commit:     b7d442c1ad60516bf1f2e25bdb4f7287ac29a0cd
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 09:30:16 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 09:30:16 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b7d442c1

sci-biology/tablet: update ebuild

New homepage, switch from svn to github, new license, switch
from picard to htsjdk

There is no ./classes/ so `ant build` does not work for me.

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

 ...-1.16.09.06.ebuild => tablet-1.17.08.17.ebuild} | 25 ++++++++++----------
 sci-biology/tablet/tablet-9999.ebuild              | 27 +++++++++++-----------
 2 files changed, 25 insertions(+), 27 deletions(-)

diff --git a/sci-biology/tablet/tablet-1.16.09.06.ebuild 
b/sci-biology/tablet/tablet-1.17.08.17.ebuild
similarity index 63%
rename from sci-biology/tablet/tablet-1.16.09.06.ebuild
rename to sci-biology/tablet/tablet-1.17.08.17.ebuild
index e72339d61..08a272961 100644
--- a/sci-biology/tablet/tablet-1.16.09.06.ebuild
+++ b/sci-biology/tablet/tablet-1.17.08.17.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
 inherit java-pkg-2 java-ant-2 python-r1
 
-# [ "$PV" == "9999" ] && inherit subversion
-inherit subversion
+[ "$PV" == "9999" ] && inherit git-r3
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/";
+HOMEPAGE="https://ics.hutton.ac.uk/tablet";
 if [ "$PV" == "9999" ]; then
-       ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/";
+       EGIT_REPO_URI="https://github.com/cropgeeks/tablet.git";
        KEYWORDS=""
 else
-       ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}";
-       KEYWORDS="~amd64 ~x86"
+       SRC_URI="https://github.com/cropgeeks/tablet/archive/${PV}.tar.gz -> 
${P}.tar.gz"
+       KEYWORDS=""
 fi
 
-LICENSE="Tablet"
+LICENSE="BSD-2"
 SLOT="0"
 IUSE=""
 
@@ -29,10 +28,10 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 DEPEND="${PYTHON_DEPS}
        >=virtual/jdk-1.8:*"
 RDEPEND="${PYTHON_DEPS}
-       >=virtual/jre-1.8:*"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
+       >=virtual/jre-1.8:*
+       >=dev-java/commons-compress-1.4.1"
+# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, 
htsjdk-2.11.0.jar
 # sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not 
sci-biology/samtools either
-# replacing picard.jar with a symlink to picard.jar from sci-biology.picard 
does not help either
 
 S="${WORKDIR}"
 
@@ -43,7 +42,7 @@ src_install() {
        java-pkg_dojar lib/flamingo.jar
        java-pkg_dojar lib/scri-commons.jar
        java-pkg_dojar lib/samtools*.jar
-       java-pkg_dojar lib/picard*.jar # is picard-1.113 in tablet-1.16.09.06
+       java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17
        java-pkg_dojar lib/sqlite-jdbc*.jar
 
        echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet

diff --git a/sci-biology/tablet/tablet-9999.ebuild 
b/sci-biology/tablet/tablet-9999.ebuild
index 467895e5d..01759c6b4 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
 inherit java-pkg-2 java-ant-2 python-r1
 
-# [ "$PV" == "9999" ] && inherit subversion
-inherit subversion
+[ "$PV" == "9999" ] && inherit git-r3
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/";
+HOMEPAGE="https://ics.hutton.ac.uk/tablet";
 if [ "$PV" == "9999" ]; then
-       ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/";
+       EGIT_REPO_URI="https://github.com/cropgeeks/tablet.git";
        KEYWORDS=""
 else
-       ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}";
+       SRC_URI="https://github.com/cropgeeks/tablet/archive/${PV}.tar.gz -> 
${P}.tar.gz"
        KEYWORDS=""
 fi
 
-LICENSE="Tablet"
+LICENSE="BSD-2"
 SLOT="0"
 IUSE=""
 
@@ -29,12 +28,12 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 DEPEND="${PYTHON_DEPS}
        >=virtual/jdk-1.8:*"
 RDEPEND="${PYTHON_DEPS}
-       >=virtual/jre-1.8:*"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
-# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not 
sci-biology/samtools either
-# replacing picard.jar with a symlink to picard.jar from sci-biology.picard 
does not help either
+       >=virtual/jre-1.8:*
+       >=dev-java/commons-compress-1.4.1"
+# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, 
htsjdk-2.11.0.jar
+# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not 
sci-biology/samtools
 
-S="${WORKDIR}"
+#S="${WORKDIR}"
 
 src_install() {
        java-pkg_dojar lib/tablet.jar
@@ -43,7 +42,7 @@ src_install() {
        java-pkg_dojar lib/flamingo.jar
        java-pkg_dojar lib/scri-commons.jar
        java-pkg_dojar lib/samtools*.jar
-       java-pkg_dojar lib/picard*.jar
+       java-pkg_dojar lib/htsjdk*.jar
        java-pkg_dojar lib/sqlite-jdbc*.jar
 
        echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet

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