Author: tille Date: 2009-03-09 11:51:10 +0000 (Mon, 09 Mar 2009) New Revision: 3161
Added: trunk/packages/biojava/ trunk/packages/biojava/trunk/ trunk/packages/biojava/trunk/debian/ trunk/packages/biojava/trunk/debian/README.Debian trunk/packages/biojava/trunk/debian/README.source trunk/packages/biojava/trunk/debian/changelog trunk/packages/biojava/trunk/debian/compat trunk/packages/biojava/trunk/debian/control trunk/packages/biojava/trunk/debian/copyright trunk/packages/biojava/trunk/debian/libbiojava-java-doc.dirs trunk/packages/biojava/trunk/debian/libbiojava-java-doc.doc-base trunk/packages/biojava/trunk/debian/libbiojava-java-doc.links trunk/packages/biojava/trunk/debian/libbiojava-java.docs trunk/packages/biojava/trunk/debian/libbiojava1.6-java.dirs trunk/packages/biojava/trunk/debian/patches/ trunk/packages/biojava/trunk/debian/patches/buildxml.patch trunk/packages/biojava/trunk/debian/patches/series trunk/packages/biojava/trunk/debian/rules trunk/packages/biojava/trunk/debian/watch Log: Injecting BioJava into Debian Med repository Added: trunk/packages/biojava/trunk/debian/README.Debian =================================================================== --- trunk/packages/biojava/trunk/debian/README.Debian (rev 0) +++ trunk/packages/biojava/trunk/debian/README.Debian 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1,19 @@ +biojava for Debian +------------------ + +All the developers of BioJava are thanked for their fine work. Special +thanks go to Colin Hardman, Andreas Prlic and Simon Brocklehurst for +reacting to my request to get a missing license information into one +of their style sheets. + +The package is not completely functional because of a dependency of +a very small fraction of code that is of little practical relevance to +the vast majority of BioJava users. This dependes on jgrapht libraries +of version 1.5 that are not in Debian. + +The packages are now all compiled with the OpenJDK, which now qualifies +them for main. However, libjgrapht in the version currently in sid is +still in contrib. This will be changed. But for now, biojava has to go to the +contrib directory, too, for exactly this reason. + + -- Steffen Moeller <[email protected]> Tue, 30 Dec 2008 01:12:41 +0100 Added: trunk/packages/biojava/trunk/debian/README.source =================================================================== --- trunk/packages/biojava/trunk/debian/README.source (rev 0) +++ trunk/packages/biojava/trunk/debian/README.source 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1,36 @@ +biojava for Debian +------------------ + +The following jars from the upstream source distribution were +substituted by Debian packages: + + bytecode.jar + commons-cli.jar + commons-collections-2.1.jar + commons-dbcp-1.1.jar + commons-pool-1.1.jar + jgrapht-jdk1.5.jar + junit-4.4.jar + +These libraries are very common (well, this probably is why they are +named this way) and hence changes in their API very likely to effect many +programs. Nevertheless, without a proper management of Java archives +in Debian, i.e., by raven/maven, it is somewhat conflict-prone to use +other Jars than the ones deployed with upstream sources. + +Exceptions is bytecode.jar which is developed by the BioJava community +and is hence always strongly coupled to this package. The jgrapht library +underwent a recent change in its API and is hence incompatible with +the latest release. + +The documentation was separated from the jar file and so was the huge +demos folder with code examples. + +If indicated as such by the string "svn" in the version string, the +sources were taken directly from the upstream subversion repository +as svn co svn://code.open-bio.org/biojava/biojava-live/trunk biojava-live + +Help to improve the packaging is appreciated. You may find more packages +of your interest at http://pkg-escience.alioth.debian.org. + + -- Steffen Moeller <[email protected]> Tue, 03 Jul 2007 01:51:06 +0200 Added: trunk/packages/biojava/trunk/debian/changelog =================================================================== --- trunk/packages/biojava/trunk/debian/changelog (rev 0) +++ trunk/packages/biojava/trunk/debian/changelog 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1,25 @@ +biojava-live (1.6.1.svn.20090306-1) experimental; urgency=low + + * Initial release (Closes:#491025). + * Added dependency to quilt. + * Moved -doc to section doc. + * Added symlinks to jar file with pseudo-soname + * Need to be placed in contrib section as a start because of dependency + to libjgrapht that is still in contrib. + + -- Steffen Moeller <[email protected]> Tue, 30 Dec 2008 19:55:36 +0100 + +biojava-live (1.6.0.svn.20080716-1) UNRELEASED; urgency=low + + * Renamed to biojava-live in analogy to upstream's name + and to keep the opportunity to add a biojava meta package + later on. + * License issue fixed that led to previous rejection of biojava. + + -- Steffen Moeller <[email protected]> Sun, 13 Jul 2008 15:56:27 +0200 + +biojava (1.5-1) UNRELEASED; urgency=low + + * New upstream release. + + -- Steffen Moeller <[email protected]> Tue, 03 Jul 2007 01:51:06 +0200 Added: trunk/packages/biojava/trunk/debian/compat =================================================================== --- trunk/packages/biojava/trunk/debian/compat (rev 0) +++ trunk/packages/biojava/trunk/debian/compat 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1 @@ +4 Added: trunk/packages/biojava/trunk/debian/control =================================================================== --- trunk/packages/biojava/trunk/debian/control (rev 0) +++ trunk/packages/biojava/trunk/debian/control 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1,67 @@ +Source: biojava-live +Section: contrib/science +Priority: optional +Maintainer: Steffen Moeller <[email protected]> +Build-Depends-Indep: libcommons-cli-java, libcommons-dbcp-java (>= 1.1), libhsqldb-java, + libcommons-collections-java (>= 2.1), libcommons-pool-java (>= 1.1), + libbytecode-java (>= 0.92.cvs.20070925), + openjdk-6-jdk|sun-java6-jdk|sun-java5-jdk|sun-j2sdk1.4|java2-compiler, ant, junit4, + libjgrapht0.7-java|libjgrapht-java (>=0.7) +Build-Depends: debhelper, quilt +Standards-Version: 3.8.0 +Vcs-Browser: http://svn.debian.org/wsvn/pkg-escience/biojava/trunk +Vcs-Svn: svn://svn.debian.org/svn/pkg-escience/biojava +Homepage: http://www.biojava.org + +Package: libbiojava1.6-java +Architecture: all +Depends: ${shlibs:Depends},${misc:Depends}, libcommons-pool-java (>= 1.1), libcommons-collections-java (>= 2.1), libcommons-dbcp-java (>= 1.1), libhsqldb-java, libbytecode-java, openjdk-6-jre|sun-java6-jre|sun-java5-jre|java2-runtime +Suggests: java-virtual-machine, libjgrapht-java, libbiojava-java, libbiojava-java-doc +Description: Java API to biological data and applications + This package presents the Open Source Java API to biological databases + and a series of mostly sequence-based algorithms. The APIs are not + compatible between versions. In analogy to the dealing with shared + libraries of the C language, the jar file of this package has the + API version in its name. It is symbolically linked to the expected + biojava.jar filename in the package libbiojava-java. This will help + keeping multiple versions of the biojava API in parallel. + +Package: libbiojava-java +Architecture: all +Depends: libbiojava1.6-java +Description: Java API to biological data and applications + BioJava is an open-source project dedicated to providing a Java framework + for processing biological data. It includes objects for manipulating + sequences, file parsers, DAS client and server support, access to BioSQL + and Ensembl databases, and powerful analysis and statistical routines + including a dynamic programming toolkit. + . + BioJava is provided by a vibrant community which meets annually at + the Bioinformatics Open Source Conference (BOSC) that traditionally + accompanies the Intelligent Systems in Molecular Biology (ISMB) + meeting. Much like BioPerl, the employment of this library is valuable + for everybody active in the field because of the many tricks of the + trade one learns just by communicating on the mailing list. + . + If using BioJava, please cite: R.C.G. Holland, T. Down, M. Pocock, + A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, + M. Heuer; M.J. Schreiber (2008) "BioJava: an Open-Source Framework + for Bioinformatics" Bioinformatics 24(18):2096-2097. + + +Package: libbiojava-java-demos +Architecture: all +Recommends: libbiojava-java +Description: Example programs for BioJava + The package comes with a wealth of use cases for BioJava. It is generated + together with the API documentation but because of its size of ~3.7MB it + was decided to distribute it separately. + + +Package: libbiojava-java-doc +Section: contrib/doc +Architecture: all +Recommends: konqueror|html-browser +Suggests: libbiojava-java-demos, libbiojava-java +Description: [Biology] Documentation for BioJava + JavaDoc generated HTML files describing the API. Added: trunk/packages/biojava/trunk/debian/copyright =================================================================== --- trunk/packages/biojava/trunk/debian/copyright (rev 0) +++ trunk/packages/biojava/trunk/debian/copyright 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1,76 @@ +This package was debianized by Steffen Moeller <[email protected]> on +Wed, 31 Dec 2008 01:26:45 +0100 + +It was downloaded from http://www.biojava.org/download/source + +Copyright: 1999-2008 the Individual authors who contributed the code, + as identified by the @authors tag of the respective source file. + +Upstream Authors: BioJava Developers <[email protected]> + Namely: Alan Li, Andreas Dräger <[email protected]>, Andreas Prlic, + Andy Hammer, Andy Yates, Andy Yates, Aroul Ramadass, Bradford Powell, + Brian Gilman, Brian King, Bubba Puryear, Colin Hardman , David Allen, + David H. Klatte, David Huen, David Scott, David Waring, Eric Haugen, + Ewan Birney, Francois Pepin, Frans Verhoef, Frederik Decouttere, Gerald + Loeffler <[email protected]>, Greg Cox, G. Waldon, Hanning + Ni ,, Horvath Tamas, Jason Stajich, Jim Balhoff, John Day Richter, + Jolyon Holdstock, Jonathan Warren, Jules Jacobsen, Kalle Naslund, + Keith James <[email protected]>, Lachlan Coin, Laurent Jourdren, Leen + Ammeraal, Lei Lai, Len Trigg, Lorna Morris, Lukas Kall, Mark Schreiber + <[email protected]>, Mark Southern, Markus Brosch, Martin + Senger <[email protected]>, Martin Szugat <[email protected]>, Mathew + Pocock, Mathieu Wiepert , Matthew Pocock, Mayo Foundation, Michael Heuer, + Michael Jones, Michael L Heurer, Mike Jones, Moses Hohman, Nimesh Singh, + Paul Seed, Peter Lackner, raemig, Rahul Karnik, Rhett Sutphin, Richard + Holland, Ronald Tschalar, Ron Kuhn, Russell Smithies, Samiul Hasan, + Shuvankar Mukherjee, Simon Brocklehurst, Simon Foote, Stuart Johnston , + Susanne Merz, Tamas Horvath, Tanya Vavouri, Thad Welch, Thomas Down, + Tim Dilks , Tobias Thierer, Todd Riley + + +License: + + BioJava is an open source project. The project is distributed under the GNU + Lesser General Public Licence. We do not consider Java class loading to + constitute the production of a derivative work. We do not consider consider + sub-classing of Java classes or implementations of Java interfaces to constitute + the production of a derivative work. + + All .java source files should include the following comment which implies the + author's agreement to the tearms of the license. + + /* + * BioJava development code + * + * This code may be freely distributed and modified under the + * terms of the GNU Lesser General Public Licence. This should + * be distributed with the code. If you do not have a copy, + * see: + * + * http://www.gnu.org/copyleft/lesser.html + * + * Copyright for this code is held jointly by the individual + * authors. These should be listed in @author doc comments. + * + * For more information on the BioJava project and its aims, + * or to join the biojava-l mailing list, visit the home page + * at: + * + * http://www.biojava.org/ + * + */ + + This package is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this package; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + +On Debian systems, the complete text of the GNU Lesser General +Public License can be found in `/usr/share/common-licenses/LGPL'. + +The Debian packaging is (C) 2007-2008, Steffen Moeller <[email protected]> +and is licensed under the LGPL, see `/usr/share/common-licenses/LGPL'. Added: trunk/packages/biojava/trunk/debian/libbiojava-java-doc.dirs =================================================================== --- trunk/packages/biojava/trunk/debian/libbiojava-java-doc.dirs (rev 0) +++ trunk/packages/biojava/trunk/debian/libbiojava-java-doc.dirs 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1 @@ +usr/share/doc/libbiojava-java Added: trunk/packages/biojava/trunk/debian/libbiojava-java-doc.doc-base =================================================================== --- trunk/packages/biojava/trunk/debian/libbiojava-java-doc.doc-base (rev 0) +++ trunk/packages/biojava/trunk/debian/libbiojava-java-doc.doc-base 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1,26 @@ +Document: biojava +Title: biojava API +Author: BioJava developers +Abstract: Javadoc-generated API for the BioJava library. + BioJava is an open-source project dedicated to providing a Java framework + for processing biological data. It includes objects for manipulating + sequences, file parsers, DAS client and server support, access to BioSQL + and Ensembl databases, and powerful analysis and statistical routines + including a dynamic programming toolkit. + . + BioJava is provided by a vibrant community which meets annually at + the Bioinformatics Open Source Conference (BOSC) that traditionally + accompanies the Intelligent Systems in Molecular Biology (ISMB) + meeting. Much like BioPerl, the employment of this library is valuable + for everybody active in the field because of the many tricks of the + trade one learns just by communicating on the mailing list. + . + If using BioJava, please cite: R.C.G. Holland, T. Down, M. Pocock, + A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates, + M. Heuer; M.J. Schreiber (2008) "BioJava: an Open-Source Framework + for Bioinformatics" Bioinformatics 24(18):2096-2097. +Section: Science/Biology + +Format: HTML +Index: /usr/share/doc/libbiojava-java/api/index.html +Files: /usr/share/doc/libbiojava-java/api/*.html /usr/share/doc/libbiojava-java/api/*/*/*.html /usr/share/doc/libbiojava-java/api/*/*/*/*.html /usr/share/doc/libbiojava-java/api/*/*/*/*/*.html /usr/share/doc/libbiojava-java/api/*/*/*/*/*/*.html /usr/share/doc/libbiojava-java-doc/api/*/*/*/*/*/*/*.html /usr/share/doc/libbiojava-java/api/*/*/*/*/*/*/*/*.html Added: trunk/packages/biojava/trunk/debian/libbiojava-java-doc.links =================================================================== --- trunk/packages/biojava/trunk/debian/libbiojava-java-doc.links (rev 0) +++ trunk/packages/biojava/trunk/debian/libbiojava-java-doc.links 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1 @@ +usr/share/doc/libbiojava-java/api usr/share/doc/libbiojava-java-doc/api Added: trunk/packages/biojava/trunk/debian/libbiojava-java.docs =================================================================== --- trunk/packages/biojava/trunk/debian/libbiojava-java.docs (rev 0) +++ trunk/packages/biojava/trunk/debian/libbiojava-java.docs 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1,4 @@ +README +README.biosql +resources +dtd Added: trunk/packages/biojava/trunk/debian/libbiojava1.6-java.dirs =================================================================== --- trunk/packages/biojava/trunk/debian/libbiojava1.6-java.dirs (rev 0) +++ trunk/packages/biojava/trunk/debian/libbiojava1.6-java.dirs 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1 @@ +usr/share/java Added: trunk/packages/biojava/trunk/debian/patches/buildxml.patch =================================================================== --- trunk/packages/biojava/trunk/debian/patches/buildxml.patch (rev 0) +++ trunk/packages/biojava/trunk/debian/patches/buildxml.patch 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1,65 @@ +--- biojava-live-1.6.svn.20080713.orig/build.xml ++++ biojava-live-1.6.svn.20080713/build.xml +@@ -51,7 +51,7 @@ + <tstamp /> + <property name="version" value="live" /> + <property name="build.compiler" value="javac1.5" /> +- <property name="classpath" value="bytecode.jar:commons-cli.jar:commons-collections-2.1.jar:commons-dbcp-1.1.jar:commons-pool-1.1.jar:hsqldb.jar:jgrapht-jdk1.5.jar:junit-4.4.jar" /> ++ <property name="classpath" value="/usr/share/java/bytecode.jar:/usr/share/java/commons-cli.jar:/usr/share/java/commons-collections.jar:/usr/share/java/commons-dbcp.jar:/usr/share/java/commons-pool.jar:/usr/share/java/hsqldb.jar:/usr/share/java/jgrapht-0.7.jar:/usr/share/java/junit4.jar" /> + <property name="ant-tasks.path" value="ant-lib/sablecc.jar:ant-lib/anttask.jar" /> + + +@@ -401,7 +401,7 @@ + source="1.5" + windowtitle="${Name.biojava}-${version} API" + doctitle="${Name.biojava}-${version}" +- maxmemory="96m"> ++ maxmemory="512m"> + <link href="http://java.sun.com/j2se/1.5.0/docs/api/"; offline="false"/> + + <group title="Core biological packages" +@@ -464,7 +464,7 @@ + source="1.5" + windowtitle="${Name.demos} API" + doctitle="${Name.demos}" +- maxmemory="96m"> ++ maxmemory="512m"> + <link href="http://java.sun.com/j2se/1.5.0/docs/api/"; offline="false"/> + <link href="../biojava" offline="true" packagelistLoc="${build.docs.biojava}/package-list}"/> + </javadoc> +@@ -485,7 +485,7 @@ + source="1.5" + windowtitle="${Name.apps} API" + doctitle="${Name.apps}" +- maxmemory="96m"> ++ maxmemory="512m"> + <link href="http://java.sun.com/j2se/1.5.0/docs/api/"; offline="false"/> + <link href="../biojava" offline="true" packagelistLoc="${build.docs.biojava}/package-list}"/> + +@@ -507,7 +507,7 @@ + description="Run all tests, can be quite slow"> + <property name="test.subtree" value="**" /> + <echo message="Running tests: ${test.subtree}" /> +- <junit maxmemory="128m" printsummary="yes" haltonfailure="no" reloading="no"> ++ <junit maxmemory="512m" printsummary="yes" haltonfailure="no" reloading="no"> + <formatter type="plain" usefile="true" /> + <classpath> + <!-- main classes from build --> +@@ -547,7 +547,7 @@ + classpath="${classpath}" + destdir="${build.doccheck.biojava}" + source="1.5" +- maxmemory="96m"> ++ maxmemory="512m"> + </javadoc> + </target> + +@@ -558,7 +558,7 @@ + description="Run clean, build and tests for CruiseControl"> + <property name="test.subtree" value="**" /> + <echo message="Running tests: ${test.subtree}" /> +- <junit maxmemory="128m" ++ <junit maxmemory="512m" + printsummary="yes" + haltonfailure="no" + reloading="no" Added: trunk/packages/biojava/trunk/debian/patches/series =================================================================== --- trunk/packages/biojava/trunk/debian/patches/series (rev 0) +++ trunk/packages/biojava/trunk/debian/patches/series 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1 @@ +buildxml.patch Added: trunk/packages/biojava/trunk/debian/rules =================================================================== --- trunk/packages/biojava/trunk/debian/rules (rev 0) +++ trunk/packages/biojava/trunk/debian/rules 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1,83 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +include /usr/share/quilt/quilt.make + +build: patch build-stamp + +build-stamp: + dh_testdir + find . -name "*.java" -o -name ReadMe -o -name "*.fa" -o -name "*.html" | xargs -r chmod 644 + # Add here commands to compile the package. + ANT_OPTS="-Xms1024m -Xmx1024m" ant package-biojava + #ant compile-demos + ant javadocs-biojava + + touch build-stamp + +clean: unpatch + dh_testdir + dh_testroot + rm -f build-stamp + + # Add here commands to clean up after the build process. + ant clean + + dh_clean + +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + + cp ant-build/biojava.jar $(CURDIR)/debian/libbiojava1.6-java/usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar + d=$(CURDIR)/debian/libbiojava-java-doc/usr/share/doc/libbiojava-java/api; \ + [ -d $$d ] || mkdir -p $$d ; \ + cp -r ant-build/docs/biojava/* $$d + for i in $(CURDIR)/debian/libbiojava-java*; do \ + if [ -d "$i" ]; then \ + find $i -name ".svn" | xargs -r rm -r ; \ + fi ; \ + done + + ant runtests + + +binary-arch: +# We have nothing to do by default. + +binary-indep: build install + dh_testdir + dh_testroot + dh_installchangelogs + dh_installdocs + dh_installexamples -plibbiojava-java-demos demos/* + #dh_installman + dh_link -p libbiojava-java /usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar /usr/share/java/biojava.jar + dh_link -p libbiojava1.6-java /usr/share/java/biojava$(DEB_UPSTREAM_VERSION).jar /usr/share/java/biojava1.6.jar + dh_link # use <pkg>.link files for version independant linking + dh_compress + dh_fixperms + dh_installdeb + dh_gencontrol + dh_md5sums + dh_builddeb + +binary: binary-indep binary-arch + +get-orig-source: + version=1.6.1.svn.`date +"%Y%m%d"|tr -d '\n'` ; \ + targetdir=biojava-live-$$version ; \ + origtargz=biojava-live_$$version.orig.tar.gz ; \ + cd .. ; \ + svn co svn://code.open-bio.org/biojava/biojava-live/trunk $$targetdir ; \ + find $$targetdir -name ".svn" | xargs -r rm -r ; \ + find $$targetdir -name "*.jar" | xargs -r rm ; \ + tar czf $$origtargz $$targetdir ; \ + rm -rf $$targetdir + +.PHONY: build clean binary-indep binary-arch binary install configure get-orig-source Property changes on: trunk/packages/biojava/trunk/debian/rules ___________________________________________________________________ Name: svn:executable + * Added: trunk/packages/biojava/trunk/debian/watch =================================================================== --- trunk/packages/biojava/trunk/debian/watch (rev 0) +++ trunk/packages/biojava/trunk/debian/watch 2009-03-09 11:51:10 UTC (rev 3161) @@ -0,0 +1,5 @@ +version=3 +# Well, this only finds updates to version 1.5 +http://www.biojava.org/download/bj15/src/BioJava(.*)-src.tar.gz +# offers no source +#http://www.biojava.org/download/bj16/src/biojava-1.6.1-all.jar _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
