Author: fxf-guest
Date: 2010-01-19 20:36:53 +0000 (Tue, 19 Jan 2010)
New Revision: 4553
Added:
trunk/packages/beast-mcmc/trunk/debian/beauti.1
trunk/packages/beast-mcmc/trunk/debian/beauti.1.xml
trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch
Modified:
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1.xml
trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu
trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch
trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch
trunk/packages/beast-mcmc/trunk/debian/patches/series
trunk/packages/beast-mcmc/trunk/debian/rules
Log:
beauti man page
updated patches
Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1.xml
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1.xml 2010-01-19
09:15:38 UTC (rev 4552)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.1.xml 2010-01-19
20:36:53 UTC (rev 4553)
@@ -59,11 +59,11 @@
</author>
</authorgroup>
<copyright>
- <year>2002–2009</year>
+ <year>2002–2010</year>
<holder>Alexei J. Drummond, Andrew Rambaut & Marc
A. Suchard (&dhproduct;)</holder>
</copyright>
<copyright>
- <year>2002–2009</year>
+ <year>2009–2010</year>
<holder>&dhusername; (This manpage)</holder>
</copyright>
<legalnotice>
Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2010-01-19
09:15:38 UTC (rev 4552)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2010-01-19
20:36:53 UTC (rev 4553)
@@ -1,6 +1,31 @@
-?package(beast-mcmc):needs="text"\
+?package(beast-mcmc):
+ needs="text"\
section="Applications/Science/Biology"\
title="BEAST"\
command="/usr/bin/beast-mcmc"\
- hints="Bayesian evolutionary analysis sampling trees"
+ hints="Bayesian evolutionary analysis sampling trees"\
+ icon="/usr/share/pixmaps/beast.png"
+?package(beast-mcmc):\
+ needs="x11"\
+ section="Applications/Science/Biology"\
+ title="BEAST"\
+ command="/usr/bin/beast-mcmc"\
+ hints="Bayesian evolutionary analysis sampling trees"\
+ icon="/usr/share/pixmaps/beast.png"
+
+?package(beast-mcmc):\
+ needs="text"\
+ section="Applications/Science/Biology"\
+ title="BEAUti"\
+ command="/usr/bin/beauti"\
+ hints="Bayesian Evolutionary Analysis Utility"\
+ icon="/usr/share/pixmaps/beast.png"
+
+?package(beast-mcmc):\
+ needs="x11"\
+ section="Applications/Science/Biology"\
+ title="BEAUti"\
+ command="/usr/bin/beauti"\
+ hints="Bayesian Evolutionary Analysis Utility"\
+ icon="/usr/share/pixmaps/beast.png"
Added: trunk/packages/beast-mcmc/trunk/debian/beauti.1
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beauti.1
(rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beauti.1 2010-01-19 20:36:53 UTC
(rev 4553)
@@ -0,0 +1,160 @@
+'\" t
+.\" Title: BEAUTI
+.\" Author: Alexei J. Drummond
+.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
+.\" Date: 01/19/2010
+.\" Manual: BEAUti Manual
+.\" Source: BEAUti 1.5.3
+.\" Language: English
+.\"
+.TH "BEAUTI" "1" "01/19/2010" "BEAUti 1.5.3" "BEAUti Manual"
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+beauti \- Bayesian Evolutionary Analysis Utility
+.SH "SYNOPSIS"
+.HP \w'\fBbeauti\fR\ 'u
+\fBbeauti\fR [\fInexus_file\ template_file\ beast_file\fR]
+.SH "DESCRIPTION"
+.PP
+BEAUti is a graphical user\-interface (GUI) application for generating
beast\-mcmc(1) XML files\&.
+.SH "BUGS"
+.PP
+The BEAUti 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
+\fBbeast-mcmc\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 BEAUti\&.
+.RE
+.PP
+\fBAndrew Rambaut\fR
+.RS 4
+Copyright holder for BEAUti\&.
+.RE
+.PP
+\fBMarc A\&. Suchard\fR
+.RS 4
+Copyright holder for BEAUti\&.
+.RE
+.PP
+\fBFelix Feyertag\fR <\&felix\&.feyer...@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 (BEAUti)
+.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
Added: trunk/packages/beast-mcmc/trunk/debian/beauti.1.xml
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beauti.1.xml
(rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beauti.1.xml 2010-01-19 20:36:53 UTC
(rev 4553)
@@ -0,0 +1,185 @@
+<?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 "[email protected]">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhrelease "1.5.3">
+ <!ENTITY dhtitle "BEAUti Manual">
+ <!ENTITY dhucpackage "BEAUTI">
+ <!ENTITY dhpackage "beauti">
+ <!ENTITY dhproduct "BEAUti">
+ <!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 Utility</refpurpose>
+ </refnamediv>
+
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ <arg choice="opt"><replaceable>nexus_file template_file
beast_file</replaceable></arg>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+
+ <refsect1 id="description">
+ <title>DESCRIPTION</title>
+ <para>
+ BEAUti is a graphical user-interface (GUI) application for
generating beast-mcmc(1) XML files.
+ </para>
+
+ </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>beast-mcmc</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/patches/beast.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch
(rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch 2010-01-19
20:36:53 UTC (rev 4553)
@@ -0,0 +1,9 @@
+--- beast-mcmc-1.5.3+svnr2672.orig/scripts/beast
++++ beast-mcmc-1.5.3+svnr2672/scripts/beast
+@@ -23,5 +23,5 @@
+ fi
+
+ BEAST_LIB=$BEAST/lib
+-java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -jar
$BEAST_LIB/beast.jar $*
++java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/lib" -cp
"$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
+
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch
2010-01-19 09:15:38 UTC (rev 4552)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch
2010-01-19 20:36:53 UTC (rev 4553)
@@ -1,50 +1,50 @@
---- beast-mcmc-1.5.2+svnr2377.orig/scripts/beast
-+++ beast-mcmc-1.5.2+svnr2377/scripts/beast
+--- beast-mcmc-1.5.3+svnr2672.orig/scripts/beast
++++ beast-mcmc-1.5.3+svnr2672/scripts/beast
@@ -22,6 +22,6 @@
cd "$saveddir"
fi
-BEAST_LIB=$BEAST/lib
-+BEAST_LIB=/usr/share/beast-mcmc/lib
- java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -jar
$BEAST_LIB/beast.jar $*
++BEAST_LIB="/usr/share/beast-mcmc/lib/"
+ java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/lib" -cp
"$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
---- beast-mcmc-1.5.2+svnr2377.orig/scripts/beauti
-+++ beast-mcmc-1.5.2+svnr2377/scripts/beauti
+--- trunk.orig/scripts/beauti
++++ trunk/scripts/beauti
@@ -22,6 +22,6 @@
cd "$saveddir"
fi
-BEAST_LIB=$BEAST/lib
-+BEAST_LIB=/usr/share/beast-mcmc/lib
++BEAST_LIB="/usr/share/beast-mcmc/lib/"
java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -jar
$BEAST_LIB/beauti.jar $*
---- beast-mcmc-1.5.2+svnr2377.orig/scripts/loganalyser
-+++ beast-mcmc-1.5.2+svnr2377/scripts/loganalyser
+--- trunk.orig/scripts/loganalyser
++++ trunk/scripts/loganalyser
@@ -22,6 +22,6 @@
cd "$saveddir"
fi
-BEAST_LIB=$BEAST/lib
-+BEAST_LIB=/usr/share/beast-mcmc/lib
++BEAST_LIB="/usr/share/beast-mcmc/lib/"
java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar
dr.app.tools.LogAnalyser $*
---- beast-mcmc-1.5.2+svnr2377.orig/scripts/logcombiner
-+++ beast-mcmc-1.5.2+svnr2377/scripts/logcombiner
+--- trunk.orig/scripts/logcombiner
++++ trunk/scripts/logcombiner
@@ -22,6 +22,6 @@
cd "$saveddir"
fi
-BEAST_LIB=$BEAST/lib
-+BEAST_LIB=/usr/share/beast-mcmc/lib
++BEAST_LIB="/usr/share/beast-mcmc/lib/"
java -Xms64m -Xmx128m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar
dr.app.tools.LogCombiner $*
---- beast-mcmc-1.5.2+svnr2377.orig/scripts/treeannotator
-+++ beast-mcmc-1.5.2+svnr2377/scripts/treeannotator
+--- trunk.orig/scripts/treeannotator
++++ trunk/scripts/treeannotator
@@ -22,6 +22,6 @@
cd "$saveddir"
fi
-BEAST_LIB=$BEAST/lib
-+BEAST_LIB=/usr/share/beast-mcmc/lib
++BEAST_LIB="/usr/share/beast-mcmc/lib/"
java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar
dr.app.tools.TreeAnnotator $*
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch
2010-01-19 09:15:38 UTC (rev 4552)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch
2010-01-19 20:36:53 UTC (rev 4553)
@@ -1,5 +1,5 @@
---- beast-mcmc-1.5.2+svnr2377.orig/native/Makefile
-+++ beast-mcmc-1.5.2+svnr2377/native/Makefile
+--- beast-mcmc-1.5.3+svnr2672.orig/native/Makefile
++++ beast-mcmc-1.5.3+svnr2672/native/Makefile
@@ -36,6 +36,6 @@
-output lib$(OUTNAME).jnilib
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/series 2010-01-19
09:15:38 UTC (rev 4552)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2010-01-19
20:36:53 UTC (rev 4553)
@@ -1,2 +1,3 @@
+beast.patch
native_flags.patch
fix_paths.patch
Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules 2010-01-19 09:15:38 UTC
(rev 4552)
+++ trunk/packages/beast-mcmc/trunk/debian/rules 2010-01-19 20:36:53 UTC
(rev 4553)
@@ -3,10 +3,7 @@
#export DH_VERBOSE=1
-#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 +12,7 @@
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:/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
+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:/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
@@ -61,23 +58,7 @@
binary-indep: build-indep install
dh_testdir
dh_testroot
- #dh_installdocs $(CURDIR)/debian/readme.html
- dh_installdocs
- dh_installman debian/beast-mcmc.1
- dh_installchangelogs
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
- dh_installdeb
- dh_perl
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-
test:
dh_testdir
$(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME)
org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml junit
@@ -86,15 +67,25 @@
dh binary-arch
binary: binary-arch
-binary-indep: # does nothing
-
-
install: build
dh_testdir
dh_testroot
dh_clean -k
dh_installdirs
+ dh_installman debian/beast-mcmc.1 debian/beauti.1
+ dh_installdocs
+ dh_installchangelogs
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_perl
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ #dh_builddeb
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/
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