debian/0000755000000000000000000000000012232464611007167 5ustar debian/control0000644000000000000000000000321712232463646010604 0ustar Source: jebl2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: java Priority: optional Build-Depends: debhelper (>= 9), javahelper Build-Depends-Indep: default-jdk, default-jdk-doc, libtrove-java, libtrove-java-doc, ant Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libjebl2-java/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/libjebl2-java/trunk/ Homepage: http://code.google.com/p/jebl2/ Package: libjebl2-java Architecture: all Depends: ${java:Depends}, ${misc:Depends} Recommends: ${java:Recommends} Description: Java Evolutionary Biology Library A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees. . This is a branch of the original JEBL on http://sourceforge.net/projects/jebl/ to develop a new API and class library. Package: libjebl2-java-doc Architecture: all Section: doc Depends: ${java:Depends}, ${misc:Depends} Recommends: ${java:Recommends} Description: Java Evolutionary Biology Library (documentation) A Java library for evolutionary biology and bioinformatics, including objects representing biomolecular sequences, multiple sequence alignments and phylogenetic trees. . This is a branch of the original JEBL on http://sourceforge.net/projects/jebl/ to develop a new API and class library. . This package provides the documentation for the library debian/libjebl2-java-doc.javadoc0000644000000000000000000000004511525536336013676 0ustar doc /usr/share/doc/libjebl2-java/api debian/rules0000755000000000000000000000044211525330135010244 0ustar #!/usr/bin/make -f JAVA_HOME=/usr/lib/jvm/default-java %: dh $@ --with javahelper override_dh_auto_clean: # build.xml does not provide a clean target rm -rf dist build doc override_dh_auto_build: dh_auto_build ant -buildfile javadoc.xml get-orig-source: . debian/get-orig-source debian/watch0000644000000000000000000000063311525534362010227 0ustar # Obtaining the source tarball of jebl is a bit tricky because there is no # explicite link to a downloadable tarball on the web page and the source is # only in SVN. There is even no versioning scheme and this watch file is just # checking for a new SVN commit version=3 opts="dversionmangle=s/0.0.r//" \ http://code.google.com/p/jebl2/source/list \ detail\?r=([\d]+) \ debian debian/get-orig-source debian/copyright0000644000000000000000000000224012232464040011114 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: JEBL2 Upstream-Contact: Andrew Rambaut Source: http://code.google.com/p/jebl2/source/checkout Files: * Copyright: © 2009-2010 Andrew Rambaut License: LGPL-3+ Files: debian/* Copyright: © 2011 Andreas Tille License: LGPL-3+ License: LGPL-3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program 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 program. If not, see . Comment: On Debian systems, you can read the full text of the GNU Lesser General Public License in ‘/usr/share/common-licenses/LGPL-3’. debian/source/0000755000000000000000000000000011414066126010467 5ustar debian/source/format0000644000000000000000000000001411414066126011675 0ustar 3.0 (quilt) debian/get-orig-source0000755000000000000000000000112312232462522012124 0ustar #!/bin/sh # get source for jebl-lib from SVN NAME=jebl2 rm -f ../detail mkdir -p ../tarballs cd ../tarballs # svn export concerves time stamps of the files, checkout does not REV=`LC_ALL=C svn export http://${NAME}.googlecode.com/svn/trunk/ ${NAME} | tail -n 1 | sed 's/^.*revision \([0-9]\+\)./\1/'` VERSION=0.0.r${REV} find ${NAME} -name .svn -type d -exec rm -rf \{\} \; rm -f ${NAME}/lib/*.jar mv ${NAME} ${NAME}-${VERSION} GZIP="--best --no-name" XZ_OPT="-6v" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.xz "${NAME}-${VERSION}" rm -rf "${NAME}-${VERSION}" debian/changelog0000644000000000000000000000075112232464163011046 0ustar jebl2 (0.0.r22-1) unstable; urgency=low * New upstream version * debian/get-orig-source: Use xz compression when creating source tarball * debian/control: - cme fix dpkg-control - debhelper 9 - canonical Vcs URLs * debian/copyright: DEP5 -- Andreas Tille Fri, 25 Oct 2013 14:21:25 +0200 jebl2 (0.0.r6-1) unstable; urgency=low * Initial Debian Upload (Closes: #613080) -- Andreas Tille Thu, 10 Feb 2011 10:26:38 +0100 debian/patches/0000755000000000000000000000000012232462721010616 5ustar debian/patches/do_not_build_jam.patch0000644000000000000000000000757712232462721015147 0ustar --- a/build.xml +++ b/build.xml @@ -7,7 +7,6 @@ - @@ -19,31 +18,9 @@ - - - - - - - - - - - - - - - - - - - - - - @@ -52,38 +29,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -105,7 +50,7 @@ - + @@ -116,7 +61,7 @@ - + + + + + + + JEBL2]]> + http://code.google.com/p/jebl2/]]> + + + + debian/compat0000644000000000000000000000000212232463606010370 0ustar 9 debian/libjebl2-java.jlibs0000644000000000000000000000001311525536306012617 0ustar dist/*.jar