diff options
Diffstat (limited to 'sci-biology/glimmerhmm')
| -rw-r--r-- | sci-biology/glimmerhmm/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/glimmerhmm/files/glimmerhmm-3.0.1-fix-data-path.patch | 20 | ||||
| -rw-r--r-- | sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild | 31 |
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} |