[med-svn] r1219 - in trunk/packages/axparafit/trunk: . debian debian/patches
hanska-guest at alioth.debian.org
hanska-guest at alioth.debian.org
Wed Jan 30 10:54:18 UTC 2008
Author: hanska-guest
Date: 2008-01-30 10:54:18 +0000 (Wed, 30 Jan 2008)
New Revision: 1219
Added:
trunk/packages/axparafit/trunk/debian/
trunk/packages/axparafit/trunk/debian/axparafit.1
trunk/packages/axparafit/trunk/debian/axparafit.1.xml
trunk/packages/axparafit/trunk/debian/axparafitblas.1
trunk/packages/axparafit/trunk/debian/axparparafit.1
trunk/packages/axparafit/trunk/debian/axparparafitblas.1
trunk/packages/axparafit/trunk/debian/axparparafitblas_random.1
trunk/packages/axparafit/trunk/debian/changelog
trunk/packages/axparafit/trunk/debian/compat
trunk/packages/axparafit/trunk/debian/control
trunk/packages/axparafit/trunk/debian/copyright
trunk/packages/axparafit/trunk/debian/dirs
trunk/packages/axparafit/trunk/debian/install
trunk/packages/axparafit/trunk/debian/patches/
trunk/packages/axparafit/trunk/debian/patches/01-fix_Makefile.patch
trunk/packages/axparafit/trunk/debian/patches/series
trunk/packages/axparafit/trunk/debian/rules
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/axparafit/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/axparafit/trunk/debian/axparafit.1
===================================================================
--- trunk/packages/axparafit/trunk/debian/axparafit.1 (rev 0)
+++ trunk/packages/axparafit/trunk/debian/axparafit.1 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1,151 @@
+.\" Title: AXPARAFIT
+.\" Author:
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: january 30, 2008
+.\" Manual:
+.\" Source:
+.\"
+.TH "AXPARAFIT" "1" "january 30, 2008" "" ""
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+axparafit, axparafitblas, axparparafit, axparparafitblas, axparparafitblas_random - optimized statistical analysis of host-parasite coevolution
+.SH "SYNOPSIS"
+.HP 10
+\fBaxparafit\fR \fB\-p\ \fR\fB\fInumberOfPermutations\fR\fR \fB\-n1\ \fR\fB\fIN1\fR\fR \fB\-n2\ \fR\fB\fIN2\fR\fR \fB\-n3\ \fR\fB\fIN3\fR\fR \fB\-n4\ \fR\fB\fIN4\fR\fR \fB\-A\ \fR\fB\fIassociationMatrix\fR\fR
+.br
+\fB\-B\ \fR\fB\fIparasiteMatrix\fR\fR \fB\-C\ \fR\fB\fIhostMatrix\fR\fR \fB\-n\ \fR\fB\fIrunID\fR\fR
+.br
+[(1)\ \ \fB\-g\fR] [(2)\ \ \fB\-t\ \fR\fB\fItraceFileName\fR\fR] [(3)\ \ \fB\-r\ \fR\fB\fInumberOfRandomLinks\fR\fR]
+.br
+\fB\-h\fR
+.HP 4
+(1) [\fB\-g\fR\ is\ \fInot\ available\fR\ in\ \fBaxparparafit\fR,\ \fBaxparparafitblas\fR\ and\ \fBaxparparafitblas_random\fR\.]
+.sp -1n
+.HP 4
+(2) [\fB\-t\fR\ is\ \fIrequired\fR\ for\ \fBaxparparafit\fR,\ \fBaxparparafitblas\fR\ and\ \fBaxparparafitblas_random\fR\.]
+.sp -1n
+.HP 4
+(3) [\fB\-r\fR\ is\ \fIonly\fR\ available\ for\ \fBaxparparafitblas_random\fR\.]
+.SH "DESCRIPTION"
+.PP
+AxParafit is a highly optimized version of Pierre Legendre\'s Parafit program for statistical analysis of host\-parasite coevolution\. AxParafit has been parallelized with MPI (Message Passing Interface) for compute clusters and was used to carry out the largest co\-evolutionary analysis to date for the paper describing the software\.
+.PP
+AxParafit will start executing individual tests of cospeciation directly\. If you want to execute only global tests of cospeciation, please use the
+[\-g]
+option\.
+.SH "OPTIONS"
+.PP
+\fB\-p\fR
+.RS 4
+Specify the number of permutations you want to execute\.
+.RE
+.PP
+\fB\-n1 \fR\fB\fIN1\fR\fR
+.RS 4
+Specify number of Rows in
+\fIassociationMatrix\fR\.
+.RE
+.PP
+\fB\-n2 \fR\fB\fIN2\fR\fR
+.RS 4
+Specify number of Columns in
+\fIassociationMatrix\fR\.
+.RE
+.PP
+\fB\-n3 \fR\fB\fIN3\fR\fR
+.RS 4
+Specify number of Rows in
+\fIhostMatrix\fR\.
+.RE
+.PP
+\fB\-n4 \fR\fB\fIN4\fR\fR
+.RS 4
+Specify number of Columns in
+\fIparasiteMatrix\fR\.
+.RE
+.PP
+\fB\-A \fR\fB\fIassociationMatrix\fR\fR
+.RS 4
+Specify file name of associaton matrix\.
+.RE
+.PP
+\fB\-B \fR\fB\fIparasiteMatrix\fR\fR
+.RS 4
+Specify file name of parasite matrix\.
+.RE
+.PP
+\fB\-C \fR\fB\fIhostMatrix\fR\fR
+.RS 4
+Specify file name of host matrix\.
+.RE
+.PP
+\fB\-n \fR\fB\fIrunID\fR\fR
+.RS 4
+Specify a run Name/ID for this run which will be appended to the output files\.
+.RE
+.PP
+[\fB\-g\fR]
+.RS 4
+Execute global test of cospeciation only\.
+.sp
+This is
+\fInot available\fR
+for
+\fBaxparparafit\fR,
+\fBaxparparafitblas\fR
+and
+\fBaxparparafitblas_random\fR\.
+.RE
+.PP
+[\fB\-t \fR\fB\fItraceFileName\fR\fR]
+.RS 4
+Specify the name of a binary trace\-file written by a global cospeciation test with AxParafit\.
+.sp
+This argument is
+\fIrequired\fR
+by
+\fBaxparparafit\fR,
+\fBaxparparafitblas\fR
+and
+\fBaxparparafitblas_random\fR\.
+.RE
+.PP
+[\fB\-r \fR\fB\fInumberOfRandomLinks\fR\fR]
+.RS 4
+Only for
+\fBaxparparafitblas_random\fR: specify the number of randomly selected individual cospeciation tests\. Defaults to the number of non\-zero entries in
+\fIassociationMatrix\fR
+(equivalent to full analysis)\.
+.RE
+.PP
+\fB\-h\fR
+.RS 4
+Displays an help message\.
+.RE
+.SH "SEE ALSO"
+.PP
+\fBaxpcoords\fR
+(1)
+.PP
+The programs are documented by
+Alexandros Stamatakis, Alexander Auch, Jan Meier\-Kolthoff, Markus Göker: "AxPcoords & Parallel AxParafit: Statistical Co\-Phylogenetic Analyses on Thousands of Taxa", BMC Bioinformatics 8:405, 2007\.
+.PP
+Homepage:
+http://icwww\.epfl\.ch/~stamatak/AxParafit\.html
+.SH "AUTHOR"
+.PP
+This manual page was written by David Paleino
+<d\.paleino at gmail\.com>
+for the
+Debian(TM)
+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 3 any later version published by the Free Software Foundation\.
+.PP
+On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>, Alexander Auch, Jan Meier-Kolthoff, Markus Göker
+.br
Added: trunk/packages/axparafit/trunk/debian/axparafit.1.xml
===================================================================
--- trunk/packages/axparafit/trunk/debian/axparafit.1.xml (rev 0)
+++ trunk/packages/axparafit/trunk/debian/axparafit.1.xml 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1,228 @@
+<?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 V4.5//EN"
+"http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
+
+<!--
+
+Process this file with an XSLT processor: `xsltproc \
+-''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
+manpages/docbook.xsl manpage.dbk'. A manual page
+<package>.<section> will be generated. You may view the
+manual page with: nroff -man <package>.<section> | less'. A
+typical entry in a Makefile or Makefile.am is:
+
+DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
+manpages/docbook.xsl
+XP=xsltproc -''-nonet
+
+manpage.1: manpage.dbk
+ $(XP) $(DB2MAN) $<
+
+The xsltproc binary is found in the xsltproc package. The
+XSL files are in docbook-xsl. Please remember that if you
+create the nroff version in one of the debian/rules file
+targets (such as build), you will need to include xsltproc
+and docbook-xsl in your Build-Depends control field.
+
+-->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>David</firstname>">
+ <!ENTITY dhsurname "<surname>Paleino</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>january 30, 2008</date>">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1). -->
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>d.paleino at gmail.com</email>">
+ <!ENTITY dhusername "David Paleino">
+ <!ENTITY dhucpackage "<refentrytitle>AXPARAFIT</refentrytitle>">
+ <!ENTITY dhpackage "axparafit">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <copyright>
+ <year>2007</year>
+ <holder>Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch></holder>
+ <holder>Alexander Auch</holder>
+ <holder>Jan Meier-Kolthoff</holder>
+ <holder>Markus Göker</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>axparafit</refname>
+ <refname>axparafitblas</refname>
+ <refname>axparparafit</refname>
+ <refname>axparparafitblas</refname>
+ <refname>axparparafitblas_random</refname>
+
+ <refpurpose>optimized statistical analysis of host-parasite coevolution</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+
+ <arg choice="plain"><option>-p <replaceable>numberOfPermutations</replaceable></option></arg>
+ <arg choice="plain"><option>-n1 <replaceable>N1</replaceable></option></arg>
+ <arg choice="plain"><option>-n2 <replaceable>N2</replaceable></option></arg>
+ <arg choice="plain"><option>-n3 <replaceable>N3</replaceable></option></arg>
+ <arg choice="plain"><option>-n4 <replaceable>N4</replaceable></option></arg>
+ <arg choice="plain"><option>-A <replaceable>associationMatrix</replaceable></option></arg>
+ <sbr />
+ <arg choice="plain"><option>-B <replaceable>parasiteMatrix</replaceable></option></arg>
+ <arg choice="plain"><option>-C <replaceable>hostMatrix</replaceable></option></arg>
+ <arg choice="plain"><option>-n <replaceable>runID</replaceable></option></arg>
+ <sbr />
+ <!-- these are optional -->
+ <arg choice="opt">
+ <synopfragmentref linkend="notavail">-g</synopfragmentref>
+ <option>-g</option>
+ </arg>
+ <arg choice="opt">
+ <synopfragmentref linkend="required">-t</synopfragmentref>
+ <option>-t <replaceable>traceFileName</replaceable></option>
+ </arg>
+ <arg choice="opt">
+ <synopfragmentref linkend="random">-r</synopfragmentref>
+ <option>-r <replaceable>numberOfRandomLinks</replaceable></option>
+ </arg>
+ <sbr />
+ <arg choice="plain"><option>-h</option></arg>
+
+ <synopfragment id="notavail">
+ <arg><option>-g</option> is <emphasis>not available</emphasis> in <command>axparparafit</command>, <command>axparparafitblas</command>
+ and <command>axparparafitblas_random</command>.</arg>
+ </synopfragment>
+
+ <synopfragment id="required">
+ <arg><option>-t</option> is <emphasis>required</emphasis> for <command>axparparafit</command>, <command>axparparafitblas</command>
+ and <command>axparparafitblas_random</command>.</arg>
+ </synopfragment>
+
+ <synopfragment id="random">
+ <arg><option>-r</option> is <emphasis>only</emphasis> available for <command>axparparafitblas_random</command>.</arg>
+ </synopfragment>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+
+ <para>AxParafit is a highly optimized version of Pierre Legendre's Parafit
+ program for statistical analysis of host-parasite coevolution. AxParafit
+ has been parallelized with MPI (Message Passing Interface) for compute
+ clusters and was used to carry out the largest co-evolutionary analysis to
+ date for the paper describing the software.</para>
+
+ <para>AxParafit will start executing individual tests of cospeciation
+ directly. If you want to execute only global tests of cospeciation, please
+ use the <arg>-g</arg> option.</para>
+
+ </refsect1>
+ <refsect1>
+ <title>OPTIONS</title>
+
+ <variablelist>
+ <varlistentry>
+ <term><option>-p</option></term>
+ <listitem><para>Specify the number of permutations you want to execute.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-n1 <replaceable>N1</replaceable></option></term>
+ <listitem><para>Specify number of Rows in <replaceable>associationMatrix</replaceable>.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-n2 <replaceable>N2</replaceable></option></term>
+ <listitem><para>Specify number of Columns in <replaceable>associationMatrix</replaceable>.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-n3 <replaceable>N3</replaceable></option></term>
+ <listitem><para>Specify number of Rows in <replaceable>hostMatrix</replaceable>.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-n4 <replaceable>N4</replaceable></option></term>
+ <listitem><para>Specify number of Columns in <replaceable>parasiteMatrix</replaceable>.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-A <replaceable>associationMatrix</replaceable></option></term>
+ <listitem><para>Specify file name of associaton matrix.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-B <replaceable>parasiteMatrix</replaceable></option></term>
+ <listitem><para>Specify file name of parasite matrix.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-C <replaceable>hostMatrix</replaceable></option></term>
+ <listitem><para>Specify file name of host matrix.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-n <replaceable>runID</replaceable></option></term>
+ <listitem><para>Specify a run Name/ID for this run which will be appended to the output files.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><optional><option>-g</option></optional></term>
+ <listitem>
+ <para>Execute global test of cospeciation only.</para>
+ <para>This is <emphasis>not available</emphasis> for <command>axparparafit</command>, <command>axparparafitblas</command> and
+ <command>axparparafitblas_random</command>.</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><optional><option>-t <replaceable>traceFileName</replaceable></option></optional></term>
+ <listitem><para>Specify the name of a binary trace-file written by a global cospeciation test with AxParafit.</para>
+ <para>This argument is <emphasis>required</emphasis> by <command>axparparafit</command>, <command>axparparafitblas</command>
+ and <command>axparparafitblas_random</command>.</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><optional><option>-r <replaceable>numberOfRandomLinks</replaceable></option></optional></term>
+ <listitem><para>Only for <command>axparparafitblas_random</command>: specify the number of randomly selected individual
+ cospeciation tests. Defaults to the number of non-zero entries in <replaceable>associationMatrix</replaceable>
+ (equivalent to full analysis).</para></listitem>
+ </varlistentry>
+ <varlistentry>
+ <term><option>-h</option></term>
+ <listitem><para>Displays an help message.</para></listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para><command>axpcoords</command> (1)</para>
+
+ <para>The programs are documented by <citetitle>Alexandros Stamatakis,
+ Alexander Auch, Jan Meier-Kolthoff, Markus Göker: "AxPcoords & Parallel
+ AxParafit: Statistical Co-Phylogenetic Analyses on Thousands of Taxa",
+ BMC Bioinformatics 8:405, 2007</citetitle>.</para>
+
+ <para>Homepage: <link>http://icwww.epfl.ch/~stamatak/AxParafit.html</link></para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <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 3 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/axparafit/trunk/debian/axparafitblas.1
===================================================================
--- trunk/packages/axparafit/trunk/debian/axparafitblas.1 (rev 0)
+++ trunk/packages/axparafit/trunk/debian/axparafitblas.1 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1 @@
+.so man1/axparafit.1
Added: trunk/packages/axparafit/trunk/debian/axparparafit.1
===================================================================
--- trunk/packages/axparafit/trunk/debian/axparparafit.1 (rev 0)
+++ trunk/packages/axparafit/trunk/debian/axparparafit.1 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1 @@
+.so man1/axparafit.1
Added: trunk/packages/axparafit/trunk/debian/axparparafitblas.1
===================================================================
--- trunk/packages/axparafit/trunk/debian/axparparafitblas.1 (rev 0)
+++ trunk/packages/axparafit/trunk/debian/axparparafitblas.1 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1 @@
+.so man1/axparafit.1
Added: trunk/packages/axparafit/trunk/debian/axparparafitblas_random.1
===================================================================
--- trunk/packages/axparafit/trunk/debian/axparparafitblas_random.1 (rev 0)
+++ trunk/packages/axparafit/trunk/debian/axparparafitblas_random.1 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1 @@
+.so man1/axparafit.1
Added: trunk/packages/axparafit/trunk/debian/changelog
===================================================================
--- trunk/packages/axparafit/trunk/debian/changelog (rev 0)
+++ trunk/packages/axparafit/trunk/debian/changelog 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1,5 @@
+axparafit (1.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #463219)
+
+ -- David Paleino <d.paleino at gmail.com> Wed, 30 Jan 2008 11:52:11 +0100
Added: trunk/packages/axparafit/trunk/debian/compat
===================================================================
--- trunk/packages/axparafit/trunk/debian/compat (rev 0)
+++ trunk/packages/axparafit/trunk/debian/compat 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1 @@
+6
Added: trunk/packages/axparafit/trunk/debian/control
===================================================================
--- trunk/packages/axparafit/trunk/debian/control (rev 0)
+++ trunk/packages/axparafit/trunk/debian/control 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1,22 @@
+Source: axparafit
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: David Paleino <d.paleino at gmail.com>
+Build-Depends: debhelper (>= 6), quilt,
+ refblas3-dev, atlas3-base-dev, libmpich1.0-dev
+Standards-Version: 3.7.3
+Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/axparafit/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/axparafit/trunk/?rev=0&sc=0
+XS-DM-Upload-Allowed: yes
+
+Package: axparafit
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: optimized statistical analysis of host-parasite coevolution
+ AxParafit is a highly optimized version of Pierre Legendre's Parafit program
+ for statistical analysis of host-parasite coevolution. AxParafit has been
+ parallelized with MPI (Message Passing Interface) for compute clusters and
+ was used to carry out the largest co-evolutionary analysis to date for the
+ paper describing the software.
Added: trunk/packages/axparafit/trunk/debian/copyright
===================================================================
--- trunk/packages/axparafit/trunk/debian/copyright (rev 0)
+++ trunk/packages/axparafit/trunk/debian/copyright 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1,24 @@
+Source: http://icwww.epfl.ch/~stamatak/AxParafit.html
+
+Files: debian/*
+Copyright: © 2008, David Paleino <d.paleino at gmail.com>
+License: GPL-3+
+ 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 3 of the License, or
+ (at your option) any later version.
+
+Files: *
+Copyright: © 2007, Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
+ Alexander Auch
+ Jan Meier-Kolthoff
+ Markus Göker
+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.
+
+On Debian systems, the complete text of the licenses can be found in:
+GPL-3 - `/usr/share/common-licenses/GPL'
+GPL-2 - `/usr/share/common-licenses/GPL-2'
Added: trunk/packages/axparafit/trunk/debian/dirs
===================================================================
--- trunk/packages/axparafit/trunk/debian/dirs (rev 0)
+++ trunk/packages/axparafit/trunk/debian/dirs 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/man/man1
Added: trunk/packages/axparafit/trunk/debian/install
===================================================================
--- trunk/packages/axparafit/trunk/debian/install (rev 0)
+++ trunk/packages/axparafit/trunk/debian/install 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1,5 @@
+AxParafit usr/bin
+AxParafitBLAS usr/bin
+AxParParafit usr/bin
+AxParParafitBLAS usr/bin
+AxParParafitBLAS_RANDOM usr/bin
Added: trunk/packages/axparafit/trunk/debian/patches/01-fix_Makefile.patch
===================================================================
--- trunk/packages/axparafit/trunk/debian/patches/01-fix_Makefile.patch (rev 0)
+++ trunk/packages/axparafit/trunk/debian/patches/01-fix_Makefile.patch 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1,38 @@
+--- AxParafit.dist.orig/Makefile
++++ AxParafit.dist/Makefile
+@@ -8,20 +8,20 @@
+ #added -D_HAND_OPTIMIZED_MM to compile poormath.c with the hand-tuned version of
+ #dense matric mult by default
+
+-CFLAGS = -O3 -fomit-frame-pointer -funroll-loops -D_HAND_OPTIMIZED_MM
++#CFLAGS = -O3 -fomit-frame-pointer -funroll-loops -D_HAND_OPTIMIZED_MM
+
+ ######################################################################################################
+ # SPECIFY 32 or 64 bit architecture
+
+ #ARCH=64
+-ARCH=32
+-ARCHFLAGS=-m$(ARCH)
++#ARCH=32
++#ARCHFLAGS=-m$(ARCH)
+
+ ######################################################################################################
+ # STATIC or DYNAMIC linking of libraries
+
+ #LINKERFLAGS=-static
+-LINKERFLAGS=
++#LINKERFLAGS=$(LDFLAGS)
+
+ ######################################################################################################
+ # AMD ACML BLAS-specific FLAGS
+@@ -54,8 +54,8 @@
+ # ATLAS BLAS-specific FLAGS
+ # ATTENTION ! ATTENTION ! adapt BLAS and BLAS_CFLAGS to your local installation/path
+
+-BLAS_CFLAGS = -O3 -fomit-frame-pointer -funroll-loops -D_USE_ATLAS -I/root/ATLAS-LIB/Linux_P4SSE2/include/
+-BLAS = -L/root/ATLAS-LIB/Linux_P4SSE2/lib/ -lm -lcblas -latlas
++#BLAS_CFLAGS = -O3 -fomit-frame-pointer -funroll-loops -D_USE_ATLAS -I/root/ATLAS-LIB/Linux_P4SSE2/include/
++#BLAS = -L/root/ATLAS-LIB/Linux_P4SSE2/lib/ -lm -lcblas -latlas
+
+ ######################################################################################################
+
Added: trunk/packages/axparafit/trunk/debian/patches/series
===================================================================
--- trunk/packages/axparafit/trunk/debian/patches/series (rev 0)
+++ trunk/packages/axparafit/trunk/debian/patches/series 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1 @@
+01-fix_Makefile.patch
Added: trunk/packages/axparafit/trunk/debian/rules
===================================================================
--- trunk/packages/axparafit/trunk/debian/rules (rev 0)
+++ trunk/packages/axparafit/trunk/debian/rules 2008-01-30 10:54:18 UTC (rev 1219)
@@ -0,0 +1,80 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+include /usr/share/quilt/quilt.make
+
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+CFLAGS = -Wall -g -fomit-frame-pointer -funroll-loops #-D_HAND_OPTIMIZED_MM
+LDFLAGS = -lm -lcblas -latlas -Wl,-z,defs,--as-needed
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+ifeq ($(DEB_BUILD_GNU_TYPE), x86-64-linux)
+ CFLAGS += -m64
+else
+ CFLAGS += -m32
+endif
+
+XP=xsltproc -o debian/ -''-nonet
+manpages: axparafit.1
+axparafit.1: debian/axparafit.1.xml
+ $(XP) $<
+
+build: build-stamp
+build-stamp: patch
+ dh_testdir
+ $(MAKE) CFLAGS="$(CFLAGS) -D_HAND_OPTIMIZED_MM" BLAS_CFLAGS="$(CFLAGS) -D_USE_ATLAS" LINKERFLAGS="$(LDFLAGS)"
+ touch $@
+
+clean: unpatch
+ dh_testdir
+ dh_testroot
+ [ ! -f Makefile ] || $(MAKE) clean
+ dh_clean build-stamp
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ dh_install
+
+binary-indep: build install
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+
+# this is here because it seems like in the install: target
+# the $(shell ...) command gets executed before dh_installdirs,
+# thus failing.
+ for i in $(shell ls $(CURDIR)/debian/axparafit/usr/bin); \
+ do \
+ #echo $$i; \
+ lowercase=$$(echo $$i | tr [A-Z] [a-z]); \
+ dir=$(CURDIR)/debian/axparafit/usr/bin; \
+ [ "$$lowercase" == "$$i" ] || mv $$dir/$$i $$dir/$$lowercase; \
+ done;
+
+ dh_installchangelogs
+ dh_installdocs
+# dh_installmenu
+ dh_installman debian/axpar*.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
Property changes on: trunk/packages/axparafit/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
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