[med-svn] r1198 - trunk/packages/glam2/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Jan 26 12:56:34 UTC 2008
Author: charles-guest
Date: 2008-01-26 12:56:34 +0000 (Sat, 26 Jan 2008)
New Revision: 1198
Added:
trunk/packages/glam2/trunk/debian/examples
trunk/packages/glam2/trunk/debian/glam2-purge.1
trunk/packages/glam2/trunk/debian/glam2mask.1
trunk/packages/glam2/trunk/debian/glam2mask.1.xml
trunk/packages/glam2/trunk/debian/install
trunk/packages/glam2/trunk/debian/manpages
Removed:
trunk/packages/glam2/trunk/debian/compat
trunk/packages/glam2/trunk/debian/glam2.dirs
trunk/packages/glam2/trunk/debian/glam2.install
Modified:
trunk/packages/glam2/trunk/debian/README.Debian
trunk/packages/glam2/trunk/debian/changelog
trunk/packages/glam2/trunk/debian/control
trunk/packages/glam2/trunk/debian/copyright
trunk/packages/glam2/trunk/debian/glam2.1
trunk/packages/glam2/trunk/debian/glam2.1.xml
trunk/packages/glam2/trunk/debian/glam2format.1
trunk/packages/glam2/trunk/debian/glam2format.1.xml
trunk/packages/glam2/trunk/debian/glam2scan.1
trunk/packages/glam2/trunk/debian/glam2scan.1.xml
trunk/packages/glam2/trunk/debian/rules
Log:
Finished manpages, converted to CDBS.
Modified: trunk/packages/glam2/trunk/debian/README.Debian
===================================================================
--- trunk/packages/glam2/trunk/debian/README.Debian 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/README.Debian 2008-01-26 12:56:34 UTC (rev 1198)
@@ -1,10 +1,6 @@
glam2 for Debian
----------------
-This is a first shot at GLAM2 in order to have it in the archive. Several issues remain:
+We renamed purge glam2-purge, to avoid namespace collision.
- * No copyright information in the sources, the upstream author confirmed "public domain" status and it is also found here: http://bioinformatics.org.au/glam2/doc/
- * man pages are missing
- * doc-base entries still missing.
-
-- Steffen Moeller <moeller at debian.org> Tue, 13 Nov 2007 00:35:50 +0100
Modified: trunk/packages/glam2/trunk/debian/changelog
===================================================================
--- trunk/packages/glam2/trunk/debian/changelog 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/changelog 2008-01-26 12:56:34 UTC (rev 1198)
@@ -1,4 +1,4 @@
-glam2 (1023-1) unstable; urgency=low
+glam2 (1056-1) unstable; urgency=low
* Initial release (Closes: #45237)
Deleted: trunk/packages/glam2/trunk/debian/compat
===================================================================
--- trunk/packages/glam2/trunk/debian/compat 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/compat 2008-01-26 12:56:34 UTC (rev 1198)
@@ -1 +0,0 @@
-5
Modified: trunk/packages/glam2/trunk/debian/control
===================================================================
--- trunk/packages/glam2/trunk/debian/control 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/control 2008-01-26 12:56:34 UTC (rev 1198)
@@ -4,8 +4,8 @@
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
XS-DM-Upload-Allowed: Yes
Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 5), libfftw3-dev
-Standards-Version: 3.7.2
+Build-Depends: debhelper (>= 5), cdbs, libfftw3-dev
+Standards-Version: 3.7.3
Homepage: http://bioinformatics.org.au/glam2/
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/glam2/trunk/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/glam2
@@ -26,4 +26,8 @@
sequences, so that weaker motifs can be found; glam2-purge — for removing
highly similar members of a set of sequences.
.
- In this package, the fast Fourier algorithm (FFT) was enabled in glam2.
+ In this package, the fast Fourier algorithm (FFT) was enabled for glam2.
+ .
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey
+ (2008) Discovering sequence motifs with arbitrary insertions and deletions,
+ PLoS Computational Biology (in press).
Modified: trunk/packages/glam2/trunk/debian/copyright
===================================================================
--- trunk/packages/glam2/trunk/debian/copyright 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/copyright 2008-01-26 12:56:34 UTC (rev 1198)
@@ -1,19 +1,66 @@
-This package was debianized by Steffen Moeller <moeller at debian.org> on
-Tue, 13 Nov 2007 00:35:50 +0100.
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Steffen Moeller <moeller at debian.org>
+X-Debinized-Date: Tue, 13 Nov 2007 00:35:50 +0100.
+X-Source-Downloaded-From: http://bioinformatics.org.au/glam2/archive/
+X-Upstream-Author: Martin C Frith <martin at cbrc.jp>
+ Timothy L Bailey <t.bailey at imb.uq.edu.au>
-It was downloaded from http://bioinformatics.org.au/glam2/archive/
+Files: debian/*
+X-Upstream-Author: 2007 Steffen Moeller <moeller at debian.org>
+ 2007-2008 Charles Plessy <charles-debian-nospam at plessy.org>
+License: PD
+ The package is in the public domain and so shall then be
+ the packaging for Debian of Steffen Moeller <moeller at debian.org>
+ and Charles Plessy <charles-debian-nospam at plessy.org>.
-Upstream Authors:
+Files: purge/*
+X-Upstream-Author: Andrew Neuwald
+License: PD
+ PUBLIC DOMAIN NOTICE
+ National Center for Biotechnology Information
+ .
+ This software/database is a "United States Government Work" under the
+ terms of the United States Copyright Act. It was written as part of
+ the author's official duties as a United States Government employee and
+ thus cannot be copyrighted. This software is freely available to the
+ public for use. The National Library of Medicine and the U.S. Government
+ have not placed any restriction on its use or reproduction.
+ .
+ Although reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any particular
+ purpose.
+ .
+ Please cite
+ .
+ Neuwald, Liu, & Lawrence (1995) "Gibbs motif sampling:
+ detection of bacterial outer membrane protein repeats"
+ Protein Science 4, 1618-1632. (for Gibbs site sampling,
+ Gibbs motif sampling, purge, and scan programs)
+ .
+ and
+ .
+ Lawrence, Altschul, Boguski, Liu, Neuwald & Wootton (1993)
+ "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy
+ for Multiple Alignment", Science 262:208-214. (for Gibbs
+ site sampling program)
+ .
+ in any work or product based on this material.
+ .
+ The data structures used in this program are part of a package
+ of C code for molecular biological applications being developed
+ by A. F. Neuwald.
- Martin C Frith <martin at cbrc.jp>
- Timothy L Bailey <t.bailey at imb.uq.edu.au>
-
-Copyright:
-
- Copyright (C) 2007 Martin C Frith
- Copyright (C) 2007 Timothy L Bailey
-
-License:
-
- The package is in the public domain and so shall then be
- the packaging for Debian of Steffen Moeller <moeller at debian.org>.
+Files: *
+X-Upstream-Author: 2007 Martin C Frith <martin at cbrc.jp>
+ 2007 Timothy L Bailey <t.bailey at imb.uq.edu.au>
+License: PD
+ GLAM2 was developed by Martin C Frith, working at the Computational Biology
+ Research Center in Tokyo, and Timothy L Bailey, working at the Institute for
+ Molecular Bioscience in Brisbane. The source code and documentation are hereby
+ released into the public domain. If you use GLAM2, please cite: MC Frith, NFW
+ Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary
+ insertions and deletions, PLoS Computational Biology (in press).
Added: trunk/packages/glam2/trunk/debian/examples
===================================================================
--- trunk/packages/glam2/trunk/debian/examples (rev 0)
+++ trunk/packages/glam2/trunk/debian/examples 2008-01-26 12:56:34 UTC (rev 1198)
@@ -0,0 +1 @@
+examples/*
Added: trunk/packages/glam2/trunk/debian/glam2-purge.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2-purge.1 (rev 0)
+++ trunk/packages/glam2/trunk/debian/glam2-purge.1 2008-01-26 12:56:34 UTC (rev 1198)
@@ -0,0 +1,92 @@
+.\" Title: GLAM2-PURGE
+.\" Author: Andrew Neuwald
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 01/26/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2\-PURGE" "1" "01/26/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2-purge - Removes redundant sequences from a FASTA file
+.SH "SYNOPSIS"
+.HP 12
+\fBglam2\-purge\fR \fIfile\fR \fBscore\fR [\fBoptions\fR]
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2\-purge\fR
+is a modified version of Andrew Neuwald\'s
+\fBpurge\fR
+program that removes redundant sequences from a FASTA file\. This is recommended in order to prevent highly similar sequences distorting the search for motifs\. Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user\. The output file is named <file>\.<score>\. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/\-1 scoring scheme for DNA\. Purge can also be used to mask tandem repeats\. It uses the XNU program for this purpose\.
+.SH "OPTIONS"
+.PP
+\fB\-n\fR
+.RS 4
+Sequences are DNA (default: protein)\.
+.RE
+.PP
+\fB\-b\fR
+.RS 4
+Use blast heuristic method (default for protein)\.
+.RE
+.PP
+\fB\-e\fR
+.RS 4
+Use an exhaustive method (default for DNA)\.
+.RE
+.PP
+\fB\-q\fR
+.RS 4
+Keep first sequence in the set\.
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+Use xnu to mask protein tandem repeats\.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2\fR(1),
+\fBglam2format\fR(1),
+\fBglam2mask\fR(1),
+\fBglam2scan\fR(1),
+\fBxnu\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\.org\.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\.
+.SH "REFERENCES"
+.PP
+Purge was written by Andy Neuwald and is described in more detail in Neuwald et al\., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618\(en1632, 1995\. Please cite it if you use Purge\.
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\.
+.SH "AUTHORS"
+.PP
+\fBAndrew Neuwald\fR
+.sp -1n
+.IP "" 4
+Author of purge, renamed glam2\-purge in Debian\.
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Modified purge to be ANSI standard C and improved the user interface\.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Modified purge to be ANSI standard C and improved the user interface\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of Purge and GLAM2 are released in the public domain\.
+.sp
Modified: trunk/packages/glam2/trunk/debian/glam2.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2.1 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/glam2.1 2008-01-26 12:56:34 UTC (rev 1198)
@@ -1,11 +1,11 @@
.\" Title: GLAM2
.\" Author: Martin Frith
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 01/23/2008
+.\" Date: 01/26/2008
.\" Manual: glam2 Manual
.\" Source: GLAM2 1056
.\"
-.TH "GLAM2" "1" "01/23/2008" "GLAM2 1056" "glam2 Manual"
+.TH "GLAM2" "1" "01/26/2008" "GLAM2 1056" "glam2 Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
@@ -157,12 +157,12 @@
\fBMartin Frith\fR
.sp -1n
.IP "" 4
-Author of GLAM2
+Author of GLAM2\.
.PP
\fBTimothy Bailey\fR
.sp -1n
.IP "" 4
-Author of GLAM2
+Author of GLAM2\.
.PP
\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
.sp -1n
@@ -170,5 +170,5 @@
Formatted this manpage in DocBook XML for the Debian distribution\.
.SH "COPYRIGHT"
.PP
-The source code and the documentation of GLAM2 are released in the public domain
+The source code and the documentation of GLAM2 are released in the public domain\.
.sp
Modified: trunk/packages/glam2/trunk/debian/glam2.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2.1.xml 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/glam2.1.xml 2008-01-26 12:56:34 UTC (rev 1198)
@@ -36,13 +36,13 @@
<firstname>Martin</firstname>
<firstname>C</firstname>
<surname>Frith</surname>
- <contrib>Author of GLAM2</contrib>
+ <contrib>Author of GLAM2.</contrib>
</author>
<author>
<firstname>Timothy</firstname>
<firstname>L</firstname>
<surname>Bailey</surname>
- <contrib>Author of GLAM2</contrib>
+ <contrib>Author of GLAM2.</contrib>
</author>
<author>
<firstname>&dhfirstname;</firstname>
@@ -54,7 +54,7 @@
</author>
</authorgroup>
<legalnotice>
- <para>The source code and the documentation of GLAM2 are released in the public domain</para>
+ <para>The source code and the documentation of GLAM2 are released in the public domain.</para>
</legalnotice>
</refentryinfo>
<refmeta>
Deleted: trunk/packages/glam2/trunk/debian/glam2.dirs
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2.dirs 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/glam2.dirs 2008-01-26 12:56:34 UTC (rev 1198)
@@ -1 +0,0 @@
-usr/bin
Deleted: trunk/packages/glam2/trunk/debian/glam2.install
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2.install 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/glam2.install 2008-01-26 12:56:34 UTC (rev 1198)
@@ -1,5 +0,0 @@
-src/glam2format /usr/bin/
-src/glam2mask /usr/bin/
-src/glam2scan /usr/bin/
-src/glam2fft /usr/bin/
-purge/purge /usr/bin
Modified: trunk/packages/glam2/trunk/debian/glam2format.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2format.1 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/glam2format.1 2008-01-26 12:56:34 UTC (rev 1198)
@@ -1,17 +1,17 @@
.\" Title: GLAM2FORMAT
.\" Author: Martin Frith
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 01/23/2008
+.\" Date: 01/26/2008
.\" Manual: glam2 Manual
.\" Source: GLAM2 1056
.\"
-.TH "GLAM2FORMAT" "1" "01/23/2008" "GLAM2 1056" "glam2 Manual"
+.TH "GLAM2FORMAT" "1" "01/26/2008" "GLAM2 1056" "glam2 Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-glam2format - Gapped Local Alignment of Motifs
+glam2format - converts GLAM2 motifs to FASTA or MSF format
.SH "SYNOPSIS"
.HP 12
\fBglam2format\fR [\fBoptions\fR] \fBmy_format\fR \fImy_motif\.glam2\fR
@@ -69,12 +69,12 @@
\fBMartin Frith\fR
.sp -1n
.IP "" 4
-Author of GLAM2
+Author of GLAM2\.
.PP
\fBTimothy Bailey\fR
.sp -1n
.IP "" 4
-Author of GLAM2
+Author of GLAM2\.
.PP
\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
.sp -1n
@@ -82,5 +82,5 @@
Formatted this manpage in DocBook XML for the Debian distribution\.
.SH "COPYRIGHT"
.PP
-The source code and the documentation of GLAM2 are released in the public domain
+The source code and the documentation of GLAM2 are released in the public domain\.
.sp
Modified: trunk/packages/glam2/trunk/debian/glam2format.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2format.1.xml 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/glam2format.1.xml 2008-01-26 12:56:34 UTC (rev 1198)
@@ -35,13 +35,13 @@
<firstname>Martin</firstname>
<firstname>C</firstname>
<surname>Frith</surname>
- <contrib>Author of GLAM2</contrib>
+ <contrib>Author of GLAM2.</contrib>
</author>
<author>
<firstname>Timothy</firstname>
<firstname>L</firstname>
<surname>Bailey</surname>
- <contrib>Author of GLAM2</contrib>
+ <contrib>Author of GLAM2.</contrib>
</author>
<author>
<firstname>&dhfirstname;</firstname>
@@ -53,7 +53,7 @@
</author>
</authorgroup>
<legalnotice>
- <para>The source code and the documentation of GLAM2 are released in the public domain</para>
+ <para>The source code and the documentation of GLAM2 are released in the public domain.</para>
</legalnotice>
</refentryinfo>
<refmeta>
@@ -62,7 +62,7 @@
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
- <refpurpose>Gapped Local Alignment of Motifs</refpurpose>
+ <refpurpose>converts GLAM2 motifs to FASTA or MSF format</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
Added: trunk/packages/glam2/trunk/debian/glam2mask.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2mask.1 (rev 0)
+++ trunk/packages/glam2/trunk/debian/glam2mask.1 2008-01-26 12:56:34 UTC (rev 1198)
@@ -0,0 +1,73 @@
+.\" Title: GLAM2MASK
+.\" Author: Martin Frith
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 01/26/2008
+.\" Manual: glam2 Manual
+.\" Source: GLAM2 1056
+.\"
+.TH "GLAM2MASK" "1" "01/26/2008" "GLAM2 1056" "glam2 Manual"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+glam2mask - masks a GLAM2 motif in sequences
+.SH "SYNOPSIS"
+.HP 10
+\fBglam2mask\fR [\fBoptions\fR] \fImy_motif\.glam2\fR \fImy_seqs\.fa\fR
+.SH "DESCRIPTION"
+.PP
+
+\fBglam2mask\fR
+masks a
+\fBglam2\fR
+motif out of sequences, so that weaker motifs can be found\. Masking replaces residues aligned to key positions with the symbol \'x\'\. By alternately applying
+\fBglam2\fR
+and
+\fBglam2mask\fR
+several times, it is possible to find the strongest, second\-strongest, third\-strongest, etc\. motifs in a set of sequences\.
+.SH "OPTIONS (DEFAULT SETTINGS)"
+.PP
+\fB\-o\fR
+.RS 4
+Output file (\fIstdout\fR)\.
+.RE
+.PP
+\fB\-x\fR
+.RS 4
+Mask character (\fIx\fR)\.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBglam2format\fR(1),
+\fBglam2\fR(1),
+\fBglam2-purge\fR(1),
+\fBglam2scan\fR(1)
+.PP
+The full Hypertext documentation of GLAM2 is available online at
+\fIhttp://bioinformatics\.org\.au/glam2/\fR
+or on this computer in
+\fI/usr/share/doc/glam2/\fR\.
+.SH "REFERENCE"
+.PP
+If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\.
+.SH "AUTHORS"
+.PP
+\fBMartin Frith\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\.
+.PP
+\fBTimothy Bailey\fR
+.sp -1n
+.IP "" 4
+Author of GLAM2\.
+.PP
+\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
+.sp -1n
+.IP "" 4
+Formatted this manpage in DocBook XML for the Debian distribution\.
+.SH "COPYRIGHT"
+.PP
+The source code and the documentation of GLAM2 are released in the public domain\.
+.sp
Added: trunk/packages/glam2/trunk/debian/glam2mask.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2mask.1.xml (rev 0)
+++ trunk/packages/glam2/trunk/debian/glam2mask.1.xml 2008-01-26 12:56:34 UTC (rev 1198)
@@ -0,0 +1,131 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl"
+ href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+ "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+
+<!-- Process this file with an XSLT processor, e.g. xsltproc: -->
+<!-- `xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1" \
+ manpage.xml' -->
+
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "1056">
+ <!ENTITY dhtitle "glam2 Manual">
+ <!ENTITY dhucpackage "GLAM2MASK">
+ <!ENTITY dhpackage "glam2mask">
+ <!ENTITY dhproduct "GLAM2">
+ <!ENTITY dhsection "1">
+
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <!-- Better put a suite name instead of &dhpackage; into productname -->
+ <productname>&dhproduct;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <authorgroup>
+ <author>
+ <firstname>Martin</firstname>
+ <firstname>C</firstname>
+ <surname>Frith</surname>
+ <contrib>Author of GLAM2.</contrib>
+ </author>
+ <author>
+ <firstname>Timothy</firstname>
+ <firstname>L</firstname>
+ <surname>Bailey</surname>
+ <contrib>Author of GLAM2.</contrib>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Formatted this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <legalnotice>
+ <para>The source code and the documentation of GLAM2 are released in the public domain.</para>
+ </legalnotice>
+ </refentryinfo>
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>masks a GLAM2 motif in sequences</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt"><option>options</option></arg>
+ <arg choice="plain"><replaceable>my_motif.glam2</replaceable></arg>
+ <arg choice="plain"><replaceable>my_seqs.fa</replaceable></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>
+ <command>&dhpackage;</command> masks a <command>glam2</command> motif out of sequences, so that weaker motifs can be found. Masking replaces residues aligned to key positions with the symbol 'x'. By alternately applying <command>glam2</command> and <command>glam2mask</command> several times, it is possible to find the strongest, second-strongest, third-strongest, etc. motifs in a set of sequences.
+ </para>
+ </refsect1>
+
+ <refsect1 id="options">
+ <title>OPTIONS (default settings)</title>
+ <variablelist>
+ <!-- Use the variablelist.term.separator and the
+ variablelist.term.break.after parameters to
+ control the term elements. -->
+ <varlistentry>
+ <term><option>-o</option></term>
+ <listitem>
+ <para>Output file (<parameter>stdout</parameter>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-x</option></term>
+ <listitem>
+ <para>Mask character (<parameter>x</parameter>).</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry>
+ <refentrytitle>glam2format</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2-purge</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>, <citerefentry>
+ <refentrytitle>glam2scan</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry></para>
+ <para>The full Hypertext documentation of GLAM2 is available online at <ulink url="http://bioinformatics.org.au/glam2/">http://bioinformatics.org.au/glam2/</ulink> or on this computer in <filename class="directory">/usr/share/doc/glam2/</filename>.</para>
+ </refsect1>
+
+ <refsect1 id="ref">
+ <title>REFERENCE</title>
+ <para>
+ If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press).
+ </para>
+ </refsect1>
+</refentry>
Modified: trunk/packages/glam2/trunk/debian/glam2scan.1
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2scan.1 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/glam2scan.1 2008-01-26 12:56:34 UTC (rev 1198)
@@ -1,17 +1,17 @@
.\" Title: GLAM2SCAN
.\" Author: Martin Frith
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 01/23/2008
+.\" Date: 01/26/2008
.\" Manual: glam2 Manual
.\" Source: GLAM2 1056
.\"
-.TH "GLAM2SCAN" "1" "01/23/2008" "GLAM2 1056" "glam2 Manual"
+.TH "GLAM2SCAN" "1" "01/26/2008" "GLAM2 1056" "glam2 Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-glam2scan - Gapped Local Alignment of Motifs
+glam2scan - finds a GLAM2 motif in a database
.SH "SYNOPSIS"
.HP 10
\fBglam2scan\fR [\fBoptions\fR] \fBalphabet\fR \fImy_motif\.glam2\fR \fImy_seqs\.fa\fR
@@ -92,12 +92,12 @@
\fBMartin Frith\fR
.sp -1n
.IP "" 4
-Author of GLAM2
+Author of GLAM2\.
.PP
\fBTimothy Bailey\fR
.sp -1n
.IP "" 4
-Author of GLAM2
+Author of GLAM2\.
.PP
\fBCharles Plessy\fR <\&charles\-debian\-nospam at plessy\.org\&>
.sp -1n
@@ -105,5 +105,5 @@
Formatted this manpage in DocBook XML for the Debian distribution\.
.SH "COPYRIGHT"
.PP
-The source code and the documentation of GLAM2 are released in the public domain
+The source code and the documentation of GLAM2 are released in the public domain\.
.sp
Modified: trunk/packages/glam2/trunk/debian/glam2scan.1.xml
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2scan.1.xml 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/glam2scan.1.xml 2008-01-26 12:56:34 UTC (rev 1198)
@@ -36,13 +36,13 @@
<firstname>Martin</firstname>
<firstname>C</firstname>
<surname>Frith</surname>
- <contrib>Author of GLAM2</contrib>
+ <contrib>Author of GLAM2.</contrib>
</author>
<author>
<firstname>Timothy</firstname>
<firstname>L</firstname>
<surname>Bailey</surname>
- <contrib>Author of GLAM2</contrib>
+ <contrib>Author of GLAM2.</contrib>
</author>
<author>
<firstname>&dhfirstname;</firstname>
@@ -54,7 +54,7 @@
</author>
</authorgroup>
<legalnotice>
- <para>The source code and the documentation of GLAM2 are released in the public domain</para>
+ <para>The source code and the documentation of GLAM2 are released in the public domain.</para>
</legalnotice>
</refentryinfo>
<refmeta>
@@ -63,7 +63,7 @@
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
- <refpurpose>Gapped Local Alignment of Motifs</refpurpose>
+ <refpurpose>finds a GLAM2 motif in a database</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
Copied: trunk/packages/glam2/trunk/debian/install (from rev 1197, trunk/packages/glam2/trunk/debian/glam2.install)
===================================================================
--- trunk/packages/glam2/trunk/debian/install (rev 0)
+++ trunk/packages/glam2/trunk/debian/install 2008-01-26 12:56:34 UTC (rev 1198)
@@ -0,0 +1,5 @@
+src/glam2format /usr/bin/
+src/glam2mask /usr/bin/
+src/glam2scan /usr/bin/
+src/glam2 /usr/bin/
+purge/glam2-purge /usr/bin
Added: trunk/packages/glam2/trunk/debian/manpages
===================================================================
--- trunk/packages/glam2/trunk/debian/manpages (rev 0)
+++ trunk/packages/glam2/trunk/debian/manpages 2008-01-26 12:56:34 UTC (rev 1198)
@@ -0,0 +1,5 @@
+debian/glam2.1
+debian/glam2format.1
+debian/glam2mask.1
+debian/glam2-purge.1
+debian/glam2scan.1
Modified: trunk/packages/glam2/trunk/debian/rules
===================================================================
--- trunk/packages/glam2/trunk/debian/rules 2008-01-25 21:26:00 UTC (rev 1197)
+++ trunk/packages/glam2/trunk/debian/rules 2008-01-26 12:56:34 UTC (rev 1198)
@@ -1,57 +1,16 @@
#!/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
+DEB_COMPRESS_EXCLUDE := .pdf
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
-build: build-stamp
-
-build-stamp:
- dh_testdir
+build/glam2::
$(MAKE) -C src
$(MAKE) -C src glam2fft
$(MAKE) -C purge
- #(cd debian; for i in glam2format.1 glam2mask.1 glam2scan.1; do ln -s glam2.1 $$i; done)
- touch $@
+ mv $(CURDIR)/src/glam2fft $(CURDIR)/src/glam
+ mv $(CURDIR)/purge/purge $(CURDIR)/purge/glam2-purge
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp configure-stamp
-
- dh_clean purge/*.o purge/purge src/*.o src/{glam2,glam2mask,glam2format,glam2scan}
-
-install: build
- dh_install
- mv $(CURDIR)/debian/glam2/usr/bin/glam2fft $(CURDIR)/debian/glam2/usr/bin/glam2
- mv $(CURDIR)/debian/glam2/usr/bin/purge $(CURDIR)/debian/glam2/usr/bin/glam2-purge
-
-binary-indep: build install
-
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs ChangeLog
- dh_installdocs
- dh_installexamples examples/*
- dh_installman debian/glam2.1
- for i in format scan mask; do \
- dh_link /usr/share/man/man1/glam2.1.gz /usr/share/man/man1/glam2$$i.1.gz; \
- done
- dh_strip
- dh_compress
- dh_fixperms
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
+clean::
+ rm -f purge/*.o purge/purge purge/glam2-purge src/*.o src/{glam2,glam2mask,glam2format,glam2scan,glam2-fft}
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