[med-svn] r10989 - in trunk/packages: . proalign proalign/trunk proalign/trunk/debian

[Andreas Tille]

Author: tille
Date: 2012-05-24 12:42:36 +0000 (Thu, 24 May 2012)
New Revision: 10989

Added:
   trunk/packages/proalign/
   trunk/packages/proalign/trunk/
   trunk/packages/proalign/trunk/debian/
   trunk/packages/proalign/trunk/debian/changelog
   trunk/packages/proalign/trunk/debian/compat
   trunk/packages/proalign/trunk/debian/control
   trunk/packages/proalign/trunk/debian/copyright
   trunk/packages/proalign/trunk/debian/upstream
   trunk/packages/proalign/trunk/debian/watch
Log:
Turn information from tasks file and WNPP in something machine readable


Added: trunk/packages/proalign/trunk/debian/changelog
===================================================================
--- trunk/packages/proalign/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/changelog	2012-05-24 12:42:36 UTC (rev 10989)
@@ -0,0 +1,5 @@
+proalign (0.603-1) unstable; urgency=low
+
+  * Initial release (Closes: #378290)
+
+ -- Andreas Tille <tille at debian.org>  Thu, 24 May 2012 14:30:13 +0200

Added: trunk/packages/proalign/trunk/debian/compat
===================================================================
--- trunk/packages/proalign/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/compat	2012-05-24 12:42:36 UTC (rev 10989)
@@ -0,0 +1 @@
+9

Added: trunk/packages/proalign/trunk/debian/control
===================================================================
--- trunk/packages/proalign/trunk/debian/control	                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/control	2012-05-24 12:42:36 UTC (rev 10989)
@@ -0,0 +1,28 @@
+Source: proalign
+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: http://ueg.ulb.ac.be/ProAlign/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/proalign/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/proalign/trunk/
+
+Package: proalign
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Probabilistic multiple alignment program
+ ProAlign performs probabilistic sequence alignments using hidden Markov
+ models (HMM). It includes a graphical interface (GUI) allowing to (i)
+ perform alignments of nucleotide or amino-acid sequences, (ii) view the
+ quality of solutions, (iii) filter the unreliable alignment regions and
+ (iv) export alignments to other softwares.
+ .
+ ProAlign uses a progressive method, such that multiple alignment is
+ created stepwise by performing pairwise alignments in the nodes of a
+ guide tree. Sequences are described with vectors of character
+ probabilities, and each pairwise alignment reconstructs the ancestral
+ (parent) sequence by computing the probabilities of different
+ characters according to an evolutionary model.
\ No newline at end of file

Added: trunk/packages/proalign/trunk/debian/copyright
===================================================================
--- trunk/packages/proalign/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/copyright	2012-05-24 12:42:36 UTC (rev 10989)
@@ -0,0 +1,35 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ProAlign
+Upstream-Contact: Ari Löytynoja & Michel C. Milinkovitch
+Source: http://ueg.ulb.ac.be/ProAlign/
+
+Files: *
+Copyright: © 2002-2003 Ari Löytynoja and Michel C. Milinkovitch.
+License: GPL-2+
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+License: GPL-2+
+ This program is free software; you can redistribute it
+ and/or modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later
+ version.
+ .
+ This program is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the implied
+ warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE.  See the GNU General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
+

Added: trunk/packages/proalign/trunk/debian/upstream
===================================================================
--- trunk/packages/proalign/trunk/debian/upstream	                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/upstream	2012-05-24 12:42:36 UTC (rev 10989)
@@ -0,0 +1,12 @@
+Reference:
+  Author: Ari Löytynoja and Michel C Milinkovitch
+  Title: A hidden Markov model for progressive multiple alignment
+  Journal: Bioinformatics
+  Year: 2003
+  Volume: 19
+  Number: 12
+  Pages: 1505-13
+  DOI: 10.1093/bioinformatics/btg193
+  PMID: 12912831
+  URL: http://bioinformatics.oxfordjournals.org/content/19/12/1505
+  eprint: http://bioinformatics.oxfordjournals.org/content/19/12/1505.full.pdf+html

Added: trunk/packages/proalign/trunk/debian/watch
===================================================================
--- trunk/packages/proalign/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/proalign/trunk/debian/watch	2012-05-24 12:42:36 UTC (rev 10989)
@@ -0,0 +1,4 @@
+version=3
+
+opts=dversionmangle=s/\.// \
+  http://ueg.ulb.ac.be/ProAlign/download/src/proalign_(.+)\.tgz