commit: cef6f206bd05567e80c11b9f9b1e850f74e06731 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Fri Jul 28 19:23:07 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Fri Jul 28 20:05:19 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cef6f206
sci-biology/nanopolish: new package Package-Manager: Portage-2.3.6, Repoman-2.3.3 sci-biology/nanopolish/metadata.xml | 12 +++++++ sci-biology/nanopolish/nanopolish-9999.ebuild | 48 +++++++++++++++++++++++++++ 2 files changed, 60 insertions(+) diff --git a/sci-biology/nanopolish/metadata.xml b/sci-biology/nanopolish/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/nanopolish/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <maintainer type="person"> + <email>mmokr...@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <maintainer type="project"> + <email>sci-biol...@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/nanopolish/nanopolish-9999.ebuild b/sci-biology/nanopolish/nanopolish-9999.ebuild new file mode 100644 index 000000000..92c5f41d3 --- /dev/null +++ b/sci-biology/nanopolish/nanopolish-9999.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit git-r3 + +DESCRIPTION="Signal-level analysis of Oxford Nanopore sequencing data" +HOMEPAGE="https://github.com/jts/nanopolish"; +EGIT_REPO_URI="https://github.com/jts/nanopolish.git"; + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +IUSE="" + +# HDF5 is not thread safe by default and nanopolish currently requires a threadsafe HDF5. +# This is one reason we download the compile it ourself (the main reason is to make it +# easier for most users). The other options cxx, fortran, mpi are not needed by nanopolish +# (we use the C bindings in nanopolish only). +# The bundled version of htslib in is 1.2.1 as of now although 1.5.1 already exists +DEPEND=">=sci-libs/hdf5-1.8.14[threads] + >=dev-cpp/eigen-3.2.5 + sci-libs/htslib:0 + sci-libs/fast5" +RDEPEND="${DEPEND} + sci-biology/biopython" + +src_prepare(){ + default + rm -rf hdf5* eigen htslib || die # TODO; zap also fast5 +} + +src_compile(){ + # >=gcc-4.8 but <gcc-7 is needed + # https://github.com/jts/nanopolish/issues/145 + emake HDF5="noinstall" EIGEN="nofetch" HTS_LIB=-lhts HTS_INCLUDE=-I/usr/include/htslib EIGEN_INCLUDE=-I/usr/include/eigen3 # TODO: FAST5_INCLUDE=-I/usr/include/fast5 +} + +src_install(){ + rm -rf lib || die # zap libs eventually compiled from the bundled copies + dobin nanopolish + # add scripts/ subdirectory to PATH +} + +src_test(){ + nanopolish_test || die +}
