sci-biology/glimmerhmm: Port to EAPI 7

Package-Manager: Portage-2.3.81, Repoman-2.3.20
Signed-off-by: David Seifert <soap@gentoo.org>

diff --git a/sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch b/sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch
new file mode 100644 (file)
index 0000000..3ad5090
--- /dev/null
+++ b/sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch
@@ -0,0 +1,20 @@
+--- a/train/trainGlimmerHMM
++++ b/train/trainGlimmerHMM
+@@ -12,7 +12,7 @@
+ use Cwd;
+ 
+ use FindBin;
+-use lib $FindBin::Bin;
++use lib "/usr/share/glimmerhmm/lib";
+ use orf;
+ use formtrain;
+ use dectree_allinfo;
+@@ -20,7 +20,7 @@
+ use splitiso;
+ 
+ my $workdir=cwd();
+-my $scriptdir=$FindBin::Bin; # directory where all training programs should be
++my $scriptdir="/usr/libexec/glimmerhmm/training_utils"; # directory where all training programs should be
+ 
+ #print "workdir=$workdir scriptdir=$scriptdir\n";exit;
+ 

diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
index 1d3cf1171d76a8be6bfb5fa22a449d3ef431673e..5424e942a7f743127952abefab105e45a0c0e843 100644 (file)
--- a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=4
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 MY_P=GlimmerHMM
 
@@ -13,27 +13,22 @@ SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz"
 
 LICENSE="Artistic"
 SLOT="0"
-IUSE=""
 KEYWORDS="amd64 x86"
 
-src_unpack() {
-       unpack ${A}
-       mv GlimmerHMM ${P}
-}
+S="${WORKDIR}/${MY_P}"
 
-src_prepare() {
-       sed \
-               -e 's|\(my $scriptdir=\)$FindBin::Bin|\1"/usr/libexec/'${PN}'/training_utils"|' \
-               -e 's|\(use lib\) $FindBin::Bin|\1 "/usr/share/'${PN}'/lib"|' \
-               -i "${S}/train/trainGlimmerHMM" || die
+PATCHES=(
+       "${FILESDIR}"/${PV}-gentoo.patch
+       "${FILESDIR}"/${PN}-3.0.1-fix-data-path.patch
+)
 
-       epatch "${FILESDIR}"/${PV}-gentoo.patch
+src_configure() {
        tc-export CC CXX
 }
 
 src_compile() {
-       emake -C "${S}/sources"
-       emake -C "${S}/train"
+       emake -C sources
+       emake -C train
 }
 
 src_install() {
@@ -41,8 +36,10 @@ src_install() {
 
        insinto /usr/share/${PN}/lib
        doins train/*.pm
+
        insinto /usr/share/${PN}/models
-       doins -r trained_dir/*
+       doins -r trained_dir/.
+
        exeinto /usr/libexec/${PN}/training_utils
        doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore}