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 6A3F5138A1A for ; Sat, 10 Jan 2015 01:21:11 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 246F7E0875; Sat, 10 Jan 2015 01:21:09 +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 A553FE0875 for ; Sat, 10 Jan 2015 01:21:08 +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 5A4F934077F for ; Sat, 10 Jan 2015 01:21:07 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 064EDF3D8 for ; Sat, 10 Jan 2015 01:21:06 +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: <1420852802.f1305f2410140aee98085c7448eae116695a4b04.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/cegma/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/cegma/ChangeLog sci-biology/cegma/cegma-2.5.ebuild sci-biology/cegma/metadata.xml X-VCS-Directories: sci-biology/cegma/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: f1305f2410140aee98085c7448eae116695a4b04 X-VCS-Branch: master Date: Sat, 10 Jan 2015 01:21:06 +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: 8a07bc10-537f-4688-8553-1f216ec4a713 X-Archives-Hash: d90aef608451c4360924e582de3e020a commit: f1305f2410140aee98085c7448eae116695a4b04 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Sat Jan 10 01:20:02 2015 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Jan 10 01:20:02 2015 +0000 URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f1305f24 new package; install *.pm into PERL5LIB/cegma and pass that via env.d --- sci-biology/cegma/ChangeLog | 8 ++++++++ sci-biology/cegma/cegma-2.5.ebuild | 36 ++++++++++++++++++++++++++++++++++++ sci-biology/cegma/metadata.xml | 9 +++++++++ 3 files changed, 53 insertions(+) diff --git a/sci-biology/cegma/ChangeLog b/sci-biology/cegma/ChangeLog new file mode 100644 index 0000000..8e87015 --- /dev/null +++ b/sci-biology/cegma/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for sci-biology/cegma +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 10 Jan 2015; Martin Mokrejs +cegma-2.5.ebuild, + +metadata.xml: + new package; install *.pm into PERL5LIB/cegma and pass that via env.d + diff --git a/sci-biology/cegma/cegma-2.5.ebuild b/sci-biology/cegma/cegma-2.5.ebuild new file mode 100644 index 0000000..ef8dfe5 --- /dev/null +++ b/sci-biology/cegma/cegma-2.5.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Use set of 458 core proteins to predict genes in a genome and use them for training to find all genes" +HOMEPAGE="http://korflab.ucdavis.edu/datasets/cegma" +SRC_URI="http://korflab.ucdavis.edu/datasets/cegma/CEGMA_v"${PV}".tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="dev-lang/perl + sci-biology/wise + >=sci-biology/hmmer-3.0 + sci-biology/geneid + sci-biology/ncbi-tools++" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/CEGMA_v${PV} + +src_install(){ + dobin bin/* + eval `perl '-V:installvendorlib'` + vendor_lib_install_dir="${installvendorlib}" + dodir ${vendor_lib_install_dir}/cegma + insinto ${vendor_lib_install_dir}/cegma + doins lib/*.pm + + echo "PERL5LIB="${vendor_lib_install_dir}"/cegma" > ${S}"/99cegma" + # echo "CEGMATMP=/var/tmp" >> ${S}"/99cegma" + doenvd ${S}"/99cegma" || die +} diff --git a/sci-biology/cegma/metadata.xml b/sci-biology/cegma/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/cegma/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +