Author: osallou-guest Date: 2011-12-14 15:59:00 +0000 (Wed, 14 Dec 2011) New Revision: 8956
Added: trunk/packages/clustalo/trunk/debian/ trunk/packages/clustalo/trunk/debian/changelog trunk/packages/clustalo/trunk/debian/clustalo.1 trunk/packages/clustalo/trunk/debian/clustalo.dirs trunk/packages/clustalo/trunk/debian/clustalo.manpages trunk/packages/clustalo/trunk/debian/compat trunk/packages/clustalo/trunk/debian/control trunk/packages/clustalo/trunk/debian/copyright trunk/packages/clustalo/trunk/debian/docs trunk/packages/clustalo/trunk/debian/libclustalo-dev.dirs trunk/packages/clustalo/trunk/debian/rules trunk/packages/clustalo/trunk/debian/source/ trunk/packages/clustalo/trunk/debian/source/format trunk/packages/clustalo/trunk/debian/watch Log: [svn-inject] Applying Debian modifications (1.0.3-1) to trunk Property changes on: trunk/packages/clustalo/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/clustalo/trunk/debian/changelog =================================================================== --- trunk/packages/clustalo/trunk/debian/changelog (rev 0) +++ trunk/packages/clustalo/trunk/debian/changelog 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1,5 @@ +clustalo (1.0.3-1) UNRELEASED; urgency=low + + * Initial release (Closes: #652031) + + -- Olivier Sallou <[email protected]> Wed, 14 Dec 2011 11:21:56 +0100 Added: trunk/packages/clustalo/trunk/debian/clustalo.1 =================================================================== --- trunk/packages/clustalo/trunk/debian/clustalo.1 (rev 0) +++ trunk/packages/clustalo/trunk/debian/clustalo.1 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1,49 @@ +.TH clustalo 1 "December 14, 2011" "version 1.1.0" "USER COMMANDS" +.SH NAME +clustalo \- General purpose multiple sequence alignment program for proteins +.SH SYNOPSIS +.B clustalo +[\-h] +.SH DESCRIPTION +Clustal-Omega is a general purpose multiple sequence alignment (MSA) +program for proteins. It produces high quality MSAs and is capable of +handling data-sets of hundreds of thousands of sequences in reasonable +time. + +In default mode, users give a file of sequences to be aligned and +these are clustered to produce a guide tree and this is used to guide +a "progressive alignment" of the sequences. There are also facilities +for aligning existing alignments to each other, aligning a sequence to +an alignment and for using a hidden Markov model (HMM) to help guide +an alignment of new sequences that are homologous to the sequences +used to make the HMM. This latter procedure is referred to as +"external profile alignment" or EPA. + +Clustal-Omega uses HMMs for the alignment engine, based on the HHalign +package from Johannes Soeding [1]. Guide trees are made using an +enhanced version of mBed [2] which can cluster very large numbers of +sequences in O(N*log(N)) time. Multiple alignment then proceeds by +aligning larger and larger alignments using HHalign, following the +clustering given by the guide tree. + +In its current form Clustal-Omega can only align protein sequences but +not DNA/RNA sequences. It is envisioned that DNA/RNA will become +available in a future version. +.PP +.SH USAGE +Tool usage is available in /usr/share/doc/clustalo/README. +.PP +.SH DEVELOPMENT +Headers and libraries are available in libclustalo-dev package. +.SH CITING +Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, + Remmert M, Söding J, Thompson JD, Higgins DG (2011). +Fast, scalable generation of high-quality protein multiple sequence alignments + using Clustal Omega. Mol Syst Biol 7. +.PP +.SH AUTHOR +Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging +Conway Institute UCD Dublin (clustalw (at) ucd.ie) - clustalo + + + Added: trunk/packages/clustalo/trunk/debian/clustalo.dirs =================================================================== --- trunk/packages/clustalo/trunk/debian/clustalo.dirs (rev 0) +++ trunk/packages/clustalo/trunk/debian/clustalo.dirs 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1 @@ +usr Added: trunk/packages/clustalo/trunk/debian/clustalo.manpages =================================================================== --- trunk/packages/clustalo/trunk/debian/clustalo.manpages (rev 0) +++ trunk/packages/clustalo/trunk/debian/clustalo.manpages 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1 @@ +debian/clustalo.1 Added: trunk/packages/clustalo/trunk/debian/compat =================================================================== --- trunk/packages/clustalo/trunk/debian/compat (rev 0) +++ trunk/packages/clustalo/trunk/debian/compat 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1 @@ +8 Added: trunk/packages/clustalo/trunk/debian/control =================================================================== --- trunk/packages/clustalo/trunk/debian/control (rev 0) +++ trunk/packages/clustalo/trunk/debian/control 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1,28 @@ +Source: clustalo +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +DM-Upload-Allowed: yes +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/clustalo/trunk/ +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/clustalo/trunk/?rev=0&sc=0 +Homepage: http://www.clustal.org/omega/ +Build-Depends: debhelper (>= 8.0.0), libargtable2-dev +Standards-Version: 3.9.2 + +Package: clustalo +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, libargtable2-0 +Description: General purpose multiple sequence alignment program for proteins + Clustal-Omega is a general purpose multiple sequence alignment (MSA) + program for proteins. It produces high quality MSAs and is capable of + handling data-sets of hundreds of thousands of sequences in reasonable + time. + +Package: libclustalo-dev +Architecture: any +Section: libdevel +Depends: ${shlibs:Depends}, ${misc:Depends}, libargtable2-dev, ${binary:Version} +Description: library to embed Clustal Omega + This package contains headers and libraries to include + Clustal Omega in a program. Added: trunk/packages/clustalo/trunk/debian/copyright =================================================================== --- trunk/packages/clustalo/trunk/debian/copyright (rev 0) +++ trunk/packages/clustalo/trunk/debian/copyright 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1,33 @@ +Format: http://dep.debian.net/deps/dep5 +Upstream-Name: clustalo +Source: http://www.clustal.org/omega/ + +License: GPL-2+ + This package 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 package 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 program. If not, see <http://www.gnu.org/licenses/> + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". + +Files: src/squid/* +Copyright: 1992-2002 Washington University School of Medicine +License: GPL-2+ + + +Files: * +Copyright: 2010 UCD Dublin <[email protected]> +License: GPL-2+ + +Files: debian/* +Copyright: 2011 Olivier Sallou <[email protected]> +License: GPL-2+ Added: trunk/packages/clustalo/trunk/debian/docs =================================================================== --- trunk/packages/clustalo/trunk/debian/docs (rev 0) +++ trunk/packages/clustalo/trunk/debian/docs 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1 @@ +README Added: trunk/packages/clustalo/trunk/debian/libclustalo-dev.dirs =================================================================== --- trunk/packages/clustalo/trunk/debian/libclustalo-dev.dirs (rev 0) +++ trunk/packages/clustalo/trunk/debian/libclustalo-dev.dirs 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1 @@ +usr Added: trunk/packages/clustalo/trunk/debian/rules =================================================================== --- trunk/packages/clustalo/trunk/debian/rules (rev 0) +++ trunk/packages/clustalo/trunk/debian/rules 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1,20 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +%: + dh $@ + +override_dh_install: + dh_install + rm -rf debian/tmp/usr/lib/pkgconfig + rm -f debian/tmp/usr/lib/libclustalo.la + mv debian/tmp/usr/include debian/libclustalo-dev/usr + mv debian/tmp/usr/lib debian/libclustalo-dev/usr + mv debian/tmp/usr/bin debian/clustalo/usr + +override_dh_clean: + dh_clean + rm -f _configs.sed Property changes on: trunk/packages/clustalo/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/clustalo/trunk/debian/source/format =================================================================== --- trunk/packages/clustalo/trunk/debian/source/format (rev 0) +++ trunk/packages/clustalo/trunk/debian/source/format 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/clustalo/trunk/debian/watch =================================================================== --- trunk/packages/clustalo/trunk/debian/watch (rev 0) +++ trunk/packages/clustalo/trunk/debian/watch 2011-12-14 15:59:00 UTC (rev 8956) @@ -0,0 +1,5 @@ +# Compulsory line, this is a version 3 file +version=3 + +http://www.clustal.org/omega/clustal-omega-(.*)\.tar\.gz + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
