[med-svn] [artemis] 02/02: Initial packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Mon Sep 21 07:34:29 UTC 2015
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 <afif at 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 <afif at 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-packaging at lists.alioth.debian.org>
+Uploaders:
+ Afif Elghraoui <afif at 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 <afif at 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 <afif at 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 <afif at 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)
--
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