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

[Horea Christian]

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/artemis-users@×××××××××.uk/msg00551.html
-# http://www.mail-archive.com/artemis-users@×××××××××.uk/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>mmokrejs@×××××××××××××××.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@g.o</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>