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
