[med-svn] r103 - in trunk/packages/sigma-align/trunk: . debian
Charles Plessy
charles-guest at costa.debian.org
Tue Sep 5 15:36:14 UTC 2006
Author: charles-guest
Date: 2006-09-05 15:36:14 +0000 (Tue, 05 Sep 2006)
New Revision: 103
Added:
trunk/packages/sigma-align/trunk/debian/
trunk/packages/sigma-align/trunk/debian/changelog
trunk/packages/sigma-align/trunk/debian/compat
trunk/packages/sigma-align/trunk/debian/control
trunk/packages/sigma-align/trunk/debian/copyright
trunk/packages/sigma-align/trunk/debian/dirs
trunk/packages/sigma-align/trunk/debian/rules
trunk/packages/sigma-align/trunk/debian/sigma.1.xml
Log:
Load newtrunk into trunk/packages/sigma-align/trunk.
Added: trunk/packages/sigma-align/trunk/debian/changelog
===================================================================
--- trunk/packages/sigma-align/trunk/debian/changelog (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/changelog 2006-09-05 15:36:14 UTC (rev 103)
@@ -0,0 +1,6 @@
+sigma-align (1.0-1) unstable; urgency=low
+
+ * Initial release Closes: #378289
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 5 Sep 2006 23:14:46 +0900
+
Added: trunk/packages/sigma-align/trunk/debian/compat
===================================================================
--- trunk/packages/sigma-align/trunk/debian/compat (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/compat 2006-09-05 15:36:14 UTC (rev 103)
@@ -0,0 +1 @@
+5
Added: trunk/packages/sigma-align/trunk/debian/control
===================================================================
--- trunk/packages/sigma-align/trunk/debian/control (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/control 2006-09-05 15:36:14 UTC (rev 103)
@@ -0,0 +1,25 @@
+Source: sigma-align
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 5), ocaml-nox, xsltproc, docbook-xsl, docbook-xml
+Standards-Version: 3.7.2
+
+Package: sigma-align
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Simple greedy multiple alignment of non-coding DNA sequences
+ Sigma ("Simple greedy multiple alignment") is an alignment program with a new
+ algorithm and scoring scheme designed specifically for non-coding DNA
+ sequence. It uses a strategy of seeking the best possible gapless local
+ alignments, at each step making the best possible alignment consistent with
+ existing alignments, and scores the significance of the alignment based on the
+ lengths of the aligned fragments and a background model which may be supplied
+ or estimated from an auxiliary file of intergenic DNA. With real data, while
+ "correctness" can't be directly quantified for the alignment, running the
+ PhyloGibbs motif finder on pre-aligned sequence suggests that Sigma's
+ alignments are superior. It has been published in BMC Bioinformatics. 2006 Mar
+ 16;7:143.
+ .
+ Homepage: http://www.imsc.res.in/~rsidd/sigma/
Added: trunk/packages/sigma-align/trunk/debian/copyright
===================================================================
--- trunk/packages/sigma-align/trunk/debian/copyright (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/copyright 2006-09-05 15:36:14 UTC (rev 103)
@@ -0,0 +1,26 @@
+This package was debianized by Charles Plessy <charles-debian-nospam at plessy.org> on
+Tue, 5 Sep 2006 23:14:46 +0900.
+
+It was downloaded from <http://www.imsc.res.in/~rsidd/sigma/>
+
+Copyright (C) Rahul Siddharthan, 2006
+
+License:
+
+ 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 package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
Added: trunk/packages/sigma-align/trunk/debian/dirs
===================================================================
--- trunk/packages/sigma-align/trunk/debian/dirs (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/dirs 2006-09-05 15:36:14 UTC (rev 103)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/sigma-align/trunk/debian/rules
===================================================================
--- trunk/packages/sigma-align/trunk/debian/rules (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/rules 2006-09-05 15:36:14 UTC (rev 103)
@@ -0,0 +1,54 @@
+#!/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.
+# Modifications by Charles Plessy during the year 2006
+# are hereby released as "public domain".
+
+
+configure:
+
+build:
+ dh_testdir
+ ocamlopt str.cmxa sigma.ml -o sigma
+ xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl debian/sigma.1.xml
+ touch build
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f sigma sigma.cmi sigma.cmx sigma.o
+ dh_clean debian/sigma.1 build
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+binary-indep:
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples
+ dh_install sigma usr/bin
+ dh_installman debian/sigma.1
+ dh_link
+ 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
Property changes on: trunk/packages/sigma-align/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/sigma-align/trunk/debian/sigma.1.xml
===================================================================
--- trunk/packages/sigma-align/trunk/debian/sigma.1.xml (rev 0)
+++ trunk/packages/sigma-align/trunk/debian/sigma.1.xml 2006-09-05 15:36:14 UTC (rev 103)
@@ -0,0 +1,164 @@
+<?xml version='1.0' encoding='ISO-8859-1'?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
+"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
+
+
+ <!ENTITY dhfirstname "<firstname>Charles</firstname>">
+ <!ENTITY dhsurname "<surname>Plessy</surname>">
+ <!ENTITY dhdate "<date>september 5, 2006</date>">
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
+ <!ENTITY dhusername "Charles Plessy">
+ <!ENTITY dhucpackage "<refentrytitle>SIGMA</refentrytitle>">
+ <!ENTITY dhpackage "sigma">
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<!-- Copyright 2006 Charles Plessy. You can use, copy, and redistribute this manpage under the GNU GPL. -->
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+<!-- <author>
+ &dhfirstname;
+ &dhsurname;
+ </author> -->
+ <copyright>
+ <year>2006</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>Simple greedy multiple alignment of non-coding DNA sequences</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt">options</arg>
+ <arg>
+ <replaceable>inputfile.fasta</replaceable>
+ </arg>
+ <arg choice="opt">
+ <replaceable>inputfile2.fasta ...</replaceable>
+ </arg>
+ </cmdsynopsis>
+
+ <para>
+ Each fasta file may contain a single sequence or multiple sequences; all sequences will be aligned together.
+ </para>
+
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para><command>Sigma</command> ("Simple greedy multiple alignment") is an alignment program with a new algorithm and scoring scheme designed specifically for non-coding DNA sequence. It uses a strategy of seeking the best possible gapless local alignments, at each step making the best possible alignment consistent with existing alignments, and scores the significance of the alignment based on the lengths of the aligned fragments and a background model which may be supplied or estimated from an auxiliary file of intergenic DNA. With real data, while "correctness" can't be directly quantified for the alignment, running the PhyloGibbs motif finder on pre-aligned sequence suggests that Sigma's alignments are superior.</para>
+
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+
+ <variablelist>
+ <varlistentry>
+ <term><option>-A</option>
+ </term>
+ <listitem>
+ <para>Aligned output (compare with <option>-F</option> option) (default: only this).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-b</option>
+ <parameter>filename</parameter>
+ </term>
+ <listitem>
+ <para>Auxiliary file from which to read background sequences (overridden by <option>-B</option>).</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term>
+ <option>-B</option>
+ <parameter>filename</parameter>
+ </term>
+ <listitem>
+ <para>File containing background probabilities.</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-F</option>
+ </term>
+ <listitem>
+ <para>fasta output (can use both <option>-A</option> and <option>-F</option> in either order)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-n</option>
+ <parameter>number</parameter>
+ </term>
+ <listitem>
+ <para>Background correlation (default <parameter>2</parameter>=dinucleotide;
+ <parameter>1</parameter>=single-site basecounts, <parameter>0</parameter>=0.25 per base)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-x</option>
+ <parameter>number</parameter>
+ </term>
+ <listitem>
+ <para>Set limit for how probable the match is by chance
+ (default 0.002, smaller=more stringent)</para>
+ </listitem>
+ </varlistentry>
+
+ <varlistentry>
+ <term><option>-help</option>,
+ <option>--help</option>
+ </term>
+ <listitem>
+ <para>Displays this list of options.</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1>
+ <title>REFERENCE</title>
+ <para>
+ Please cite Sigma: Rahul Siddharthan (2006) Multiple alignment of weakly-conserved non-coding DNA sequence BMC Bioinformatics 2006, 7:143 doi:10.1186/1471-2105-7-143 Published 16 March 2006, available online at http://www.biomedcentral.com/1471-2105/7/143/</para>
+ </refsect1>
+
+ <refsect1>
+ <title>COPYRIGHTS</title>
+
+ <para>Copyright (C) 2006 Rahul Siddharthan <email>rsidd at imsc.res.in</email>. Sigma 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.</para>
+
+ <para>This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+ </para>
+
+ <para>
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+ </para>
+
+ </refsect1>
+</refentry>
+
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