commit: 2fe25927e87d9c3339465453ae165b366ff2d8f2 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Tue Mar 18 19:24:38 2014 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Tue Mar 18 19:24:38 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2fe25927
sci-biology/khmer: Unbundle zlib and bzpi2; bump to disturils-r1; respect CFLAGS Package-Manager: portage-2.2.8-r1 --- sci-biology/khmer/ChangeLog | 6 ++++++ sci-biology/khmer/khmer-0.8.ebuild | 38 +++++++++++++++++++++++++++++++++++++ sci-biology/khmer/khmer-9999.ebuild | 21 ++++++++++++++++++-- 3 files changed, 63 insertions(+), 2 deletions(-) diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog index 4f2f8a6..a2834e6 100644 --- a/sci-biology/khmer/ChangeLog +++ b/sci-biology/khmer/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*khmer-0.8 (18 Mar 2014) + + 18 Mar 2014; Justin Lecher <j...@gentoo.org> +khmer-0.8.ebuild, + khmer-9999.ebuild: + Unbundle zlib and bzpi2; bump to disturils-r1; respect CFLAGS + 16 Mar 2014; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> khmer-9999.ebuild: sci-biology/khmer: revert to distutils to obey sandbox violation diff --git a/sci-biology/khmer/khmer-0.8.ebuild b/sci-biology/khmer/khmer-0.8.ebuild new file mode 100644 index 0000000..7566b3c --- /dev/null +++ b/sci-biology/khmer/khmer-0.8.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences" +HOMEPAGE="https://github.com/ged-lab/khmer"; +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS=" ~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="" +RDEPEND="sci-biology/screed" + +python_prepare_all(){ + rm -rf lib/{bzip2,zlib} || die + + sed \ + -e 's:zlib/zlib.h:zlib.h:g' \ + -e 's:bzip2/bzlib.h:bzlib.h:g' \ + -i lib/read_parsers.hh lib/counting.cc || die + + sed \ + -e "/extra_objects/d" \ + -e '/libraries/s:, ]:, "z", "bz2", ]:g' \ + -e "s:'-O3',::g" \ + -i setup.py || die + + distutils-r1_python_prepare_all +} diff --git a/sci-biology/khmer/khmer-9999.ebuild b/sci-biology/khmer/khmer-9999.ebuild index ab29463..4ac1a8b 100644 --- a/sci-biology/khmer/khmer-9999.ebuild +++ b/sci-biology/khmer/khmer-9999.ebuild @@ -6,7 +6,7 @@ EAPI=5 PYTHON_COMPAT=( python2_7 ) -inherit distutils git-r3 +inherit distutils-r1 git-r3 DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences" HOMEPAGE="https://github.com/ged-lab/khmer"; @@ -19,4 +19,21 @@ KEYWORDS="" IUSE="" DEPEND="" -RDEPEND="${DEPEND}" +RDEPEND="sci-biology/screed" + +python_prepare_all(){ + rm -rf lib/{bzip2,zlib} || die + + sed \ + -e 's:zlib/zlib.h:zlib.h:g' \ + -e 's:bzip2/bzlib.h:bzlib.h:g' \ + -i lib/read_parsers.hh lib/counting.cc || die + + sed \ + -e "/extra_objects/d" \ + -e '/libraries/s:, ]:, "z", "bz2", ]:g' \ + -e "s:'-O3',::g" \ + -i setup.py || die + + distutils-r1_python_prepare_all +}
