diff options
Diffstat (limited to 'sci-biology/shrimp/shrimp-2.2.3.ebuild')
-rw-r--r-- | sci-biology/shrimp/shrimp-2.2.3.ebuild | 82 |
1 files changed, 0 insertions, 82 deletions
diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild deleted file mode 100644 index 2b57b032a1b2..000000000000 --- a/sci-biology/shrimp/shrimp-2.2.3.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit flag-o-matic python-single-r1 toolchain-funcs - -MY_PV=${PV//./_} - -DESCRIPTION="SHort Read Mapping Package" -HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/" -SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz" - -LICENSE="shrimp" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="custom-cflags +cpu_flags_x86_sse2" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# file collision on /usr/bin/utils #453044 -DEPEND="!sci-mathematics/cado-nfs" -RDEPEND="${DEPEND} - ${PYTHON_DEPS}" - -S=${WORKDIR}/SHRiMP_${MY_PV} - -pkg_pretend() { - use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU" -} - -pkg_setup() { - if [[ ${CC} == *gcc* ]] && ! tc-has-openmp; then - elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc" - die "C compiler lacks OPENMP support" - fi - python-single-r1_pkg_setup -} - -src_prepare() { - sed \ - -e '1 a #include <stdint.h>' \ - -i common/dag_glue.cpp || die - # respect LDFLAGS wrt 331823 - sed \ - -e "s/LDFLAGS/LIBS/" \ - -e "s/\$(LD)/& \$(LDFLAGS)/" \ - -e 's/-static//' \ - -i Makefile || die - - append-flags -fopenmp - if ! use custom-cflags; then - append-flags -O3 - replace-flags -O* -O3 - fi - tc-export CXX - - cd utils || die - sed -e '/^#!/d' -i *py || die - sed -e '1i#!/usr/bin/python' -i *py || die -} - -src_compile() { - emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" -} - -src_install() { - local i - newdoc bin/README README.bin && rm bin/README - dobin bin/* utils/split-contigs utils/temp-sink - dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES - - pushd utils > /dev/null - - python_doscript *py - - rm *.py *.o *.c split-contigs temp-sink || die - insinto /usr/share/${PN} - doins -r * -} |