From ca7355423fa229cebfe243f837792abb9bf1ef4c Mon Sep 17 00:00:00 2001 From: Horea Christian Date: Sun, 27 Sep 2020 05:20:21 -0400 Subject: 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 --- sci-biology/artemis/Manifest | 2 - sci-biology/artemis/artemis-9999.ebuild | 70 --------------------------------- sci-biology/artemis/metadata.xml | 12 ------ 3 files changed, 84 deletions(-) delete mode 100644 sci-biology/artemis/Manifest delete mode 100644 sci-biology/artemis/artemis-9999.ebuild delete mode 100644 sci-biology/artemis/metadata.xml diff --git a/sci-biology/artemis/Manifest b/sci-biology/artemis/Manifest deleted file mode 100644 index 230e664f0..000000000 --- a/sci-biology/artemis/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST artemis-9999.html_build.zip 2284822 BLAKE2B 4b29d2f503418e12433d9528bab618e1c98d3b6d54704dc8b7e443c9bbddd716a063810559a0680015ba396d76cedc4f76cc98bd822c97207ac17b9d98162631 SHA512 80c952fe20f98b647f38a08a469cb351bb44aa1b0a7d1a9b997fabbd37107d5d934a6d52fa2abfde243f90f4e752c99d418c4ad6b634d82de9744d089eb1cf8a -DIST artemis-9999.manual.pdf 1149449 BLAKE2B 683583db0238bda801cd7fa3c915be41da53eb9d3b4e6e1fa1dfa5ce70585e483892263cd6d6a68ab6689d5663243897d6e6a758024a3a9644681ffe917bc972 SHA512 1c3056dab7239c3a68b2e76491d77612f22ac8f83eaf32e0ab0a3901e03d3c65d5ac02f5758d2d7728d94dd44c29517a498fa94a947d5d319ded43ddec4ba5fb 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@sanger.ac.uk/msg00551.html -# http://www.mail-archive.com/artemis-users@sanger.ac.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 @@ - - - - - mmokrejs@fold.natur.cuni.cz - Martin Mokrejs - - - sci-biology@gentoo.org - Gentoo Biology Project - - -- cgit v1.2.3-65-gdbad