URL: http://bioinformatics.oxfordjournals.org/content/19/3/427.short
+  eprint: http://bioinformatics.oxfordjournals.org/content/19/3/427.full.pdf+html