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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +Uploaders: Pjotr Prins <[email protected]>, Steffen Moeller <[email protected]> +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 <[email protected]> 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 <[email protected]> + +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 <[email protected]> + +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) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
