[med-svn] r4549 - trunk/packages/beast-mcmc/trunk/debian
Felix Feyertag
fxf-guest at alioth.debian.org
Mon Jan 18 23:59:36 UTC 2010
Author: fxf-guest
Date: 2010-01-18 23:59:36 +0000 (Mon, 18 Jan 2010)
New Revision: 4549
Added:
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1.xml
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu
Modified:
trunk/packages/beast-mcmc/trunk/debian/changelog
trunk/packages/beast-mcmc/trunk/debian/rules
Log:
New upstream release.
Added man page.
Added: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1 (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1 2010-01-18 23:59:36 UTC (rev 4549)
@@ -0,0 +1,228 @@
+'\" t
+.\" Title: BEAST-MCMC
+.\" Author: Alexei J. Drummond
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 01/19/2010
+.\" Manual: BEAST-MCMC Manual
+.\" Source: BEAST 1.5.3
+.\" Language: English
+.\"
+.TH "BEAST\-MCMC" "1" "01/19/2010" "BEAST 1.5.3" "BEAST-MCMC Manual"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+beast-mcmc \- Bayesian evolutionary analysis sampling trees
+.SH "SYNOPSIS"
+.HP \w'\fBbeast\-mcmc\fR\ 'u
+\fBbeast\-mcmc\fR [\fBOPTIONS\fR] [\fIinput\&.xml\fR]
+.HP \w'\fBbeast\-mcmc\fR\ 'u
+\fBbeast\-mcmc\fR [\fB\-verbose\fR | \fB\-strict\fR | \fB\-window\fR | \fB\-options\fR | \fB\-working\fR | \fB\-seed\fR | \fB\-errors\ i\fR | \fB\-threads\ i\fR | \fB\-java\fR | \fB\-beagle\fR | \fB\-beagle_info\fR | \fB\-beagle_resource_order\fR | \fB\-help\fR | \fBinput\&.xml\fR]
+.SH "DESCRIPTION"
+.PP
+BEAST is a cross\-platform program for Bayesian MCMC analysis of molecular sequences\&. It is orientated towards rooted, time\-measured phylogenies inferred using strict or relaxed molecular clock models\&. It is intended both as a method of reconstructing phylogenies and as a framework for testing evolutionary hypotheses without conditioning on a single tree topology\&. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability\&. We include a simple to use user\-interface program for setting up standard analyses and a suite of programs for analysing the results\&. There are three main areas of research for which the BEAUti/BEAST package is particularly applicable\&. These areas are species phylogenies for molecular dating, coalescent\-based population genetics and measurably evolving populations (ancient DNA or time\-stamped viral sequence data sets)\&.
+.SH "OPTIONS"
+.PP
+\fB\-verbose\fR
+.RS 4
+verbose XML parsing messages
+.RE
+.PP
+\fB\-strict\fR
+.RS 4
+fail on non conforming BEAST XML file
+.RE
+.PP
+\fB\-window\fR
+.RS 4
+provide a console window
+.RE
+.PP
+\fB\-options\fR
+.RS 4
+display an options dialog
+.RE
+.PP
+\fB\-working\fR
+.RS 4
+change working directory to input file\'s directory
+.RE
+.PP
+\fB\-seed\fR
+.RS 4
+specify a random number generator seed
+.RE
+.PP
+\fB\-errors \fR\fB\fIi\fR\fR
+.RS 4
+maximum number of numerical errors before stopping
+.RE
+.PP
+\fB\-threads \fR\fB\fIi\fR\fR
+.RS 4
+the number of computational threads to use (default 1)
+.RE
+.PP
+\fB\-java\fR
+.RS 4
+use Java only, no native implementations
+.RE
+.PP
+\fB\-beagle\fR
+.RS 4
+use beagle library if available
+.RE
+.PP
+\fB\-beagle_info\fR
+.RS 4
+show information on available beagle resources
+.RE
+.PP
+\fB\-beagle_resource_order\fR
+.RS 4
+set order of beagle resources
+.RE
+.PP
+\fB\-help\fR
+.RS 4
+print usage screen
+.RE
+.SH "BUGS"
+.PP
+The BEAST bug tracking system can be found at
+\m[blue]\fB\%http://code.google.com/p/beast-mcmc/issues/list\fR\m[]\&.
+.SH "SEE ALSO"
+.PP
+\fBbeauti\fR(1)\&.
+.SH "REFERENCES"
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees\&." BMC Evolutionary Biology 7:214\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185\-1192\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307\-1320\&.
+.RE
+.SH "AUTHORS"
+.PP
+\fBAlexei J\&. Drummond\fR
+.RS 4
+Copyright holder for BEAST\&.
+.RE
+.PP
+\fBAndrew Rambaut\fR
+.RS 4
+Copyright holder for BEAST\&.
+.RE
+.PP
+\fBMarc A\&. Suchard\fR
+.RS 4
+Copyright holder for BEAST\&.
+.RE
+.PP
+\fBFelix Feyertag\fR <\&felix\&.feyertag at googlemail\&.com\&>
+.RS 4
+Prepared this manpage in DocBook XML for the Debian distribution\&.
+.RE
+.SH "COPYRIGHT"
+.br
+CopyrightCopyright \(co 2002\(en2009 Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (BEAST)
+.br
+Copyright \(co 2002\(en2009 Felix Feyertag (This manpage)
+.br
+.PP
+The binaries and source code are made available and can be distributed subject to the following conditions:
+.PP
+BEAST is Copyright (C) 2002\-2006 Alexei Drummond and Andrew Rambaut BEAST is distributed under the terms of the GNU Lesser General Public License\&. See the notice in individual files and the file LICENSE for licensing details\&.
+.PP
+BEAST includes software libraries from projects whose licensing terms require that the following notices be included when they are distributed in binary form and that the recipient be given a copy of their respective licenses\&.
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+This product includes software developed by the JDOM Project (http://www\&.jdom\&.org/)
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+This product includes software developed by The Apache Software Foundation (http://www\&.apache\&.org/)
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+The license for JDOM can be read in the LICENSE\&.txt file in the source distribution available at http://www\&.jdom\&.org/
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+The license for the Commons Math library can be read at http://www\&.apache\&.org/licenses/LICENSE\-2\&.0 or in the LICENSE\&.txt file in the source distribution available at http://jakarta\&.apache\&.org/commons/math/
+.RE
+.PP
+This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\&.
+.sp
Property changes on: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1.xml
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1.xml (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1.xml 2010-01-18 23:59:36 UTC (rev 4549)
@@ -0,0 +1,325 @@
+<?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" [
+
+<!-- Template from docbook-xsl-1.73.2.dfsg.1-3 -->
+
+<!-- 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 "Felix">
+ <!ENTITY dhsurname "Feyertag">
+ <!ENTITY dhemail "felix.feyertag at googlemail.com">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "1.5.3">
+ <!ENTITY dhtitle "BEAST-MCMC Manual">
+ <!ENTITY dhucpackage "BEAST-MCMC">
+ <!ENTITY dhpackage "beast-mcmc">
+ <!ENTITY dhproduct "BEAST">
+ <!ENTITY dhsection "1">
+]>
+
+<refentry>
+ <refentryinfo>
+ <title>&dhtitle;</title>
+ <productname>&dhproduct;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <authorgroup>
+ <author>
+ <firstname>Alexei J.</firstname>
+ <surname>Drummond</surname>
+ <contrib>Copyright holder for &dhproduct;.</contrib>
+ </author>
+ <author>
+ <firstname>Andrew</firstname>
+ <surname>Rambaut</surname>
+ <contrib>Copyright holder for &dhproduct;.</contrib>
+ </author>
+ <author>
+ <firstname>Marc A.</firstname>
+ <surname>Suchard</surname>
+ <contrib>Copyright holder for &dhproduct;.</contrib>
+ </author>
+ </authorgroup>
+ <authorgroup>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Prepared this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <copyright>
+ <year>2002–2009</year>
+ <holder>Alexei J. Drummond, Andrew Rambaut & Marc A. Suchard (&dhproduct;)</holder>
+ </copyright>
+ <copyright>
+ <year>2002–2009</year>
+ <holder>&dhusername; (This manpage)</holder>
+ </copyright>
+ <legalnotice>
+ <para>
+ The binaries and source code are made available and can be distributed subject to the following conditions:
+ </para>
+ <para>
+BEAST is Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
+BEAST is distributed under the terms of the GNU Lesser General Public License.
+See the notice in individual files and the file LICENSE for licensing details.
+ </para>
+ <para>
+BEAST includes software libraries from projects whose licensing
+terms require that the following notices be included when they are
+distributed in binary form and that the recipient be given a copy of
+their respective licenses.
+ </para>
+ <itemizedlist>
+ <listitem>
+ <para>
+This product includes software developed by the
+JDOM Project (http://www.jdom.org/)
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+This product includes software developed by
+The Apache Software Foundation (http://www.apache.org/)
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+The license for JDOM can be read in the LICENSE.txt file in the
+source distribution available at http://www.jdom.org/
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+The license for the Commons Math library can be read at
+http://www.apache.org/licenses/LICENSE-2.0 or in the LICENSE.txt file
+in the source distribution available at
+http://jakarta.apache.org/commons/math/
+ </para>
+ </listitem>
+ </itemizedlist>
+ </legalnotice>
+ <legalnotice>
+ <para>
+ This manual page and its XML source can be used, modified, and redistributed as if it were in public domain.
+ </para>
+ </legalnotice>
+ </refentryinfo>
+
+ <refmeta>
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
+
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+ <refpurpose>Bayesian evolutionary analysis sampling trees</refpurpose>
+ </refnamediv>
+
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt"><option>OPTIONS</option></arg>
+ <arg choice="opt"><replaceable>input.xml</replaceable></arg>
+ </cmdsynopsis>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <!-- Normally the help and version options make the programs stop
+ right after outputting the requested information. -->
+ <group choice="opt">
+ <arg choice="plain"><option>-verbose</option></arg>
+ <arg choice="plain"><option>-strict</option></arg>
+ <arg choice="plain"><option>-window</option></arg>
+ <arg choice="plain"><option>-options</option></arg>
+ <arg choice="plain"><option>-working</option></arg>
+ <arg choice="plain"><option>-seed</option></arg>
+ <arg choice="plain"><option>-errors i</option></arg>
+ <arg choice="plain"><option>-threads i</option></arg>
+ <arg choice="plain"><option>-java</option></arg>
+ <arg choice="plain"><option>-beagle</option></arg>
+ <arg choice="plain"><option>-beagle_info</option></arg>
+ <arg choice="plain"><option>-beagle_resource_order</option></arg>
+ <arg choice="plain"><option>-help</option></arg>
+ <arg choice="plain"><option>input.xml</option></arg>
+ </group>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>
+BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is orientated towards rooted,
+time-measured phylogenies inferred using strict or relaxed molecular clock models. It is intended both as a method of
+reconstructing phylogenies and as a framework for testing evolutionary hypotheses without conditioning on a single tree
+topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior
+probability. We include a simple to use user-interface program for setting up standard analyses and a suite of programs
+for analysing the results. There are three main areas of research for which the BEAUti/BEAST package is particularly
+applicable. These areas are species phylogenies for molecular dating, coalescent-based population genetics and
+measurably evolving populations (ancient DNA or time-stamped viral sequence data sets).
+ </para>
+
+ </refsect1>
+
+ <refsect1 id="options">
+ <title>OPTIONS</title>
+
+ <variablelist>
+ <varlistentry>
+ <term>
+ <option>-verbose</option>
+ </term>
+ <listitem>
+ <para>verbose XML parsing messages</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-strict</option>
+ </term>
+ <listitem>
+ <para>fail on non conforming BEAST XML file</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-window</option>
+ </term>
+ <listitem>
+ <para>provide a console window</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-options</option>
+ </term>
+ <listitem>
+ <para>display an options dialog</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-working</option>
+ </term>
+ <listitem>
+ <para>change working directory to input file's directory</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-seed</option>
+ </term>
+ <listitem>
+ <para>specify a random number generator seed</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-errors <replaceable class="parameter">i</replaceable></option>
+ </term>
+ <listitem>
+ <para>maximum number of numerical errors before stopping</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-threads <replaceable class="parameter">i</replaceable></option>
+ </term>
+ <listitem>
+ <para>the number of computational threads to use (default 1)</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-java</option>
+ </term>
+ <listitem>
+ <para>use Java only, no native implementations</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-beagle</option>
+ </term>
+ <listitem>
+ <para>use beagle library if available</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-beagle_info</option>
+ </term>
+ <listitem>
+ <para>show information on available beagle resources</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-beagle_resource_order</option>
+ </term>
+ <listitem>
+ <para>set order of beagle resources</para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
+ <term>
+ <option>-help</option>
+ </term>
+ <listitem>
+ <para>print usage screen</para>
+ </listitem>
+ </varlistentry>
+ </variablelist>
+ </refsect1>
+
+ <refsect1 id="bugs">
+ <!-- Or use this section to tell about upstream BTS. -->
+ <title>BUGS</title>
+ <para>The &dhproduct; bug tracking system can be found at <ulink url="http://code.google.com/p/beast-mcmc/issues/list"/>.</para>
+ </refsect1>
+
+ <refsect1 id="see_also">
+ <title>SEE ALSO</title>
+ <!-- In alpabetical order. -->
+ <para><citerefentry>
+ <refentrytitle>beauti</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>.</para>
+ </refsect1>
+
+ <refsect1 id="references">
+ <title>REFERENCES</title>
+ <itemizedlist>
+ <listitem>
+ <para>
+ Drummond AJ, Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7:214.
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Drummond AJ, Ho SYW, Phillips MJ & Rambaut A (2006) PLoS Biology 4, e88.
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Drummond AJ, Rambaut A & Shapiro B and Pybus OG (2005) Mol Biol Evol 22, 1185-1192.
+ </para>
+ </listitem>
+ <listitem>
+ <para>
+ Drummond AJ, Nicholls GK, Rodrigo AG & Solomon W (2002) Genetics 161, 1307-1320.
+ </para>
+ </listitem>
+ </itemizedlist>
+ </refsect1>
+</refentry>
Added: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2010-01-18 23:59:36 UTC (rev 4549)
@@ -0,0 +1,6 @@
+?package(beast-mcmc):needs="text"\
+ section="Applications/Science/Biology"\
+ title="BEAST"\
+ command="/usr/bin/beast-mcmc"\
+ hints="Bayesian evolutionary analysis sampling trees"
+
Modified: trunk/packages/beast-mcmc/trunk/debian/changelog
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/changelog 2010-01-18 16:57:55 UTC (rev 4548)
+++ trunk/packages/beast-mcmc/trunk/debian/changelog 2010-01-18 23:59:36 UTC (rev 4549)
@@ -1,3 +1,9 @@
+beast-mcmc (1.5.3+svnr2672-1) karmic; urgency=low
+
+ * New upstream release
+
+ -- Felix Feyertag <fx at atalanta> Mon, 18 Jan 2010 18:13:41 +0100
+
beast-mcmc (1.5.2+svnr2377-1) UNRELEASED; urgency=low
* Initial release. (Closes: #552101)
Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules 2010-01-18 16:57:55 UTC (rev 4548)
+++ trunk/packages/beast-mcmc/trunk/debian/rules 2010-01-18 23:59:36 UTC (rev 4549)
@@ -3,10 +3,10 @@
#export DH_VERBOSE=1
-#include /usr/share/cdbs/1/rules/debhelper.mk
#include /usr/share/cdbs/1/class/ant.mk
#include /usr/share/cdbs/1/rules/simple-patchsys.mk
include /usr/share/quilt/quilt.make
+#include /usr/share/cdbs/1/rules/debhelper.mk
PACKAGE = beast-mcmc
@@ -15,7 +15,7 @@
TARBALL = $(PACKAGE)_$(SRC_VERSION).orig.tar.gz
JAVA := /usr/lib/jvm/java-6-openjdk/bin/java
-CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:lib/beagle.jar:lib/commons-math-1.2.jar:lib/itext-1.4.5.jar:lib/jdom.jar:lib/JRI.jar:lib/libjri.jnilib:lib/mtj.jar:lib/colt.jar:lib/figtreepanel.jar:lib/jam.jar:lib/jebl.jar:lib/junit-4.4.jar:lib/mpj.jar:lib/options.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar
+CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:lib/beagle.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/itext-1.4.5.jar:lib/commons-math-2.0.jar:lib/beagle.jar:lib/jebl.jar:lib/mpj.jar:lib/jam.jar:lib/org.boehn.kmlframework_20090320.jar:lib/junit-4.4.jar:lib/JRI.jar:lib/figtreepanel.jar:lib/colt.jar:lib/jdom.jar:lib/options.jar:lib/mtj.jar
ANT_HOME := /usr/share/ant
ANT_BIN := $(ANT_HOME)/bin/ant
ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true
@@ -39,7 +39,7 @@
dh_testroot
rm -f build-stamp configure-stamp
## Add here commands to clean up after the build process.
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_BEAST_MCMC.xml clean
+ #$(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml clean
rm -f native/*\.o
dh_clean
@@ -48,24 +48,13 @@
configure-stamp:
dh_testdir
# Add here commands to configure the package.
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_BEAST_MCMC.xml init
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_coalsim.xml init
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_pathogen.xml init
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_treestat.xml init
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_vcs.xml init
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml init
touch configure-stamp
build: build-stamp
build-stamp: patch
dh_testdir
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_BEAST_MCMC.xml compile-all dist_all_BEAST
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_coalsim.xml compile-all
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_pathogen.xml compile-all dist
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_treestat.xml compile-all
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_vcs.xml compile-all
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml build-project
+ $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml build_jar_all_BEAST_NoJUnitTest
cd native && make linux
touch build-stamp
@@ -74,7 +63,7 @@
dh_testroot
#dh_installdocs $(CURDIR)/debian/readme.html
dh_installdocs
- dh_installman debian/mencal.1
+ dh_installman debian/beast-mcmc.1
dh_installchangelogs
dh_link
dh_strip
@@ -91,7 +80,7 @@
test:
dh_testdir
- $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build_BEAST_MCMC.xml junit
+ $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml junit
binary-arch: build install
dh binary-arch
@@ -106,7 +95,8 @@
dh_testroot
dh_clean -k
dh_installdirs
- install $(CURDIR)/scripts/beast $(CURDIR)/debian/beast-mcmc/usr/bin/
+ mv $(CURDIR)/scripts/beast $(CURDIR)/scripts/beast-mcmc
+ install $(CURDIR)/scripts/beast-mcmc $(CURDIR)/debian/beast-mcmc/usr/bin/
install $(CURDIR)/scripts/beauti $(CURDIR)/debian/beast-mcmc/usr/bin/
install $(CURDIR)/scripts/loganalyser $(CURDIR)/debian/beast-mcmc/usr/bin/
install $(CURDIR)/scripts/logcombiner $(CURDIR)/debian/beast-mcmc/usr/bin/
@@ -117,7 +107,8 @@
install -m 664 $(CURDIR)/release/common/icons/beast.png $(CURDIR)/debian/beast-mcmc/usr/share/pixmaps/
install -m 664 $(CURDIR)/doc/*pdf $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/doc
install -m 664 $(CURDIR)/doc/Virus\ Practical\ Tex/*pdf $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/doc
- install -d -m 664 $(CURDIR)/examples $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/examples
+ install -m 664 $(CURDIR)/examples/*\.xml $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/examples
+ install -m 664 $(CURDIR)/examples/*\.nex $(CURDIR)/debian/beast-mcmc/usr/share/beast-mcmc/examples
dh_desktop
dh_installmenu
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