commit: c86c2b38245dd48b5de81f6359c993a3d72cdac7 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jan 10 00:59:00 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Jan 10 00:59:00 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c86c2b38
sci-biology/idba: distinguish openmp cflags, fix compile and install steps Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/idba/idba-1.1.1.ebuild | 22 ++++++++++++++++++++-- sci-biology/idba/idba-9999.ebuild | 25 ++++++++++++++++++++++--- 2 files changed, 42 insertions(+), 5 deletions(-) diff --git a/sci-biology/idba/idba-1.1.1.ebuild b/sci-biology/idba/idba-1.1.1.ebuild index d061f9a..2c923af 100644 --- a/sci-biology/idba/idba-1.1.1.ebuild +++ b/sci-biology/idba/idba-1.1.1.ebuild @@ -12,19 +12,37 @@ SRC_URI="https://storage.googleapis.com/google-code-archive-downloads/v2/code.go LICENSE="GPL-2+" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" +IUSE="openmp" DEPEND="" RDEPEND="${DEPEND}" +pkg_setup() { + use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler" +} + src_prepare(){ # Makefile.am also forces '-fopenmp -pthread', do we care? + #code stolen from velvet-1.2.10.ebuild + if [[ $(tc-getCC) =~ gcc ]]; then + local eopenmp=-fopenmp + elif [[ $(tc-getCC) =~ icc ]]; then + local eopenmp=-openmp + sed -e 's/-fopenmp/-openmp/' -i BUILD || die + else + elog "Cannot detect compiler type so not setting openmp support" + fi find . -name Makefile.in | while read f; do \ - sed -e 's/-Wall -O3//' -i $f || die + sed -e "s/-Wall -O3//" -i $f || die done || die + sed -e 's/"-Wall", "-O3", //' -i BUILD || die default } +src_compile(){ + sh build.sh || die +} + src_install(){ default # https://github.com/loneknightpy/idba/issues/23 diff --git a/sci-biology/idba/idba-9999.ebuild b/sci-biology/idba/idba-9999.ebuild index da7f888..1932d8c 100644 --- a/sci-biology/idba/idba-9999.ebuild +++ b/sci-biology/idba/idba-9999.ebuild @@ -4,7 +4,7 @@ EAPI=6 -inherit git-r3 +inherit git-r3 toolchain-funcs DESCRIPTION="De novo De Bruijn graph assembler iteratively using multimple k-mers" HOMEPAGE="http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud"; @@ -13,21 +13,40 @@ EGIT_REPO_URI="https://github.com/loneknightpy/idba.git"; LICENSE="GPL-2+" SLOT="0" KEYWORDS="" -IUSE="" +IUSE="openmp" DEPEND="" RDEPEND="${DEPEND}" +pkg_setup() { + use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler" +} + src_prepare(){ + if [[ $(tc-getCC) =~ gcc ]]; then + local eopenmp=-fopenmp + elif [[ $(tc-getCC) =~ icc ]]; then + local eopenmp=-openmp + sed -e 's/-fopenmp/-openmp/' -i BUILD || die + else + elog "Cannot detect compiler type so not setting openmp support" + fi find . -name Makefile.in | while read f; do \ - sed -e 's/-Wall -O3//' -i $f || die + sed -e "s/-Wall -O3 ${eopenmp}//" -i $f || die done + sed -e 's/"-Wall", "-O3", //' -i BUILD || die default } +src_compile(){ + sh build.sh || die +} + src_install(){ default # https://github.com/loneknightpy/idba/issues/23 + mkdir -p "${D}"/usr/bin || die + mv "${D}"/usr/local/bin/* "${D}"/usr/bin/ || die rm "${D}"/usr/bin/scan.py "${D}"/usr/bin/run-unittest.py || die rm bin/test bin/*.o bin/Makefile* || die # avoid file collision dobin bin/* # https://github.com/loneknightpy/idba/issues/23
