gentoo resync : 15.12.2019

3 files changed, 36 insertions, 18 deletions

diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest
index 24f25f908fc3..4de35b164fb1 100644
--- a/sci-biology/glimmerhmm/Manifest
+++ b/sci-biology/glimmerhmm/Manifest
@@ -1,4 +1,5 @@
 AUX 3.0.1-gentoo.patch 4235 BLAKE2B 8263516018df83c39da08e906bcdbfb8445ef26c064a82d8edf547fba5b569921905dd32476a99726f1864cc24ec5464fbc48db55e08cca0b9555647dddae120 SHA512 e0350a4b604fe76462bbb7139264a9b2916c050c335589031bdca0cf0c6a653bbf84d9827f5c2096ff13f1007d4ef2e93698814758f787a98e4dd818be44bc3d
+AUX glimmerhmm-3.0.1-fix-data-path.patch 512 BLAKE2B fc37954be58eaaec074fbb3ff9a8109907fc71be39365aa07e62c884a78c910d0ffcceaee907736107b56d97f0e7c9baf30f9fd71f239ede6cebe4bc9bcfb59e SHA512 0e1b65887a7a27c8d9adbf88a904ddbb4afc56e5052a6693ca57ae160bc9c6dab8589b633d364aead873fc1aaa671580bfc0deed9bde153f5069a0351244ef51
 DIST GlimmerHMM-3.0.1.tar.gz 45475952 BLAKE2B 355f4e9f26c31167e0935de8012fa99a243838d0dd47e0e46ae4cb1df4eaf188a13fb365025bc4be82805c89f36f534a9907030515f96b9422340e9e966f4ea6 SHA512 15307d1982527bd83433882552cd3e12c76a65a2a119b6911a748dc801f80b1fc5732cb769a52e5c6281bdd48cf619a02edbd1b96ee40319fc620a3a7cdd82b7
-EBUILD glimmerhmm-3.0.1-r1.ebuild 1190 BLAKE2B ab0c495ffc681f595d466b236826df1eea014424c8797013e9627cffc9cb1e37411955ebccadcaf0f678c13d159b32187b0f6e6a3f3ffdc572208c0e61c0d681 SHA512 9faea51c07ef865eb0dfd9028077ef7a3e42a633ca39dd1a66caf817a35a75236ecda3ed58f9941bd18c925f43a4319e65f1f03510032bfe92f0cae81076dd9d
+EBUILD glimmerhmm-3.0.1-r1.ebuild 989 BLAKE2B 7b411464fe1fd149ee78db9f067ff9c549854cf0ee8d572df30d0d03c3081bfe66c7ad26ad3051313909a51fc0ef0ac7e6e13f0ec378bf23929d2d4267d3b764 SHA512 1a55d81a6294016b4c90c952f49810ddf0a34f5b6b299f0040775a6a7cebe94aad5730d864143d4f09457b6616032fae2da3c893f47501d7c7effe60616a7196
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
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}