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\&.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 (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 "[email protected]"> + <!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 <f...@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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
