[med-svn] r8956 - in trunk/packages/clustalo/trunk: . debian debian/source
olivier sallou
osallou-guest at alioth.debian.org
Wed Dec 14 15:59:01 UTC 2011
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 <olivier.sallou at irisa.fr> 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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <olivier.sallou at irisa.fr>
+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 <clustalw at ucd.ie>
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+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
+
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