blob: d23a32e729764f510f40439ed676a257e1ab437d (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
|
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
JAVA_PKG_IUSE="doc source test"
WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4"
inherit java-pkg-2 java-ant-2
DESCRIPTION="Java-based command-line utilities that manipulate SAM/BAM/CRAM/VCF files"
HOMEPAGE="http://picard.sourceforge.net
http://broadinstitute.github.io/picard"
#SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"
SRC_URI="https://github.com/broadinstitute/picard/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="Apache-2.0" # 2.2.2 is MIT instead, not sure when it changed away from Apache
SLOT="0"
IUSE=""
KEYWORDS=""
CDEPEND="dev-java/snappy:1.0
dev-java/cofoja:0
dev-java/commons-jexl:2
dev-java/ant-core:0"
DEPEND=">=virtual/jdk-1.7
dev-java/ant-apache-bcel:0
test? (
dev-java/testng:0
dev-lang/R
)
${CDEPEND}"
RDEPEND=">=virtual/jre-1.7
${CDEPEND}"
EANT_BUILD_TARGET="all"
EANT_TEST_TARGET="test"
EANT_NEEDS_TOOLS="true"
JAVA_ANT_REWRITE_CLASSPATH="true"
EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core"
EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng"
java_prepare() {
mkdir -p "${S}"/lib || die
# TODO: update the patch
#epatch "${FILESDIR}"/${PV}-gentoo.patch
mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die
}
src_install() {
cd dist || die
for i in *-${PV}.jar; do
java-pkg_newjar $i ${i/-${PV}/}
rm $i || die
done
java-pkg_dojar *.jar
for i in *.jar; do
java-pkg_dolauncher ${i/.jar/} --jar $i;
done
use source && java-pkg_dosrc "${S}"/src/java/*
use doc && java-pkg_dojavadoc "${S}"/javadoc
}
src_test() {
java-pkg-2_src_test
}
|
GitWeb
