From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 85843138CDD for ; Tue, 9 Jun 2015 10:25:15 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 477C2E0830; Tue, 9 Jun 2015 10:25:13 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id D9F33E0830 for ; Tue, 9 Jun 2015 10:25:12 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 438BA3406A7 for ; Tue, 9 Jun 2015 10:25:11 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id C884EA30 for ; Tue, 9 Jun 2015 10:25:09 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1433845456.d33eacc4b6316885d2d31c3ef5774bb731242cd7.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/artemis/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/artemis/ChangeLog sci-biology/artemis/artemis-9999.ebuild X-VCS-Directories: sci-biology/artemis/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: d33eacc4b6316885d2d31c3ef5774bb731242cd7 X-VCS-Branch: master Date: Tue, 9 Jun 2015 10:25:09 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: d26475f1-ed91-4c59-989a-9d5795590d92 X-Archives-Hash: 1334120c5e14815d6d8da0b50311bb5d commit: d33eacc4b6316885d2d31c3ef5774bb731242cd7 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Jun 9 10:24:16 2015 +0000 Commit: Martin Mokrejs fold natur cuni 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 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 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" +}