[med-svn] r5468 - in trunk/packages: . pal2nal pal2nal/trunk pal2nal/trunk/debian pal2nal/trunk/debian/source
Steffen Möller
moeller at alioth.debian.org
Tue Nov 23 15:37:37 UTC 2010
Author: moeller
Date: 2010-11-23 15:37:36 +0000 (Tue, 23 Nov 2010)
New Revision: 5468
Added:
trunk/packages/pal2nal/
trunk/packages/pal2nal/trunk/
trunk/packages/pal2nal/trunk/debian/
trunk/packages/pal2nal/trunk/debian/README.Debian
trunk/packages/pal2nal/trunk/debian/README.source
trunk/packages/pal2nal/trunk/debian/changelog
trunk/packages/pal2nal/trunk/debian/compat
trunk/packages/pal2nal/trunk/debian/control
trunk/packages/pal2nal/trunk/debian/copyright
trunk/packages/pal2nal/trunk/debian/docs
trunk/packages/pal2nal/trunk/debian/examples
trunk/packages/pal2nal/trunk/debian/pal2nal.install
trunk/packages/pal2nal/trunk/debian/rules
trunk/packages/pal2nal/trunk/debian/source/
trunk/packages/pal2nal/trunk/debian/source/format
Log:
Added package for pal2nal. It seems to work, a few bits are
pending, in particular there is no license for it, yet.
Added: trunk/packages/pal2nal/trunk/debian/README.Debian
===================================================================
--- trunk/packages/pal2nal/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/README.Debian 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1,7 @@
+pal2nal for Debian
+------------------
+
+This package comes without a license and as such remains unredistributable
+untils this has been clarified with upstream.
+
+ -- Steffen Moeller <steffen_moeller at gmx.de> Tue, 23 Nov 2010 16:18:36 +0100
Added: trunk/packages/pal2nal/trunk/debian/README.source
===================================================================
--- trunk/packages/pal2nal/trunk/debian/README.source (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/README.source 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1,7 @@
+pal2nal for Debian
+------------------
+
+All source files where left intact,
+the name of the directory was changed
+to pal2nal-13, only.
+
Added: trunk/packages/pal2nal/trunk/debian/changelog
===================================================================
--- trunk/packages/pal2nal/trunk/debian/changelog (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/changelog 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1,5 @@
+pal2nal (13-1) unstable; urgency=low
+
+ * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+
+ -- Steffen Moeller <steffen_moeller at gmx.de> Tue, 23 Nov 2010 16:18:36 +0100
Added: trunk/packages/pal2nal/trunk/debian/compat
===================================================================
--- trunk/packages/pal2nal/trunk/debian/compat (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/compat 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1 @@
+7
Added: trunk/packages/pal2nal/trunk/debian/control
===================================================================
--- trunk/packages/pal2nal/trunk/debian/control (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/control 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1,33 @@
+Source: pal2nal
+Section: science
+Priority: extra
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Pjotr Prins <pjotr.debian at thebird.nl>, Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 7.0.50~)
+Standards-Version: 3.9.1
+Homepage: http://www.bork.embl.de/pal2nal
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/pal2nal/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pal2nal/trunk/?rev=0&sc=0
+
+Package: pal2nal
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: paml
+Description: converts proteins to genomic DNA alignment
+ PAL2NAL is a program that converts a multiple sequence alignment
+ of proteins and the corresponding DNA (or mRNA) sequences into
+ a codon-based DNA alignment. The program automatically assigns
+ the corresponding codon sequence even if the input DNA sequence
+ has mismatches with the input protein sequence, or contains UTRs,
+ polyA tails. It can also deal with frame shifts in the input
+ alignment, which is suitable for the analysis of pseudogenes.
+ The resulting codon-based DNA alignment can further be subjected
+ to the calculation of synonymous (Ks) and non-synonymous (Ka)
+ substitution rates.
+ .
+ If you use PAL2NAL, please cite the following paper:
+ Mikita Suyama, David Torrents, and Peer Bork (2006)
+ PAL2NAL: robust conversion of protein sequence alignment into
+ the corresponding codon alignments.
+ Nucleic Acids Res. 34:W609-W612.
+
Added: trunk/packages/pal2nal/trunk/debian/copyright
===================================================================
--- trunk/packages/pal2nal/trunk/debian/copyright (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/copyright 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1,27 @@
+This work was packaged for Debian by:
+
+ Steffen Moeller <moeller at debian.org> on Tue, 23 Nov 2010 16:18:36 +0100
+
+It was downloaded from:
+
+ http://www.bork.embl.de/pal2nal/distribution/pal2nal.v13.tar.gz
+
+Upstream Authors:
+
+ Mikita Suyama <mikita at genome.med.kyoto-u.ac.jp>
+
+Copyright:
+
+ Copyright (C) 2006-2010 Mikita Suyama, David Torrents, and Peer Bork
+ and their respective employing institute.
+
+License:
+
+ <Put the license of the package here indented by 4 spaces>
+
+The Debian packaging is:
+
+ Copyright (C) 2010 Steffen Moeller <moeller at debian.org>
+
+and is licensed under the GPL version 3,
+see "/usr/share/common-licenses/GPL-3".
Added: trunk/packages/pal2nal/trunk/debian/docs
===================================================================
--- trunk/packages/pal2nal/trunk/debian/docs (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/docs 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1 @@
+README
Added: trunk/packages/pal2nal/trunk/debian/examples
===================================================================
--- trunk/packages/pal2nal/trunk/debian/examples (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/examples 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1,2 @@
+test.aln
+test.nuc
Added: trunk/packages/pal2nal/trunk/debian/pal2nal.install
===================================================================
--- trunk/packages/pal2nal/trunk/debian/pal2nal.install (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/pal2nal.install 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1 @@
+./pal2nal.pl /usr/bin
Added: trunk/packages/pal2nal/trunk/debian/rules
===================================================================
--- trunk/packages/pal2nal/trunk/debian/rules (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/rules 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
Property changes on: trunk/packages/pal2nal/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/pal2nal/trunk/debian/source/format
===================================================================
--- trunk/packages/pal2nal/trunk/debian/source/format (rev 0)
+++ trunk/packages/pal2nal/trunk/debian/source/format 2010-11-23 15:37:36 UTC (rev 5468)
@@ -0,0 +1 @@
+3.0 (quilt)
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