commit: ca7355423fa229cebfe243f837792abb9bf1ef4c Author: Horea Christian <chr <AT> chymera <DOT> eu> AuthorDate: Sun Sep 27 09:20:21 2020 +0000 Commit: Horea Christian <horea.christ <AT> gmail <DOT> com> CommitDate: Sun Sep 27 09:20:21 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca735542
sci-biology/artemis: remove unmaintained package Package is not discontinued upstream, but would need a major overhaul from present live ebuild: https://github.com/sanger-pathogens/Artemis Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Horea Christian <chr <AT> chymera.eu> sci-biology/artemis/artemis-9999.ebuild | 70 --------------------------------- sci-biology/artemis/metadata.xml | 12 ------ 2 files changed, 82 deletions(-) diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild deleted file mode 100644 index 162cc67e7..000000000 --- a/sci-biology/artemis/artemis-9999.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit java-pkg-2 java-ant-2 git-r3 - -DESCRIPTION="DNA sequence viewer/annotation (Artemis) and comparison (ACT) tool" -HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"; -SRC_URI=" - ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf -> ${P}.manual.pdf - ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/art_html_build.zip -> ${P}.html_build.zip" -EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"; - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="" -IUSE="" - -# uses its own BamView -RDEPEND=" - sci-biology/samtools:0 - >=virtual/jre-1.6:*" -DEPEND="${RDEPEND} - !sci-biology/artemis-bin - dev-java/ant-core - >=virtual/jdk-1.6:* - dev-java/log4j - dev-java/jdbc-postgresql - dev-java/jakarta-regexp - dev-java/batik - dev-java/j2ssh - sci-biology/picard - dev-java/biojava" -# some more dependencies extracted from /usr/bin/act -# JacORB.jar, jemAlign.jar, macos.jar, chado-14-interface.jar, iBatis, biojava.jar, -# - -# http://www.mail-archive.com/[email protected]/msg00551.html -# http://www.mail-archive.com/[email protected]/msg00561.html -# http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial - -# BamView is at http://bamview.sourceforge.net/ - -src_unpack(){ - unzip "${DISTDIR}"/art_html_build.zip || die -} - -src_compile(){ - ant || die -} - -src_install(){ - dobin act act.command art dnaplotter gff2embl - java-pkg_dojar ant-build/artemis.jar - dodoc "${DISTDIR}"/"${P}".manual.pdf README - insinto /usr/share/doc/"${PN}"/html - doins art_html_build/* -} - -# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files -# artemis_v16.0.11.jar and sartemis_v16.0.11.jar -# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.11/ - -pkg_postinst(){ - einfo "For BAM file support please install sci-biology/BamView" - einfo "You may find interesting the additional web resources:" - einfo "http://www.webact.org/WebACT"; - einfo "http://www.hpa-bioinfotools.org.uk/pise/double_act.html"; -} diff --git a/sci-biology/artemis/metadata.xml b/sci-biology/artemis/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/artemis/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata>
