[gentoo-commits] proj/sci:master commit in: sci-biology/cramtools/

[gentoo-commits] proj/sci:master commit in: sci-biology/cramtools/

[Martin Mokrejs]

commit:     d8114ce881aac5e2972066606955071fa0ae4fde
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jul 12 16:04:10 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jul 12 16:04:10 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d8114ce8

sci-biology/cramtools: new package, not working yet

will not compile with java8 until upstream issue #59 is fixed

contains bundled dev-java/htsjdk (although other apps do not keep up
with the API changes in htsjdk so it does have a reason)

Package-Manager: portage-2.2.28

 sci-biology/cramtools/cramtools-3.0.ebuild | 32 ++++++++++++++++++++++++++++++
 sci-biology/cramtools/metadata.xml         | 12 +++++++++++
 2 files changed, 44 insertions(+)

diff --git a/sci-biology/cramtools/cramtools-3.0.ebuild b/sci-biology/cramtools/cramtools-3.0.ebuild
new file mode 100644
index 0000000..9d903a2
--- /dev/null
+++ b/sci-biology/cramtools/cramtools-3.0.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Java tools and APIs for efficient compression of sequence read data"
+HOMEPAGE="http://www.ebi.ac.uk/ena/software/cram-toolkit
+	https://github.com/enasequence/cramtools"
+SRC_URI="https://github.com/enasequence/cramtools/archive/v3.0.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+	>=virtual/jdk-1.7:*
+	dev-java/ant-core
+	dev-java/htsjdk"
+RDEPEND="
+	${DEPEND}
+	>=virtual/jre-1.7:*"
+
+# TODO: zap bundled htsjdk to ensure it uses dev-java/htsjdk?
+# https://github.com/enasequence/cramtools/issues/58
+# https://github.com/enasequence/cramtools/issues/59
+src_compile(){
+	ant -f build/build.xml runnable || die
+}

diff --git a/sci-biology/cramtools/metadata.xml b/sci-biology/cramtools/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/cramtools/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

[gentoo-commits] proj/sci:master commit in: sci-biology/cramtools/

[Andrew Ammerlaan]

commit:     97692d227a146db8714608d39f07cbdfd57e1b02
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb  1 10:38:51 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb  1 10:38:51 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=97692d22

sci-biology/cramtools: EAPI bump, fix install, add keywords

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/cramtools/cramtools-3.0.ebuild | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/sci-biology/cramtools/cramtools-3.0.ebuild b/sci-biology/cramtools/cramtools-3.0.ebuild
index f0b8d7ac5..b57f4fb26 100644
--- a/sci-biology/cramtools/cramtools-3.0.ebuild
+++ b/sci-biology/cramtools/cramtools-3.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit java-pkg-2 java-ant-2
 
@@ -12,8 +12,7 @@ SRC_URI="https://github.com/enasequence/cramtools/archive/v3.0.tar.gz -> ${P}.ta
 
 LICENSE="Apache-2.0"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
 
 DEPEND="
 	>=virtual/jdk-1.7:*
@@ -29,3 +28,7 @@ RDEPEND="
 src_compile(){
 	ant -f build/build.xml runnable || die
 }
+
+src_install() {
+	java-pkg_newjar "${P}.jar" "${PN}.jar"
+}