Upgrading to GitLab 12.1.0.

Commit b91b1f18 authored by Olivier Sallou's avatar Olivier Sallou

[svn-inject] Applying Debian modifications (1.0.3-1) to trunk

parent b88aea89
clustalo (1.0.3-1) UNRELEASED; urgency=low
* Initial release (Closes: #652031)
-- Olivier Sallou <olivier.sallou@irisa.fr> Wed, 14 Dec 2011 11:21:56 +0100
.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
Source: clustalo
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Olivier Sallou <olivier.sallou@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.
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@ucd.ie>
License: GPL-2+
Files: debian/*
Copyright: 2011 Olivier Sallou <olivier.sallou@irisa.fr>
License: GPL-2+
#!/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
# Compulsory line, this is a version 3 file
version=3
http://www.clustal.org/omega/clustal-omega-(.*)\.tar\.gz
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