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 B8A0259CA9 for ; Wed, 30 Mar 2016 16:33:24 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 1DD4121C024; Wed, 30 Mar 2016 16:33:24 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id A7C9821C024 for ; Wed, 30 Mar 2016 16:33:23 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 3117434045C for ; Wed, 30 Mar 2016 16:33:22 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id F2549845 for ; Wed, 30 Mar 2016 16:33:20 +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: <1459355441.4215f67e0da1eb2a2600f0b30a9e6032ddea342c.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/exomiser-bin/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild X-VCS-Directories: sci-biology/exomiser-bin/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 4215f67e0da1eb2a2600f0b30a9e6032ddea342c X-VCS-Branch: master Date: Wed, 30 Mar 2016 16:33:20 +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: 654de9ae-2039-4615-a7ad-f0c17d04ccb3 X-Archives-Hash: 0f030e06ca4da57e46403d076d13af7d commit: 4215f67e0da1eb2a2600f0b30a9e6032ddea342c Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Mar 30 16:30:41 2016 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Mar 30 16:30:41 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4215f67e sci-biology/exomiser-bin: improve ebuild, fix LICENSE, a 19GB files should be fetched manually but the ebuild should get access to it, unpack it and install as the files make grounding for a usable workspace Package-Manager: portage-2.2.28 sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild | 23 ---------------- sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild | 31 ++++++++++++++++++++++ 2 files changed, 31 insertions(+), 23 deletions(-) diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild deleted file mode 100644 index c58cabf..0000000 --- a/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Id$ - -EAPI=5 - -DESCRIPTION="Annotate VCF files from whole-exome sequencing (Jannovar, UCSC KnownGenes, hg19)" -HOMEPAGE="http://www.sanger.ac.uk/resources/software/exomiser" -SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}.BETA-distribution.zip" -# 1.16GB ! - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="sci-biology/Jannovar-bin" -RDEPEND="${DEPEND}" - -pkg_postinst(){ - einfo "Please download 3.7GB file from ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/h2_db_dumps/exomiser-${PV}.BETA.h2.db.gz" - einfo "and follow README.md" -} diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild new file mode 100644 index 0000000..1346fd2 --- /dev/null +++ b/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +DESCRIPTION="Annotate VCF files and prioritize genome/exome mutations (Jannovar, UCSC KnownGenes, hg19)" +HOMEPAGE="http://www.sanger.ac.uk/science/tools/exomiser" +SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}-distribution.zip + ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/GenomiserREADME -> ${PN}.README + ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/README.md -> ${PN}.README.md" +# 1.16GB ! + +LICENSE="AGPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="sci-biology/Jannovar-bin" +RDEPEND="${DEPEND}" + +src_install(){ + dodoc "${DISTDIR}"/${PN}.README "${DISTDIR}"/${PN}.README.md +} + +pkg_postinst(){ + einfo "Please download 3.7GB file from ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/h2_db_dumps/exomiser-${PV}.BETA.h2.db.gz" + einfo "and follow README.md" + einfo "The is also 19GB file ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-7.2.1-data.zip" + einfo "with test data" +}