commit: 6948e2872a1c6182e8e325edd5e48a21bd713443 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sun Apr 30 13:23:16 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sun Apr 30 13:23:16 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6948e287
sci-biology/samtools: version bump Compiles fine against htslib-1.4 but because htslib-1.4 is not KEYWORDed keeping samtools-1.4 masked as well. Package-Manager: Portage-2.3.5, Repoman-2.3.2 sci-biology/samtools/samtools-1.4.ebuild | 82 ++++++++++++++++++++++++++++++++ 1 file changed, 82 insertions(+) diff --git a/sci-biology/samtools/samtools-1.4.ebuild b/sci-biology/samtools/samtools-1.4.ebuild new file mode 100644 index 000000000..b0bd40b82 --- /dev/null +++ b/sci-biology/samtools/samtools-1.4.ebuild @@ -0,0 +1,82 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map) and BAM files" +HOMEPAGE="http://www.htslib.org/"; +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +# KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +CDEPEND=" + sys-libs/ncurses:0= + >=sci-libs/htslib-${PV}" + +RDEPEND="${CDEPEND} + dev-lang/lua + dev-lang/perl" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +src_prepare() { + find htslib-* -delete || die + + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + + tc-export CC AR + + sed \ + -e '/htslib.mk/d' \ + -i Makefile || die +} + +src_compile() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + CC=$(tc-getCC) CFLAGS="${CFLAGS}" + ) + emake "${mymakeargs[@]}" +} + +src_test() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test +} + +src_install() { + dobin samtools $(find misc -type f -executable) + + python_replicate_script "${ED}"/usr/bin/varfilter.py + #dolib.so libbam.so* + dolib libbam.a + + insinto /usr/include/bam + doins *.h + + doman ${PN}.1 + dodoc AUTHORS NEWS README + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +}
