[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[Justin Lecher]

commit:     c3ab7823c9462b681b308ab69346acc77cea683f
Author:     Johann Schmitz <ercpe <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 24 06:08:19 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 24 06:10:23 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=c3ab7823

dev-java/htsjdk: New ebuild (dependency of picard-2)

Package-Manager: portage-2.2.26

 dev-java/htsjdk/htsjdk-2.2.2.ebuild | 47 +++++++++++++++++++++++++++++++++++++
 dev-java/htsjdk/metadata.xml        | 15 ++++++++++++
 2 files changed, 62 insertions(+)

diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.2.2.ebuild
new file mode 100644
index 0000000..9950f1f
--- /dev/null
+++ b/dev-java/htsjdk/htsjdk-2.2.2.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="6"
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats."
+HOMEPAGE="https://samtools.github.io/htsjdk/"
+SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="dev-java/commons-jexl:2
+	dev-java/commons-compress:0
+	dev-java/commons-logging:0"
+
+DEPEND=">=virtual/jdk-1.8
+	${CDEPEND}"
+RDEPEND=">=virtual/jre-1.8
+	${CDEPEND}"
+
+EANT_BUILD_TARGET="all"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
+
+java_prepare() {
+	rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
+}
+
+src_install() {
+	cd dist || die
+
+	for i in *.jar; do
+		java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
+	done
+
+	use source && java-pkg_dosrc "${S}"/src/java/*
+	use doc && java-pkg_dojavadoc "${S}"/javadoc
+}

diff --git a/dev-java/htsjdk/metadata.xml b/dev-java/htsjdk/metadata.xml
new file mode 100644
index 0000000..513e863
--- /dev/null
+++ b/dev-java/htsjdk/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>ercpe@gentoo.org</email>
+		<name>Johann Schmitz (ercpe)</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="sourceforge">picard</remote-id>
+	</upstream>
+</pkgmetadata>

[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[Justin Lecher]

commit:     f14032b578bf9d6b6bd840a05ad00f47867207f8
Author:     Johann Schmitz <ercpe <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 24 06:13:12 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 24 06:13:12 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f14032b5

dev-java/htsjdk: Fixed error with EAPI=6

Package-Manager: portage-2.2.26

 dev-java/htsjdk/htsjdk-2.2.2.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.2.2.ebuild
index 9950f1f..ca2cdd9 100644
--- a/dev-java/htsjdk/htsjdk-2.2.2.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.2.2.ebuild
@@ -32,6 +32,7 @@ JAVA_ANT_REWRITE_CLASSPATH="true"
 EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
 
 java_prepare() {
+	default
 	rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
 }
 

[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[Martin Mokrejs]

commit:     091fd4549ad2edd83419e0f645cc902a2f71ae23
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 15:53:53 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 15:53:53 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=091fd454

dev-java/htsjdk: version bump, moved from ant to gradle, SANDBOX VIOLATION

Package-Manager: portage-2.2.28

 dev-java/htsjdk/{htsjdk-2.2.2.ebuild => htsjdk-2.5.1.ebuild} | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.5.1.ebuild
similarity index 89%
rename from dev-java/htsjdk/htsjdk-2.2.2.ebuild
rename to dev-java/htsjdk/htsjdk-2.5.1.ebuild
index ca2cdd9..b63c0d2 100644
--- a/dev-java/htsjdk/htsjdk-2.2.2.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.5.1.ebuild
@@ -15,7 +15,7 @@ SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
 LICENSE="MIT"
 SLOT="0"
 IUSE=""
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="" # SANDBOX VIOLATION
 
 CDEPEND="dev-java/commons-jexl:2
 	dev-java/commons-compress:0
@@ -31,9 +31,12 @@ EANT_NEEDS_TOOLS="true"
 JAVA_ANT_REWRITE_CLASSPATH="true"
 EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
 
-java_prepare() {
+java_prepare(){
 	default
-	rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
+}
+
+src_compile(){
+	./gradlew build || die
 }
 
 src_install() {

[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[Martin Mokrejs]

commit:     691de03a081a82665985b69eb879c6be3ecd7f7e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 16:31:39 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 16:31:39 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=691de03a

dev-java/htsjdk: added 2.1.0 version needed=bundled so far in cramtools-3.0

Package-Manager: portage-2.2.28

 dev-java/htsjdk/htsjdk-2.1.0.ebuild | 48 +++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
new file mode 100644
index 0000000..ca2cdd9
--- /dev/null
+++ b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="6"
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats."
+HOMEPAGE="https://samtools.github.io/htsjdk/"
+SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="dev-java/commons-jexl:2
+	dev-java/commons-compress:0
+	dev-java/commons-logging:0"
+
+DEPEND=">=virtual/jdk-1.8
+	${CDEPEND}"
+RDEPEND=">=virtual/jre-1.8
+	${CDEPEND}"
+
+EANT_BUILD_TARGET="all"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
+
+java_prepare() {
+	default
+	rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
+}
+
+src_install() {
+	cd dist || die
+
+	for i in *.jar; do
+		java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
+	done
+
+	use source && java-pkg_dosrc "${S}"/src/java/*
+	use doc && java-pkg_dojavadoc "${S}"/javadoc
+}

[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[Martin Mokrejs]

commit:     9ce6536356df2dffa9672161ae47b8de609c7682
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 16:28:58 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 16:28:58 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ce65363

dev-java/htsjdk: re-added back 2.2.2 version due to picard-2

Package-Manager: portage-2.2.28

 dev-java/htsjdk/htsjdk-2.2.2.ebuild | 48 +++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)

diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.2.2.ebuild
new file mode 100644
index 0000000..ca2cdd9
--- /dev/null
+++ b/dev-java/htsjdk/htsjdk-2.2.2.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="6"
+
+JAVA_PKG_IUSE="doc source"
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats."
+HOMEPAGE="https://samtools.github.io/htsjdk/"
+SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+CDEPEND="dev-java/commons-jexl:2
+	dev-java/commons-compress:0
+	dev-java/commons-logging:0"
+
+DEPEND=">=virtual/jdk-1.8
+	${CDEPEND}"
+RDEPEND=">=virtual/jre-1.8
+	${CDEPEND}"
+
+EANT_BUILD_TARGET="all"
+EANT_NEEDS_TOOLS="true"
+JAVA_ANT_REWRITE_CLASSPATH="true"
+EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
+
+java_prepare() {
+	default
+	rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
+}
+
+src_install() {
+	cd dist || die
+
+	for i in *.jar; do
+		java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
+	done
+
+	use source && java-pkg_dosrc "${S}"/src/java/*
+	use doc && java-pkg_dojavadoc "${S}"/javadoc
+}

[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[Martin Mokrejs]

commit:     d0811884dba63b23093aa0cf580171e4ba51a36f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 21:42:07 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 21:42:07 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d0811884

dev-java/htsjdk: make gradle use relocated $HOME/.gradle/ inside sanbox paths

This dies later because .git/ directory does not exist (probably $HOME/.git/ was
looked up).

Package-Manager: portage-2.2.28

 dev-java/htsjdk/htsjdk-2.5.1.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild b/dev-java/htsjdk/htsjdk-2.5.1.ebuild
index b63c0d2..0f1e162 100644
--- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.5.1.ebuild
@@ -36,7 +36,9 @@ java_prepare(){
 }
 
 src_compile(){
-	./gradlew build || die
+	# work around gradle writing $HOME/.gradle
+	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
 }
 
 src_install() {

[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[Martin Mokrejs]

commit:     6e6616f8521d20074bbca6522e2a5570718d5736
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 11 23:26:50 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 11 23:26:50 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6e6616f8

dev-java/htsjdk: add a live ebuild, add a note

Not sure if current build system still creates $HOME/.git but from
reading github Issues it seem it is still needed: users are even asked
to run 'git clone' to work around the issue when gradle fails to do that.

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 dev-java/htsjdk/htsjdk-2.5.1.ebuild                |  4 ++--
 .../{htsjdk-2.5.1.ebuild => htsjdk-9999.ebuild}    | 26 +++++++++++-----------
 2 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild b/dev-java/htsjdk/htsjdk-2.5.1.ebuild
index 0f1e162..6ba163f 100644
--- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.5.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -36,7 +36,7 @@ java_prepare(){
 }
 
 src_compile(){
-	# work around gradle writing $HOME/.gradle
+	# work around gradle writing $HOME/.gradle and $HOME/.git
 	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
 	GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
 }

diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild b/dev-java/htsjdk/htsjdk-9999.ebuild
similarity index 59%
copy from dev-java/htsjdk/htsjdk-2.5.1.ebuild
copy to dev-java/htsjdk/htsjdk-9999.ebuild
index 0f1e162..e957674 100644
--- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild
+++ b/dev-java/htsjdk/htsjdk-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -6,11 +6,11 @@ EAPI="6"
 
 JAVA_PKG_IUSE="doc source"
 
-inherit java-pkg-2 java-ant-2
+inherit git-r3 java-pkg-2 java-ant-2
 
 DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats."
 HOMEPAGE="https://samtools.github.io/htsjdk/"
-SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
+EGIT_REPO_URI="https://github.com/samtools/htsjdk.git"
 
 LICENSE="MIT"
 SLOT="0"
@@ -36,18 +36,18 @@ java_prepare(){
 }
 
 src_compile(){
-	# work around gradle writing $HOME/.gradle
+	# work around gradle writing $HOME/.gradle and $HOME/.git
 	# https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965
-	GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die
+	GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die
 }
 
 src_install() {
-	cd dist || die
-
-	for i in *.jar; do
-		java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
-	done
-
-	use source && java-pkg_dosrc "${S}"/src/java/*
-	use doc && java-pkg_dojavadoc "${S}"/javadoc
+	cd build/libs || die
+
+	#for i in *-SNAPSHOT.jar; do
+	#	java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
+	#done
+	java-pkg_newjar "${S}"/build/libs/*-SNAPSHOT.jar htsjdk.jar
+	use source && java-pkg_dosrc "${S}"/build/libs/*-sources.jar
+	use doc && java-pkg_dojavadoc "${S}"/build/libs/*-javadoc.jar
 }

[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[Martin Mokrejs]

commit:     6d3f8d736bf1a9653f516c3e959a97948c61f843
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 11:08:21 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 11:08:21 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d3f8d73

dev-java/htsjdk: 2.3.0 which was the last using Apache ant

Bump to EAPI7

Building does not work since sandbox has now no network access.

Downloading https://services.gradle.org/distributions/gradle-5.2.1-bin.zip

Exception in thread "main" java.net.SocketException: Network
is unreachable (connect failed)

htsjdk calls some `gradlew` wrapper so the recent ebuilds
need more work to use dev-java/gradle-bin package.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 dev-java/htsjdk/htsjdk-2.1.0.ebuild                           | 4 ++--
 dev-java/htsjdk/{htsjdk-2.5.1.ebuild => htsjdk-2.19.0.ebuild} | 7 ++++---
 dev-java/htsjdk/{htsjdk-2.2.2.ebuild => htsjdk-2.3.0.ebuild}  | 4 ++--
 dev-java/htsjdk/htsjdk-9999.ebuild                            | 7 ++++---
 4 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
index fc2dd6e8a..c94f79781 100644
--- a/dev-java/htsjdk/htsjdk-2.1.0.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 JAVA_PKG_IUSE="doc source"
 

diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild b/dev-java/htsjdk/htsjdk-2.19.0.ebuild
similarity index 91%
rename from dev-java/htsjdk/htsjdk-2.5.1.ebuild
rename to dev-java/htsjdk/htsjdk-2.19.0.ebuild
index 755a6fa1f..349e56673 100644
--- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.19.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 JAVA_PKG_IUSE="doc source"
 
@@ -18,7 +18,8 @@ KEYWORDS=""
 
 CDEPEND="dev-java/commons-jexl:2
 	dev-java/commons-compress:0
-	dev-java/commons-logging:0"
+	dev-java/commons-logging:0
+	dev-java/gradle-bin:*"
 
 DEPEND=">=virtual/jdk-1.8
 	${CDEPEND}"

diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.3.0.ebuild
similarity index 95%
rename from dev-java/htsjdk/htsjdk-2.2.2.ebuild
rename to dev-java/htsjdk/htsjdk-2.3.0.ebuild
index fc2dd6e8a..c94f79781 100644
--- a/dev-java/htsjdk/htsjdk-2.2.2.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.3.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 JAVA_PKG_IUSE="doc source"
 

diff --git a/dev-java/htsjdk/htsjdk-9999.ebuild b/dev-java/htsjdk/htsjdk-9999.ebuild
index b4a3c1441..2123bbc55 100644
--- a/dev-java/htsjdk/htsjdk-9999.ebuild
+++ b/dev-java/htsjdk/htsjdk-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 JAVA_PKG_IUSE="doc source"
 
@@ -18,7 +18,8 @@ KEYWORDS=""
 
 CDEPEND="dev-java/commons-jexl:2
 	dev-java/commons-compress:0
-	dev-java/commons-logging:0"
+	dev-java/commons-logging:0
+	dev-java/gradle-bin:*"
 
 DEPEND=">=virtual/jdk-1.8
 	${CDEPEND}"

[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

[Martin Mokrejs]

commit:     a12a2d7f3f65eb66e44d3fc907f4b24e85ef201a
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 11:50:28 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 11:50:28 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a12a2d7f

dev-java/htsjdk: drop old 2.1.0 version

 dev-java/htsjdk/htsjdk-2.1.0.ebuild | 47 -------------------------------------
 1 file changed, 47 deletions(-)

diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
deleted file mode 100644
index c94f79781..000000000
--- a/dev-java/htsjdk/htsjdk-2.1.0.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/"
-SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/commons-jexl:2
-	dev-java/commons-compress:0
-	dev-java/commons-logging:0"
-
-DEPEND=">=virtual/jdk-1.8
-	${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
-	${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare() {
-	default
-	rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
-}
-
-src_install() {
-	cd dist || die
-
-	for i in *.jar; do
-		java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
-	done
-
-	use source && java-pkg_dosrc "${S}"/src/java/*
-	use doc && java-pkg_dojavadoc "${S}"/javadoc
-}