This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository artemis.
commit e88eb7d85e9f2f12c91ea4281f5e11735b6b90c5 Author: Afif Elghraoui <a...@ghraoui.name> Date: Mon Sep 21 00:33:45 2015 -0700 Initial packaging --- debian/TODO | 1 + debian/changelog | 5 ++++ debian/compat | 1 + debian/control | 33 +++++++++++++++++++++ debian/copyright | 50 ++++++++++++++++++++++++++++++++ debian/docs | 1 + debian/patches/class-path.patch | 63 +++++++++++++++++++++++++++++++++++++++++ debian/patches/java6.patch | 15 ++++++++++ debian/patches/series | 2 ++ debian/rules | 14 +++++++++ debian/source/format | 1 + 11 files changed, 186 insertions(+) diff --git a/debian/TODO b/debian/TODO new file mode 100644 index 0000000..c3aaff0 --- /dev/null +++ b/debian/TODO @@ -0,0 +1 @@ +* populate license fields in d/copyright diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..ad56814 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,5 @@ +artemis (16.0.0+dfsg-1) unstable; urgency=low + + * Initial release (Closes: #nnnn) + + -- Afif Elghraoui <a...@ghraoui.name> Sun, 20 Sep 2015 19:52:30 -0700 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..023aeab --- /dev/null +++ b/debian/control @@ -0,0 +1,33 @@ +Source: artemis +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> +Uploaders: + Afif Elghraoui <a...@ghraoui.name> +Build-Depends: + debhelper (>= 9), + default-jdk, + javahelper, + libbiojava-java, + libj2ssh-java, + libibatis-java, + liblog4j1.2-java, + libpostgresql-jdbc-java, + picard-tools, + libsam-java, + libcommons-net2-java, + libbatik-java +Standards-Version: 3.9.6 +Homepage: https://www.sanger.ac.uk/resources/software/artemis/ +Vcs-Git: git://anonscm.debian.org/debian-med/artemis.git +Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/artemis.git + +Package: artemis +Architecture: all +Depends: + ${misc:Depends}, + ${java:Depends} +Description: genome browser and annotation tool + Artemis is a genome browser and annotation tool that allows visualisation of + sequence features, next generation data and the results of analyses within the + context of the sequence, and also its six-frame translation. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..302c99f --- /dev/null +++ b/debian/copyright @@ -0,0 +1,50 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: artemis +Source: https://github.com/sanger-pathogens/Artemis +Files-Excluded: + lib/* + test/lib/* + +Files: * +Copyright: + 1998-2013 Genome Research Limited + 2013 Wellcome Trust Sanger Institute +License: GPL-2+ + +Files: uk/ac/sanger/artemis/components/variant/TabixReader.java +Copyright: + 2010 Broad Institute +License: ? + +Files: + uk/ac/sanger/artemis/components/filetree/FileList.java + uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java + uk/ac/sanger/artemis/components/filetree/TransferableFileNodeList.java +Copyright: Tim Carver +License: ? + +Files: docs/copyright.sgml +Copyright: 1989, 1991 Free Software Foundation +License: ? + +Files: debian/* +Copyright: + 2015 Afif Elghraoui <a...@ghraoui.name> +License: GPL-2+ + +License: GPL-2+ + This package 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; either version 2 of the License, or + (at your option) any later version. + . + 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 General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/> + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". diff --git a/debian/docs b/debian/docs new file mode 100644 index 0000000..e845566 --- /dev/null +++ b/debian/docs @@ -0,0 +1 @@ +README diff --git a/debian/patches/class-path.patch b/debian/patches/class-path.patch new file mode 100644 index 0000000..b2cf540 --- /dev/null +++ b/debian/patches/class-path.patch @@ -0,0 +1,63 @@ +Description: Look for jars in /usr/share/java rather than ./lib + The bundled jar files in lib/ have been removed for Debian, so the + build system ought to find the packaged versions in /usr/share/java. + This patch essentially implements s#lib#/usr/share/java# with some + manual modifications afterwards. +Author: Afif Elghraoui <a...@ghraoui.name> +Forwarded: not-needed +Last-Update: 2015-09-21 +--- artemis.orig/Makefile ++++ artemis/Makefile +@@ -8,7 +8,7 @@ + + JAVAC := javac -source 1.5 -target 1.5 $(OPT_FLAGS) $(EXTRA_FLAGS) + +-REAL_CLASSPATH := CLASSPATH=lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/picard/sam.jar:lib/commons-net-2.2.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. ++REAL_CLASSPATH := CLASSPATH=/usr/share/java/biojava.jar:/usr/share/java/jemAlign.jar:/usr/share/java/j2ssh/j2ssh-core.jar:/usr/share/java/ibatis.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/postgresql-jdbc3.jar:/usr/share/java/picard.jar:/usr/share/java/sam.jar:/usr/share/java/commons-net-2.2.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:. + + # NAMES:= \ + # uk/ac/sanger/artemis/OptionChangeListener \ +@@ -279,7 +279,7 @@ + mkdir tar_build/artemis + rm -f artemis_compiled_latest.tar.gz + tar cf - $(OTHER_FILES) act art Makefile corba etc | (cd tar_build/artemis; tar xf -) +- tar cf - artemis_sqlmap dnaplotter uk org nsdb type seqdb lib | (cd tar_build/artemis; tar xf -) ++ tar cf - artemis_sqlmap dnaplotter uk org nsdb type seqdb /usr/share/java | (cd tar_build/artemis; tar xf -) + (cd tar_build; find . -name 'CVS' -print | xargs rm -rf; find . -name '.svn' -print | xargs rm -rf; tar cvf ../artemis_compiled.tar artemis) + + jar : all artemis.jar +@@ -289,28 +289,28 @@ + rm -f artemis.jar + cd jar_build; \ + if [ ! -d org ]; then \ +- for fileJar in ../lib/*.jar; do \ ++ for fileJar in /usr/share/java/*.jar; do \ + jar xvf $$fileJar; \ + rm -rf META-INF/MANIFEST.MF; \ + done; \ +- for fileJar in ../lib/j2ssh/*.jar; do \ ++ for fileJar in /usr/share/java/j2ssh/*.jar; do \ + jar xvf $$fileJar; \ + rm -rf META-INF/MANIFEST.MF; \ + done; \ +- for fileJar in ../lib/ibatis/*.jar; do \ ++ for fileJar in /usr/share/java/ibatis/*.jar; do \ + jar xvf $$fileJar; \ + rm -rf META-INF/MANIFEST.MF; \ + done; \ +- for fileJar in ../lib/batik/*.jar; do \ ++ for fileJar in /usr/share/java/batik/*.jar; do \ + jar xvf $$fileJar; \ + rm -rf META-INF/MANIFEST.MF; \ + done; \ +- for fileJar in ../lib/picard/*.jar; do \ ++ for fileJar in /usr/share/java/picard/*.jar; do \ + jar xvf $$fileJar; \ + rm -rf META-INF/MANIFEST.MF; \ + done; \ + fi; \ +- cp -R ../lib/LICENSE.Apache ../uk ../org ../nsdb ../type ../seqdb ../etc ../images ../lib/j2ssh/j2ssh.properties \ ++ cp -R ../uk ../org ../nsdb ../type ../seqdb ../etc ../images \ + ../images/PSUlogo.gif ../images/icon.gif ../README ../artemis_sqlmap . + find jar_build -name '*.java' -print | xargs rm -f + find jar_build -name '.svn' -print | xargs rm -rf diff --git a/debian/patches/java6.patch b/debian/patches/java6.patch new file mode 100644 index 0000000..a10bfa7 --- /dev/null +++ b/debian/patches/java6.patch @@ -0,0 +1,15 @@ +Description: Don't force javac to use Java5 +Author: Afif Elghraoui <a...@ghraoui.name> +Forwarded: no +Last-Update: 2015-09-21 +--- artemis.orig/Makefile ++++ artemis/Makefile +@@ -6,7 +6,7 @@ + + #OPT_FLAGS = -g -deprecation + +-JAVAC := javac -source 1.5 -target 1.5 $(OPT_FLAGS) $(EXTRA_FLAGS) ++JAVAC := javac $(OPT_FLAGS) $(EXTRA_FLAGS) + + REAL_CLASSPATH := CLASSPATH=/usr/share/java/biojava.jar:/usr/share/java/jemAlign.jar:/usr/share/java/j2ssh/j2ssh-core.jar:/usr/share/java/ibatis.jar:/usr/share/java/log4j-1.2.jar:/usr/share/java/postgresql-jdbc3.jar:/usr/share/java/picard.jar:/usr/share/java/sam.jar:/usr/share/java/commons-net-2.2.jar:/usr/share/java/batik-awt-util.jar:/usr/share/java/batik-dom.jar:/usr/share/java/batik-ext.jar:/usr/share/java/batik-svggen.jar:/usr/share/java/batik-util.jar:/usr/share/java/batik-xml.jar:. + diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..091507a --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,2 @@ +class-path.patch +java6.patch diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..8513f81 --- /dev/null +++ b/debian/rules @@ -0,0 +1,14 @@ +#!/usr/bin/make -f + +#DH_VERBOSE = 1 + +DPKG_EXPORT_BUILDFLAGS = 1 +include /usr/share/dpkg/default.mk + +JAVA_HOME=/usr/lib/jvm/default-java + +%: + dh $@ + +override_dh_auto_build: + $(MAKE) jar 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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/artemis.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit