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 <[email protected]> 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 <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
