From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1Rjv2H-0003gL-KL for garchives@archives.gentoo.org; Sun, 08 Jan 2012 15:51:54 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id C184321C028; Sun, 8 Jan 2012 15:51:43 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 831EF21C028 for ; Sun, 8 Jan 2012 15:51:43 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id A0ACB1B4017 for ; Sun, 8 Jan 2012 15:51:42 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id D5E6180044 for ; Sun, 8 Jan 2012 15:51:41 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1afb461b204933db48bfe976a37203c92846930d.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 sci-biology/artemis/metadata.xml X-VCS-Directories: sci-biology/artemis/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 1afb461b204933db48bfe976a37203c92846930d Date: Sun, 8 Jan 2012 15:51:41 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: 65b22664-c8d7-4437-9d01-0478bc37a117 X-Archives-Hash: 3ffd671ec8d8e7429219de9c95164c77 commit: 1afb461b204933db48bfe976a37203c92846930d Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Sun Jan 8 15:49:57 2012 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Jan 8 15:49:57 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D1afb461b sci-biology/artemis: DNA sequence viewer, annotation (Artemis) and compar= ison (ACT) tool --- sci-biology/artemis/ChangeLog | 10 ++++++++ sci-biology/artemis/artemis-9999.ebuild | 39 +++++++++++++++++++++++++= ++++++ sci-biology/artemis/metadata.xml | 9 +++++++ 3 files changed, 58 insertions(+), 0 deletions(-) diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLo= g new file mode 100644 index 0000000..8a33496 --- /dev/null +++ b/sci-biology/artemis/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/artemis +# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*artemis-9999 (08 Jan 2012) + + 08 Jan 2012; Martin Mokrejs + +artemis-9999.ebuild, +metadata.xml: + initial, not yet working ebuild + diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemi= s/artemis-9999.ebuild new file mode 100644 index 0000000..ff8d52d --- /dev/null +++ b/sci-biology/artemis/artemis-9999.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3D3 + +inherit java-pkg-2 java-ant-2 + +[ "$PV" =3D=3D "9999" ] && inherit git-2 + +DESCRIPTION=3D"DNA sequence viewer, annotation (Artemis) and comparison = (ACT) tool" +HOMEPAGE=3D"http://www.sanger.ac.uk/resources/software/artemis" + +if [ "$PV" =3D=3D "9999" ]; then + EGIT_REPO_URI=3D"https://github.com/sanger-pathogens/Artemis" + KEYWORDS=3D"" +else + SRC_URI=3D"ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v= "${PV}"/artemis_compiled_v"${PV}".tar.gz" + KEYWORDS=3D"~amd64 ~x86" +fi + +LICENSE=3D"GPL-2" +SLOT=3D"0" +KEYWORDS=3D"~amd64 ~x86" +IUSE=3D"" + +DEPEND=3D"sci-biology/samtools + sci-biology/bamview + >=3Dvirtual/jdk-1.5 + >=3Ddev-java/sun-jdk-1.5 + dev-java/ant-core" +RDEPEND=3D"${DEPEND} + >=3Dvirtual/jre-1.5" + +src_compile() { + ant compile || die + + einfo "Need to figure out where does the GeneBuilder application come f= rom so that one could use Chado for automated gene prediction pipeline" +} diff --git a/sci-biology/artemis/metadata.xml b/sci-biology/artemis/metad= ata.xml new file mode 100644 index 0000000..07b5255 --- /dev/null +++ b/sci-biology/artemis/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +