sci-biology/kat: execute the build_boost.sh and autogen.sh logic

Execute the commands from within ebuild to ease debugging of errors.

See https://github.com/TGAC/KAT/issues/92

Package-Manager: Portage-2.3.28, Repoman-2.3.9

2 files changed, 31 insertions, 5 deletions

diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild
index 466b5431e..1df9f4430 100644
--- a/sci-biology/kat/kat-2.4.1.ebuild
+++ b/sci-biology/kat/kat-2.4.1.ebuild
@@ -32,8 +32,10 @@ S="${WORKDIR}"/KAT-Release-"${PV}"
 
 src_prepare(){
 	default
-	sh build_boost.sh || die
-	sh autogen.sh || die
+	# autogen.sh
+	test -n "$srcdir" || local srcdir=`dirname "$0"`
+	test -n "$srcdir" || local srcdir=.
+	eautoreconf --force --install --verbose "$srcdir"
 }
 
 src_configure(){
@@ -42,3 +44,12 @@ src_configure(){
 	use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.20/configure
 	PYTHON_VERSION=3 econf ${myconf[@]}
 }
+
+src_compile(){
+	# build_boost.sh
+	cd deps/boost || die
+	./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die
+	./b2 headers || die
+	./b2 install || die
+	cd ../.. || die
+}
diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild
index 39107167a..d46f6d3e8 100644
--- a/sci-biology/kat/kat-9999.ebuild
+++ b/sci-biology/kat/kat-9999.ebuild
@@ -6,7 +6,7 @@ EAPI=6
 PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features with >=3.5
 # https://github.com/Ensembl/Bio-DB-HTS/issues/30
 
-inherit git-r3 eutils flag-o-matic
+inherit git-r3 eutils flag-o-matic autotools
 
 DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
 HOMEPAGE="https://github.com/TGAC/KAT"
@@ -29,10 +29,25 @@ RDEPEND="${DEPEND}"
 # contains embedded sci-biology/seqan
 
 src_prepare(){
-	sh build_boost.sh || die
-	sh autogen.sh . || die
+	default
+	# autogen.sh
+	test -n "$srcdir" || local srcdir=`dirname "$0"`
+	test -n "$srcdir" || local srcdir=.
+	eautoreconf --force --install --verbose "$srcdir"
+}
+
+src_configure(){
 	local myconf=()
 	myconf+=( --disable-gnuplot ) # python3 does better image rendering, no need for gnuplot
 	use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) # pass down to jellyfish-2.20/configure
 	PYTHON_VERSION=3 econf ${myconf[@]}
 }
+
+src_compile(){
+	# build_boost.sh
+	cd deps/boost || die
+	./bootstrap.sh --prefix=build --with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace || die
+	./b2 headers || die
+	./b2 install || die
+	cd ../.. || die
+}