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

[Martin Mokrejs]

commit:     aca4c5886f2dc4991a59805666245be2a627f0ea
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 22 08:57:59 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 22 08:57:59 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=aca4c588

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

 sci-biology/kat/kat-2.4.1.ebuild | 15 +++++++++++++--
 sci-biology/kat/kat-9999.ebuild  | 21 ++++++++++++++++++---
 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
+}