[med-svn] [libjloda-java] 02/02: Add initial packaging
Andreas Tille
tille at debian.org
Wed Nov 2 20:56:20 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository libjloda-java.
commit e6626db89e23e0221f54bfc4e5be662cdd463589
Author: Andreas Tille <tille at debian.org>
Date: Wed Nov 2 21:55:38 2016 +0100
Add initial packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 24 ++++++++++++++++++++++++
debian/copyright | 28 ++++++++++++++++++++++++++++
debian/get-orig-source | 28 ++++++++++++++++++++++++++++
debian/patches/fix_build_xml.patch | 18 ++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 26 ++++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 8 ++++++++
debian/watch | 3 +++
11 files changed, 143 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..6002b36
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+libjloda-java (0.0+20161018-1) UNRELEASED; urgency=medium
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Tue, 11 Oct 2016 20:08:16 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..e4eeec0
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: libjloda-java
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ javahelper,
+ default-jdk,
+ ant,
+ libbatik-java,
+ libjama-java
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libjloda-java.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/libjloda-java.git
+Homepage: https://github.com/danielhuson/jloda
+
+Package: libjloda-java
+Architecture: all
+Depends: ${java:Depends},
+ ${misc:Depends}
+Description: Java library of data structures and algorithms for bioinformatics
+ The jloda Java library provides some basic data structures and
+ algorithms used by bioinformatics applications like SplitsTree,
+ Dendroscope and MEGAN.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..1beaa41
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: JLODA
+Upstream-Contact: Daniel Huson <daniel.huson at uni-tuebingen.de>
+Source: https://github.com/danielhuson/jloda
+Files-Excluded: */jars/batik*
+ */jars/Jama-*
+ */.DS_Store
+
+Files: *
+Copyright: 2000-2016 Alexander Herbig, Frank Maixner, Kirsten I. Bos, Albert Zink, Johannes Krause, Daniel H. Huson
+License: GPL-3
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: GPL-3
+
+License: GPL-3
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation version 3 of the License.
+ .
+ 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 General Public License for more details.
+ .
+ On a Debian system the GNU GPL license version 3 is distributed in
+ /usr/share/common-licenses/GPL-3.
diff --git a/debian/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..9b5be60
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,28 @@
+#!/bin/sh -e
+
+COMPRESS=xz
+
+NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+ONAME=`echo $NAME | sed 's/lib\(.*\)-java/\1/'`
+MVERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'`
+
+mkdir -p ../tarballs
+cd ../tarballs
+# need to clean up the tarballs dir first because upstream tarball might
+# contain a directory with unpredictable name
+rm -rf *
+git clone --quiet https://github.com/danielhuson/${ONAME} ${NAME}
+cd $NAME
+VERSION=${MVERSION}+`date -d @$(git show --format="%at" | head -n1) +%Y%m%d`
+# for esthetical reasons set file timestamps (if git-restore-mtime is installed)
+git restore-mtime || true
+cd ..
+TARDIR=${NAME}-${VERSION}
+mv ${NAME} ${TARDIR}
+rm -rf ${TARDIR}/.git
+rm -rf ${TARDIR}/jars/batik*
+rm -rf ${TARDIR}/jars/Jama-*
+find ${TARDIR} -name .DS_Store -delete
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
+rm -rf ${TARDIR}
diff --git a/debian/patches/fix_build_xml.patch b/debian/patches/fix_build_xml.patch
new file mode 100644
index 0000000..7763f83
--- /dev/null
+++ b/debian/patches/fix_build_xml.patch
@@ -0,0 +1,18 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 11 Oct 2016 20:08:16 +0200
+Description: Fix classpath
+
+--- a/antbuild/build.xml
++++ b/antbuild/build.xml
+@@ -2,9 +2,8 @@
+
+
+ <path id="build.classpath">
+- <fileset dir="../../jloda/jars" includes="*.jar"/>
+- <fileset dir="../../jloda/jars/batik-1.8" includes="*.jar"/>
+-
++ <fileset dir="../jars" includes="*.jar"/>
++ <fileset dir="/usr/share/java" includes="**/*.jar"/>
+ </path>
+
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..e5ac080
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix_build_xml.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..88d6f05
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,26 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+export LC_ALL=C.UTF-8
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables, you can
+# include /usr/share/dpkg/default.mk
+# and use what is set there.
+
+%:
+ dh $@
+
+override_dh_auto_build:
+ ant -buildfile antbuild/build.xml
+
+get-orig-source:
+ . debian/get-orig-source
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..495acc8
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,8 @@
+Reference:
+ Author: Alexander Herbig and Frank Maixner and Kirsten I. Bos and Albert Zink and Johannes Krause and Daniel H. Huson
+ Title: "MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman"
+ Journal: bioRxiv
+ Year: 2016
+ DOI: 10.1101/050559
+ URL: http://biorxiv.org/content/early/2016/04/27/050559
+ eprint: http://biorxiv.org/content/early/2016/04/27/050559.full.pdf
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..3483b3d
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://github.com/danielhuson/jloda/releases .*/archive/.*(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
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