[gentoo-commits] proj/sci:master commit in: sci-biology/lumpy-sv/

[Andrew Ammerlaan]

commit:     b0ebcbef4027efb671812d1c0d9be250935b3c2b
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar  6 11:55:27 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar  6 11:55:27 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b0ebcbef

sci-biology/lumpy-sv: EAPI bump, fix build

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 ...{lumpy-sv-9999.ebuild => lumpy-sv-0.3.1.ebuild} | 28 ++++++++++------------
 1 file changed, 13 insertions(+), 15 deletions(-)

diff --git a/sci-biology/lumpy-sv/lumpy-sv-9999.ebuild 
b/sci-biology/lumpy-sv/lumpy-sv-0.3.1.ebuild
similarity index 64%
rename from sci-biology/lumpy-sv/lumpy-sv-9999.ebuild
rename to 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
 }