[med-svn] [varscan] 01/01: Get some basic package

[Andreas Tille]

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tille pushed a commit to branch master
in repository varscan.

commit fbaf3e40a5903ac7b64e88742a37da78bb3a0b14
Author: Andreas Tille <tille at debian.org>
Date:   Thu Apr 17 10:18:28 2014 +0200

    Get some basic package
---
 debian/{manifest => __manifest__} |  6 +++---
 debian/bin/varscan                |  3 +++
 debian/control                    |  8 ++++++--
 debian/install                    |  1 +
 debian/jlibs                      |  1 +
 debian/rules                      | 22 ++++++----------------
 6 files changed, 20 insertions(+), 21 deletions(-)

diff --git a/debian/manifest b/debian/__manifest__
similarity index 95%
rename from debian/manifest
rename to debian/__manifest__
index 416f0ea..86bb3ad 100644
--- a/debian/manifest
+++ b/debian/__manifest__
@@ -1,3 +1,3 @@
-Manifest-Version: 1.0
-Main-Class: net.sf.varscan.VarScan
-
+Manifest-Version: 1.0
+Main-Class: net.sf.varscan.VarScan
+
diff --git a/debian/bin/varscan b/debian/bin/varscan
new file mode 100755
index 0000000..2aefcd3
--- /dev/null
+++ b/debian/bin/varscan
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+java $JAVA_OPTS -jar /usr/share/java/`basename $0`.jar $@
diff --git a/debian/control b/debian/control
index 8b244ee..971b0a8 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,10 @@ Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 9)
+Build-Depends: debhelper (>= 9),
+               javahelper (>=0.25),
+               default-jdk,
+               ant
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/varscan.git
 Vcs-Git: git://anonscm.debian.org/debian-med/varscan.git
@@ -11,7 +14,8 @@ Homepage: http://varscan.sourceforge.net/
 
 Package: varscan
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${misc:Depends},
+         ${java:Depends}
 Description: variant detection in next-generation sequencing data 
  Variant detection in massively parallel sequencing. For one sample,
  calls SNPs, indels, and consensus genotypes. For tumor-normal pairs,
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..8e71dae
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+debian/bin	usr
diff --git a/debian/jlibs b/debian/jlibs
new file mode 100644
index 0000000..0ef7c6d
--- /dev/null
+++ b/debian/jlibs
@@ -0,0 +1 @@
+dist/*.jar
diff --git a/debian/rules b/debian/rules
index 58ec00b..6712aa4 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,22 +2,12 @@
 
 # DH_VERBOSE := 1
 
-# 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))
+export JAVA_HOME=/usr/lib/jvm/default-java
 
-# alternatively to manually set those variables you can
-#  include /usr/share/cdbs/1/rules/buildvars.mk
-# and use what is set there.  Any hint whether dh might set variables in
-# a similar manner are welcome.
+override_dh_auto_build:
+	cp debian/build.xml build.xml
+	dh_auto_build
+	rm -f build.xml
 
 %:
-	dh $@
-
-#get-orig-source:
-#	. debian/get-orig-source
+	dh $@ --with javahelper

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