Author: tille Date: 2011-02-16 14:57:27 +0000 (Wed, 16 Feb 2011) New Revision: 6002
Added: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu trunk/packages/beast-mcmc/trunk/debian/control trunk/packages/beast-mcmc/trunk/debian/get-orig-source trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch trunk/packages/beast-mcmc/trunk/debian/patches/series trunk/packages/beast-mcmc/trunk/debian/rules Log: Get rid of more binary jars, rebuild prebuilded pdf files instead of shipping them in tarball (Build-Depends from texlive needs to be added!) Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2011-02-16 12:38:05 UTC (rev 6001) +++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.menu 2011-02-16 14:57:27 UTC (rev 6002) @@ -5,7 +5,7 @@ command="x-terminal-emulator -e sh -c \"/usr/bin/beast-mcmc; read\""\ hints="Bayesian evolutionary analysis sampling trees"\ icon="/usr/share/pixmaps/beast.xpm" - + ?package(beast-mcmc):\ needs="x11"\ section="Applications/Science/Biology"\ Modified: trunk/packages/beast-mcmc/trunk/debian/control =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/control 2011-02-16 12:38:05 UTC (rev 6001) +++ trunk/packages/beast-mcmc/trunk/debian/control 2011-02-16 14:57:27 UTC (rev 6002) @@ -7,7 +7,8 @@ Andreas Tille <[email protected]> Build-Depends: debhelper (>= 7.1), javahelper (>=0.25), quilt (>= 0.47), ant, ant-optional, openjdk-6-jdk, libgcj10-dev, - libjebl2-java, libjam-java, r-cran-rjava, libcommons-math-java, libjdom1-java + libjebl2-java, libjam-java, figtree, + r-cran-rjava, libcommons-math-java, libjdom1-java, junit4 Standards-Version: 3.9.1 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/beast-mcmc/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/beast-mcmc/trunk/ Modified: trunk/packages/beast-mcmc/trunk/debian/get-orig-source =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2011-02-16 12:38:05 UTC (rev 6001) +++ trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2011-02-16 14:57:27 UTC (rev 6002) @@ -17,12 +17,29 @@ for jar in \ JRI.jar \ commons-math-2.0.jar \ + figtreepanel.jar \ jam.jar \ jdom.jar \ jebl.jar \ + junit-4.4.jar \ ; do rm -rf ${TARDIR}/lib/$jar done +rm -rf ${TARDIR}/release/Mac ${TARDIR}/release/Windows ${TARDIR}/release/Linux/lib/* + +set -x +# remove duplicated docs +for pdf in \ + release/common/doc/PackageStructure.pdf \ + release/common/doc/Practical_BEAST.pdf \ + "doc/Virus*Tex/Practical_BEAST.pdf" \ + 'doc/Virus*Tex/Practical_BEAST.aux' \ + release/common/doc/Yule.pdf \ + doc/Yule.pdf \ + doc/StarBEAST/STARBEAST.pdf \ + ; do + rm -rf ${TARDIR}/$pdf +done + GZIP="--best --no-name" tar czf ${TARBALL} ${TARDIR} - Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2011-02-16 12:38:05 UTC (rev 6001) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2011-02-16 14:57:27 UTC (rev 6002) @@ -8,19 +8,21 @@ <property name="dist" location="${build}/dist" /> <property name="main_class_BEAST" value="dr.app.beast.BeastMain" /> -@@ -20,6 +21,11 @@ +@@ -20,6 +21,13 @@ <path id="classpath"> <fileset dir="${lib}" includes="**/*.jar"/> + <fileset dir="${deblib}" includes="commons-math.jar"/> ++ <fileset dir="${deblib}" includes="figtree.jar"/> + <fileset dir="${deblib}" includes="jam.jar"/> + <fileset dir="${deblib}" includes="jdom1.jar"/> + <fileset dir="${deblib}" includes="jebl.jar"/> + <fileset dir="/usr/lib/R/site-library/rJava/jri/" includes="JRI.jar"/> ++ <fileset dir="${deblib}" includes="junit4.jar"/> </path> <!-- start --> -@@ -130,12 +136,8 @@ +@@ -130,12 +138,8 @@ <include name="org/virion/jam/**/*.png" /> <include name="dr/**/*.properties" /> </fileset> @@ -33,7 +35,7 @@ <zipgroupfileset dir="${lib}" includes="colt.jar" /> <zipgroupfileset dir="${lib}" includes="beagle.jar" /> </jar> -@@ -193,8 +195,6 @@ +@@ -193,8 +197,6 @@ <fileset dir="${src}"> <include name="dr/**/*.png" /> </fileset> @@ -44,22 +46,25 @@ <zipgroupfileset dir="${lib}" includes="mtj.jar" /> --- beast-mcmc-1.6.1+svnr3660.orig.orig/.classpath +++ beast-mcmc-1.6.1+svnr3660.orig/.classpath -@@ -3,13 +3,13 @@ +@@ -3,14 +3,14 @@ <classpathentry kind="src" path="src"/> <classpathentry kind="lib" path="lib/beagle.jar"/> <classpathentry kind="lib" path="lib/colt.jar"/> - <classpathentry kind="lib" path="lib/commons-math-1.2.jar"/> +- <classpathentry kind="lib" path="lib/figtreepanel.jar"/> + <classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/> - <classpathentry kind="lib" path="lib/figtreepanel.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/figtree.jar"/> <classpathentry kind="lib" path="lib/itext-1.4.5.jar"/> - <classpathentry kind="lib" path="lib/jam.jar"/> - <classpathentry kind="lib" path="lib/jdom.jar"/> - <classpathentry kind="lib" path="lib/jebl.jar"/> - <classpathentry kind="lib" path="lib/JRI.jar"/> +- <classpathentry kind="lib" path="lib/junit-4.4.jar"/> + <classpathentry kind="lib" path="/usr/share/java/jam.jar"/> + <classpathentry kind="lib" path="/usr/share/java/jdom1.jar"/> + <classpathentry kind="lib" path="/usr/share/java/jebl.jar"/> + <classpathentry kind="lib" path="/usr/lib/R/site-library/rJava/jri/JRI.jar"/> - <classpathentry kind="lib" path="lib/junit-4.4.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/junit4.jar"/> <classpathentry kind="lib" path="lib/libjri.jnilib"/> <classpathentry kind="lib" path="lib/mpj.jar"/> + <classpathentry kind="lib" path="lib/mtj.jar"/> Added: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch 2011-02-16 14:57:27 UTC (rev 6002) @@ -0,0 +1,40 @@ +--- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/StarBEAST/STARBEAST.tex ++++ beast-mcmc-1.6.1+svnr3660.orig/doc/StarBEAST/STARBEAST.tex +@@ -8,7 +8,7 @@ + + \author{Joseph Heled, Alexei J Drummond and Walter Xie} + +-\date{\today{}} ++\date{October 8, 2010} + + \maketitle + +--- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/Yule.tex ++++ beast-mcmc-1.6.1+svnr3660.orig/doc/Yule.tex +@@ -35,6 +35,7 @@ + \begin{document} + + \title{\textbf{The Yule model}} ++\date{22. May, 2007} + + \author{\textsc{Alexei J. Drummond}} + +--- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/BookSection/BookSection.tex ++++ beast-mcmc-1.6.1+svnr3660.orig/doc/BookSection/BookSection.tex +@@ -1,7 +1,7 @@ + + \NeedsTeXFormat{LaTeX2e}[1996/06/01] + +-\documentclass[cup7b, english]{cupbook} ++\documentclass[english]{report} + + + \usepackage{graphicx} +@@ -32,6 +32,7 @@ + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% User specified LaTeX commands. + + \title{The Phylogenetics Handbook} ++\date{September 14, 2007} + + \makeatother + \begin{document} Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/series 2011-02-16 12:38:05 UTC (rev 6001) +++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2011-02-16 14:57:27 UTC (rev 6002) @@ -1,3 +1,4 @@ beast.patch fix_gcc_options.patch fix_classpath_in_build_xml.patch +patch_tex_docs.patch Modified: trunk/packages/beast-mcmc/trunk/debian/rules =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-16 12:38:05 UTC (rev 6001) +++ trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-16 14:57:27 UTC (rev 6002) @@ -10,7 +10,7 @@ TARBALL=$(PACKAGE)_$(SRC_VERSION).orig.tar.gz DEBJAR := /usr/share/java -CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/itext-1.4.5.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:lib/junit-4.4.jar:lib/figtreepanel.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jar.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar +CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/itext-1.4.5.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jar.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar # to run the test suite JAVA := /usr/lib/jvm/java-6-openjdk/bin/java @@ -31,6 +31,12 @@ CLASSPATH=$(CLASS_PATH) ant build ; \ cd native && /bin/sh compileNativeLinux.sh # + # Build extra LaTeX documentation + cd doc/BookSection; pdflatex BookSection.tex; pdflatex BookSection.tex + cd doc/StarBEAST; pdflatex STARBEAST.tex; bibtex STARBEAST; pdflatex STARBEAST.tex; pdflatex STARBEAST.tex + cd doc/Virus\ Practical\ Tex; pdflatex Practical_BEAST.tex; pdflatex Practical_BEAST.tex + cd doc; pdflatex Yule.tex; pdflatex Yule.tex + # ##################################################################### ## Run test suite ## ## -------------- ## _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
