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69 lines
1.5 KiB
69 lines
1.5 KiB
7 months ago
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# Copyright 1999-2024 Gentoo Authors
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4 years ago
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# Distributed under the terms of the GNU General Public License v2
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7 months ago
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EAPI=8
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4 years ago
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7 months ago
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inherit cmake flag-o-matic
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4 years ago
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DESCRIPTION="Near-optimal RNA-Seq quantification"
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HOMEPAGE="http://pachterlab.github.io/kallisto/"
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if [[ ${PV} == *9999 ]]; then
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inherit git-r3
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EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git"
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else
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SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
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fi
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LICENSE="BSD"
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SLOT="0"
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IUSE="hdf5 test"
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RESTRICT="!test? ( test )"
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RDEPEND="
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sci-libs/htslib:=
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sys-libs/zlib:=
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hdf5? ( sci-libs/hdf5:= )"
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DEPEND="
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${RDEPEND}
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test? (
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7 months ago
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>=dev-cpp/catch-3:0
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4 years ago
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sci-libs/hdf5
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)"
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BDEPEND="virtual/pkgconfig"
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PATCHES=(
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"${FILESDIR}"/${P}-cmake.patch
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"${FILESDIR}"/${P}-htslib.patch
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"${FILESDIR}"/${P}-catch2.patch
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"${FILESDIR}"/${P}-gcc11.patch
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)
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src_prepare() {
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cmake_src_prepare
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# bundled catch2
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rm -r ext || die
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# bundled htslib structs
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rm src/kseq.h || die
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# the test suite is cheesy and relies on a
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# specific builddir nesting structure.
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sed -e "s|../test/input/short_reads.fastq|$(readlink -f unit_tests/input/short_reads.fastq)|g" \
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-i unit_tests/test_kmerhashtable.cpp || die
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7 months ago
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# This randomly hardcodes a particular std, which unfortunately is too old for catch2.
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sed -i '/CMAKE_CXX_STANDARD/d' CMakeLists.txt || die
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append-cxxflags -std=c++14
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4 years ago
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}
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src_configure() {
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local mycmakeargs=(
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-DUSE_HDF5=$(usex hdf5)
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-DBUILD_TESTING=$(usex test)
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# convenience library only
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-DBUILD_SHARED_LIBS=OFF
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)
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cmake_src_configure
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}
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