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authorDavid Seifert <soap@gentoo.org>2019-12-11 00:48:09 +0100
committerDavid Seifert <soap@gentoo.org>2019-12-11 00:48:09 +0100
commitcc28b9f8549047216b17ff331deedda1141b337e (patch)
tree0e5da9dec531b103a8d01311abd6f813b267677e /sci-biology
parent*/*: [QA] Fix trivial cases of MissingTestRestrict (diff)
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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>
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch20
-rw-r--r--sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild31
2 files changed, 34 insertions, 17 deletions
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
index 000000000000..3ad5090086eb
--- /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=$scriptdir\n";exit;
+
diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
index 1d3cf1171d76..5424e942a7f7 100644
--- a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
+++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=4
+EAPI=7
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
MY_P=GlimmerHMM
@@ -13,27 +13,22 @@ SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${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}