[med-svn] r94 - in trunk/packages/poa/trunk: . debian

Charles Plessy charles-guest at costa.debian.org
Wed Aug 23 13:49:51 UTC 2006


Author: charles-guest
Date: 2006-08-23 13:49:50 +0000 (Wed, 23 Aug 2006)
New Revision: 94

Added:
   trunk/packages/poa/trunk/debian/
   trunk/packages/poa/trunk/debian/README.debian
   trunk/packages/poa/trunk/debian/changelog
   trunk/packages/poa/trunk/debian/compat
   trunk/packages/poa/trunk/debian/control
   trunk/packages/poa/trunk/debian/copyright
   trunk/packages/poa/trunk/debian/dirs
   trunk/packages/poa/trunk/debian/docs
   trunk/packages/poa/trunk/debian/examples
   trunk/packages/poa/trunk/debian/install
   trunk/packages/poa/trunk/debian/manpages
   trunk/packages/poa/trunk/debian/poa.1.xml
   trunk/packages/poa/trunk/debian/rules
   trunk/packages/poa/trunk/debian/watch
Log:
Load poa-2.0 into trunk/packages/poa/trunk.


Added: trunk/packages/poa/trunk/debian/README.debian
===================================================================
--- trunk/packages/poa/trunk/debian/README.debian	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/README.debian	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,11 @@
+poa for Debian
+--------------
+
+POA needs a matrix file to operate. The one shipped in the sources of POA can
+be found at /usr/lib/poa/blosum80.mat
+
+You can test POA with the following command:
+
+poa -read_fasta /usr/share/doc/poa/examples/multidom.seq -clustal /dev/stdout -v /usr/share/poa/blosum80.mat
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org>, Sun, 20 Aug 2006 11:21:24 +0900

Added: trunk/packages/poa/trunk/debian/changelog
===================================================================
--- trunk/packages/poa/trunk/debian/changelog	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/changelog	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,6 @@
+poa (2.0-1) unstable; urgency=low
+
+  * Initial release Closes: #378288
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Sun, 20 Aug 2006 11:21:24 +0900
+

Added: trunk/packages/poa/trunk/debian/compat
===================================================================
--- trunk/packages/poa/trunk/debian/compat	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/compat	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1 @@
+5

Added: trunk/packages/poa/trunk/debian/control
===================================================================
--- trunk/packages/poa/trunk/debian/control	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/control	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,24 @@
+Source: poa
+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), xsltproc, docbook-xsl, docbook-xml
+Standards-Version: 3.7.2
+
+Package: poa
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Partial Order Alignment for multiple sequence alignment
+ POA is Partial Order Alignment, a fast program for multiple sequence
+ alignment (MSA) in bioinformatics. Its advantages are speed,
+ scalability, sensitivity, and the superior ability to handle branching
+ / indels in the alignment. Partial order alignment is an approach to
+ MSA, which can be combined with existing methods such as progressive
+ alignment. POA optimally aligns a pair of MSAs and which therefore can
+ be applied directly to progressive alignment methods such as CLUSTAL.
+ For large alignments, Progressive POA is 10-30 times faster than
+ CLUSTALW. POA is published in Bioinformatics. 2004 Jul
+ 10;20(10):1546-56.
+ .
+  Homepage: http://www.bioinformatics.ucla.edu/poa

Added: trunk/packages/poa/trunk/debian/copyright
===================================================================
--- trunk/packages/poa/trunk/debian/copyright	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/copyright	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,32 @@
+This package was debianized by Charles Plessy
+<charles-debian-nospam at plessy.org> on Sun, 20 Aug 2006 11:21:24 +0900. The
+packaging work is in the public domain unless stated otherwise. The manpage for
+poa and its source are licenced under the GPL.
+
+It was downloaded from http://sourceforge.net/project/showfiles.php?group_id=168080&package_id=191162&release_id=418237 
+
+Copyright 2001, 2006 Christopher Lee <leec at mbi.ucla.edu>
+
+The project page on the SourceForge website indicates that this program is
+licenced under the GNU General Public Licence.
+(see: http://sourceforge.net/projects/poamsa/)
+
+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/poa/trunk/debian/dirs
===================================================================
--- trunk/packages/poa/trunk/debian/dirs	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/dirs	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/poa

Added: trunk/packages/poa/trunk/debian/docs
===================================================================
--- trunk/packages/poa/trunk/debian/docs	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/docs	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1 @@
+README

Added: trunk/packages/poa/trunk/debian/examples
===================================================================
--- trunk/packages/poa/trunk/debian/examples	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/examples	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,2 @@
+multidom.seq
+

Added: trunk/packages/poa/trunk/debian/install
===================================================================
--- trunk/packages/poa/trunk/debian/install	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/install	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,2 @@
+poa		/usr/bin
+blosum80.mat	/usr/share/poa

Added: trunk/packages/poa/trunk/debian/manpages
===================================================================
--- trunk/packages/poa/trunk/debian/manpages	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/manpages	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,2 @@
+debian/poa.1
+

Added: trunk/packages/poa/trunk/debian/poa.1.xml
===================================================================
--- trunk/packages/poa/trunk/debian/poa.1.xml	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/poa.1.xml	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,262 @@
+<?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>august 20, 2006</date>">
+  <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
+  <!ENTITY dhemail     "<email>charles-debian-nospam at plessy.org</email>">
+  <!ENTITY dhusername  "Charles Plessy">
+  <!ENTITY dhucpackage "<refentrytitle>POA</refentrytitle>">
+  <!ENTITY dhpackage   "poa">
+  <!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>performs multiple alignment of biological sequences.</refpurpose>
+  </refnamediv>
+  <refsynopsisdiv>
+    <cmdsynopsis>
+      <command>&dhpackage;</command>
+      <arg choice="opt">Options</arg>
+      <arg choice="opt">
+        <replaceable>matrixfile</replaceable>
+      </arg>
+    </cmdsynopsis>
+  </refsynopsisdiv>
+  <refsect1>
+    <title>DESCRIPTION</title>
+
+    <para><command>POA</command> is Partial Order Alignment, a fast program for multiple sequence alignment (MSA) in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment. Partial order alignment is an approach to MSA, which can be combined with existing methods such as progressive alignment. POA optimally aligns a pair of MSAs and which therefore can be applied directly to progressive alignment methods such as CLUSTAL. For large alignments, Progressive POA is 10 to 30 times faster than CLUSTALW.</para>
+    
+  </refsect1>
+  <refsect1>
+    <title>OPTIONS</title>
+  <refsect2>
+    <title>INPUT</title>
+    <variablelist>
+      <varlistentry>
+        <term><option>-read_fasta</option>
+        <parameter>FILENAME</parameter>
+        </term>
+        <listitem>
+          <para>Reads in FASTA sequence file.</para>
+        </listitem>
+      </varlistentry>
+            
+      <varlistentry>
+        <term><option>-tolower</option>
+        </term>
+        <listitem>
+          <para>Forces FASTA sequences to lowercase (nucleotides in our matrix files).</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-toupper</option>
+        </term>
+        <listitem>
+          <para>Forces FASTA sequences to UPPERCASE (amino acids in our matrix files).</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-read_po</option>
+        <parameter>FILENAME</parameter>
+        </term>
+        <listitem>
+          <para>Reads in PO file.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-subset</option>
+          <parameter>FILENAME</parameter>
+        </term>
+        <listitem>
+          <para>Filters PO-MSA to include list of seqs in file.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-remove</option>
+        <parameter>FILENAME</parameter>
+        </term>
+        <listitem>
+          <para> Filters PO-MSA to exclude list of seqs in file.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+    </refsect2>
+    
+    <refsect2>
+      <title>ALIGNMENT</title>
+      
+    <variablelist>
+      <varlistentry>
+        <term><option>-pair_score</option>
+        <parameter>FILENAME</parameter>
+        </term>
+        <listitem>
+          <para>Reads tab-delimited file of sequence-sequence similarity scores for constructing a guide-tree and performing progressive alignment using PO-PO alignment steps.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-fuse_all</option>
+        </term>
+        <listitem>
+          <para>Fuses identical letters on align rings.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+    </refsect2>
+    
+    <refsect2>
+      <title>ANALYSIS</title>
+      
+    <variablelist>
+      <varlistentry>
+        <term><option>-hb</option>
+        </term>
+        <listitem>
+          <para>Performs heaviest bundling to generate consensi.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-hbmin</option>
+        <parameter>VALUE</parameter>
+       </term>
+        <listitem>
+          <para> Bundles into heaviest bundle seqs with percent id &gt;= <parameter>value</parameter>.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+    </refsect2>
+
+    <refsect2>
+      <title>OUTPUT</title>
+      
+    <variablelist>
+      <varlistentry>
+        <term><option>-best</option>
+        </term>
+        <listitem>
+          <para>Restricts MSA output to heaviest bundles.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-pir</option>
+        <parameter>FILENAME</parameter>
+        </term>
+        <listitem>
+          <para>Writes out MSA in PIR format.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-clustal</option>
+        <parameter>FILENAME</parameter>
+        </term>
+        <listitem>
+          <para>Writes out MSA in CLUSTAL format.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-po</option>
+        <parameter>FILENAME</parameter>
+        </term>
+        <listitem>
+          <para>Writes out MSA in PO format.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-printmatrix</option>
+        <parameter>LETTERSET</parameter>
+        </term>
+        <listitem>
+          <para>Prints score matrix to stdout.</para>
+        </listitem>
+      </varlistentry>
+      
+      <varlistentry>
+        <term><option>-v</option>
+          <option></option>
+        </term>
+        <listitem>
+          <para>Runs in verbose mode.</para>
+        </listitem>
+      </varlistentry>
+    </variablelist>
+  </refsect2>
+  
+  <para>Note:  Either the <option>-read_fasta</option> or <option>-read_po</option> argument must be used with poa, since a FASTA file or PO file must be read in by poa.</para>
+  
+  </refsect1>
+ 
+  <refsect1>
+    <title>REFERENCE</title>
+    <para>
+      Please cite Grasso C, Lee C. (2004) Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics. 2004 Jul 10;20(10):1546-56. Epub 2004 Feb 12. 
+    </para>
+  </refsect1>
+    
+  
+  <refsect1>
+    <title>SEE ALSO</title>
+    <para>The homepage of POA is <ulink url="http://www.bioinformatics.ucla.edu/poa">http://www.bioinformatics.ucla.edu/poa</ulink>
+    </para>
+  </refsect1>
+  
+  <refsect1>
+    <title>COPYRIGHTS</title>
+
+    <para>Copyright (C) 2001, 2006 Christopher Lee <email>leec at mbi.ucla.edu</email>. POA 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>
+

Added: trunk/packages/poa/trunk/debian/rules
===================================================================
--- trunk/packages/poa/trunk/debian/rules	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/rules	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,62 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Build rules for the Debian package poa
+# 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"
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+	CFLAGS += -O0
+else
+	CFLAGS += -O2
+endif
+
+build:
+	dh_testdir
+	$(MAKE) poa
+	xsltproc -o debian/ -''-nonet /usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl debian/poa.1.xml
+	touch build-stamp
+
+clean:
+	dh_testdir
+	dh_testroot
+	rm -f build-stamp configure-stamp
+	-$(MAKE) clean
+	dh_clean debian/poa.1
+
+
+install: build
+	dh_testdir
+	dh_testroot
+	dh_clean -k 
+	dh_installdirs
+
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+	dh_testdir
+	dh_testroot
+	dh_installchangelogs 
+	dh_installdocs
+	dh_installexamples
+	dh_install
+	dh_installman
+	dh_link
+	dh_strip
+	dh_compress
+	dh_fixperms
+	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/poa/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/poa/trunk/debian/watch
===================================================================
--- trunk/packages/poa/trunk/debian/watch	2006-08-23 13:46:18 UTC (rev 93)
+++ trunk/packages/poa/trunk/debian/watch	2006-08-23 13:49:50 UTC (rev 94)
@@ -0,0 +1,6 @@
+version=3
+
+# Uncomment to find new files on sourceforge, for debscripts >= 2.9
+ http://sf.net/poamsa/poa_release_(.*)_(.*)\.tar\.gz
+
+




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