commit: d33eacc4b6316885d2d31c3ef5774bb731242cd7 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jun 9 10:24:16 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Jun 9 10:24:16 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d33eacc4
sci-biology/artemis: ebuild cleanup; officially there is not install and one needs to keep the structure of the source tree and execute directly from there; therefore the ebuild does not work yet Package-Manager: portage-2.2.18 sci-biology/artemis/ChangeLog | 5 +++++ sci-biology/artemis/artemis-9999.ebuild | 38 ++++++++++++++++++++++++++++----- 2 files changed, 38 insertions(+), 5 deletions(-) diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog index 4bebaff..818f34c 100644 --- a/sci-biology/artemis/ChangeLog +++ b/sci-biology/artemis/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 09 Jun 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> artemis-9999.ebuild: + sci-biology/artemis: ebuild cleanup; officially there is not install and one + needs to keep the structure of the source tree and execute directly from + there; therefore the ebuild does not work yet + 18 Feb 2015; Justin Lecher <j...@gentoo.org> artemis-9999.ebuild: sci-biology/artemis: fix SLOT operators diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild index 630e392..8db5509 100644 --- a/sci-biology/artemis/artemis-9999.ebuild +++ b/sci-biology/artemis/artemis-9999.ebuild @@ -6,9 +6,9 @@ EAPI=5 inherit java-pkg-2 java-ant-2 git-r3 -DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool" +DESCRIPTION="DNA sequence viewer/annotation (Artemis) and comparison (ACT) tool" HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"; -SRC_URI="" +SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf"; EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"; LICENSE="GPL-2" @@ -21,13 +21,41 @@ RDEPEND=" sci-biology/samtools >=virtual/jre-1.6:*" DEPEND="${RDEPEND} + !sci-biology/artemis-bin dev-java/ant-core - >=virtual/jdk-1.6:*" + >=virtual/jdk-1.6:* + dev-java/log4j + dev-java/jdbc-postgresql + dev-java/jakarta-regexp + dev-java/batik + dev-java/j2ssh + sci-biology/picard + dev-java/biojava" +# some more dependencies extracted from /usr/bin/act +# JacORB.jar, jemAlign.jar, macos.jar, chado-14-interface.jar, iBatis, biojava.jar, +# # http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html # http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html # http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial -# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf - # BamView is at http://bamview.sourceforge.net/ + +src_compile(){ + ant || die +} + +src_install(){ + dobin act act.command art dnaplotter gff2embl + java-pkg_dojar ant-build/artemis.jar + dodoc "${DISTDIR}"/artemis.pdf README +} + +# 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 " from http://bamview.sourceforge.net"; +}
