diff options
Diffstat (limited to 'sci-biology/lumpy-sv')
| -rw-r--r-- | sci-biology/lumpy-sv/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild (renamed from sci-biology/lumpy-sv/lumpy-sv-9999.ebuild) | 28 |
2 files changed, 14 insertions, 15 deletions
diff --git a/sci-biology/lumpy-sv/Manifest b/sci-biology/lumpy-sv/Manifest new file mode 100644 index 000000000..df35426fc --- /dev/null +++ b/sci-biology/lumpy-sv/Manifest @@ -0,0 +1 @@ +DIST lumpy-sv-0.3.1.tar.gz 56671785 BLAKE2B d3878f66a5f001c11b4e78fc015102f6b357e72403545bc9c4c8e2104dbcb692fb2d9a53eb9be996ccfa788bac5b03c72be8a591636abb84731b4bab702ceea3 SHA512 efa6992f94005464b49f01c350855ead1b8d5f1006305c09634adee33e0621b0b19b55eaa2ad57583b2b9dc5365e70663892591de85a156eb08d6f14aa0f7c11 diff --git a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild b/sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild index 4c565c0c0..f98892b95 100644 --- a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild +++ b/sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild @@ -1,24 +1,26 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 - -inherit git-r3 +EAPI=7 DESCRIPTION="Probabilistic framework for structural variant discovery" HOMEPAGE="https://github.com/arq5x/lumpy-sv" -EGIT_REPO_URI="https://github.com/arq5x/lumpy-sv.git" +SRC_URI="https://github.com/arq5x/lumpy-sv/archive/v${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT" SLOT="0" -KEYWORDS="" -IUSE="" +KEYWORDS="~amd64" -# contains bundled htslib -CDEPEND="dev-util/cmake" -DEPEND="" +DEPEND="sci-libs/htslib" RDEPEND="${DEPEND}" +src_prepare() { + default + # do not build bundled htslib, link to system lib + sed -i -e 's/lumpy_filter: htslib/lumpy_filter:/g' Makefile || die + sed -i -e 's/-I..\/..\/lib\/htslib\///' -e 's/..\/..\/lib\/htslib\/libhts.a/-lhts/g' src/filter/Makefile || die +} + src_install(){ cat > "${T}"/99lumpy-sv <<- EOF LUMPY_HOME=${EPREFIX}/usr/share/lumpy-sv @@ -35,9 +37,5 @@ src_install(){ rm scripts/"$f" || die done doins scripts/* - dodoc README.md - insinto /usr/share/lumpy-sv/scripts/bamkit - cd scripts/bamkit || die - doins *.py sectosupp - newdoc README.md README_bamkit.md + einstalldocs } |