From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id C55051382C5 for ; Sun, 1 Apr 2018 15:04:46 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id BD5E9E095E; Sun, 1 Apr 2018 15:04:45 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 8193AE095E for ; Sun, 1 Apr 2018 15:04:44 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 38EAD335D99 for ; Sun, 1 Apr 2018 15:04:43 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id A1BF8266 for ; Sun, 1 Apr 2018 15:04:41 +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: <1522595065.4efdba16fdc718fde4b8679fb805cb382df46fef.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/seq_crumbs/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/seq_crumbs/metadata.xml sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild X-VCS-Directories: sci-biology/seq_crumbs/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 4efdba16fdc718fde4b8679fb805cb382df46fef X-VCS-Branch: master Date: Sun, 1 Apr 2018 15:04:41 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 583a4286-0df9-4970-b3d4-21e39dd53146 X-Archives-Hash: 3d3bf6c274f39572e7ae8fa6438db147 commit: 4efdba16fdc718fde4b8679fb805cb382df46fef Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Sun Apr 1 15:04:25 2018 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sun Apr 1 15:04:25 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4efdba16 sci-biology/seq_crumbs: new package The fix to setup.py to respect DESTDIR is probably not ideal. Needs a fix to avoid file collisions. Package-Manager: Portage-2.3.27, Repoman-2.3.9 sci-biology/seq_crumbs/metadata.xml | 12 +++++++ sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild | 46 ++++++++++++++++++++++++++ 2 files changed, 58 insertions(+) diff --git a/sci-biology/seq_crumbs/metadata.xml b/sci-biology/seq_crumbs/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/seq_crumbs/metadata.xml @@ -0,0 +1,12 @@ + + + + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + + + sci-biology@gentoo.org + Gentoo Biology Project + + diff --git a/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild b/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild new file mode 100644 index 000000000..94ce00a94 --- /dev/null +++ b/sci-biology/seq_crumbs/seq_crumbs-0.1.9.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 eutils + +DESCRIPTION="Filter, split and trim NGS sequence data" +HOMEPAGE="https://github.com/JoseBlanca/seq_crumbs" +SRC_URI="https://github.com/JoseBlanca/"${PN}"/archive/v"${PV}".tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=" + >=sci-biology/biopython-1.60 + >=sci-biology/pysam-0.8 + >=dev-python/rpy-2 + dev-python/matplotlib + dev-python/configobj + dev-python/toolz" +RDEPEND="${DEPEND}" + +# TODO fix file collisions +# * Detected file collision(s): +# * +# * /usr/share/man/man1/index.1.bz2 +# * /usr/share/man/man1/install.1.bz2 +# * +# * Searching all installed packages for file collisions... +# * +# * Press Ctrl-C to Stop +# * +# * sys-apps/coreutils-8.29:0::gentoo +# * /usr/share/man/man1/install.1.bz2 +# * +# * media-libs/netpbm-10.76.00:0::gentoo +# * /usr/share/man/man1/index.1.bz2 +src_prepare(){ + sed -e "s#sys.prefix#os.getenv('ED')+'/usr/'#" -i setup.py || die + default +}