diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
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committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/glimmerhmm |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/glimmerhmm')
-rw-r--r-- | sci-biology/glimmerhmm/Manifest | 6 | ||||
-rw-r--r-- | sci-biology/glimmerhmm/files/3.0.1-gentoo.patch | 153 | ||||
-rw-r--r-- | sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild | 50 | ||||
-rw-r--r-- | sci-biology/glimmerhmm/metadata.xml | 8 |
4 files changed, 217 insertions, 0 deletions
diff --git a/sci-biology/glimmerhmm/Manifest b/sci-biology/glimmerhmm/Manifest new file mode 100644 index 000000000000..a3814accc62d --- /dev/null +++ b/sci-biology/glimmerhmm/Manifest @@ -0,0 +1,6 @@ +AUX 3.0.1-gentoo.patch 4235 SHA256 04eef55bb0cdb4455d143bec7fd0113491caee72fa9a6c56237024b4f18abbf4 SHA512 e0350a4b604fe76462bbb7139264a9b2916c050c335589031bdca0cf0c6a653bbf84d9827f5c2096ff13f1007d4ef2e93698814758f787a98e4dd818be44bc3d WHIRLPOOL 890fd4dfdae05f846b9fe2fae239e68b90c80c7de8ae4f3449c340f99e25f93f9b0e3075756f61dc700c41b973e38b7147de518813d6012c5f640b7218487a59 +DIST GlimmerHMM-3.0.1.tar.gz 45475952 SHA256 c956838a398483003ff1af867c65aca082b82340d8b302b9ada77d1b246954e4 SHA512 15307d1982527bd83433882552cd3e12c76a65a2a119b6911a748dc801f80b1fc5732cb769a52e5c6281bdd48cf619a02edbd1b96ee40319fc620a3a7cdd82b7 WHIRLPOOL f2cc0f6cea083c223273dd59f9474a054c049b697fc122925d4f5820170ade67bfa76c6dd218ab10be5675fe0a2a2a9fa5172be540509770332cc5a1d6862ff7 +EBUILD glimmerhmm-3.0.1-r1.ebuild 1190 SHA256 8aa3d25d87b788b27f2c8b2cab541f007dd8506e90137eac8d22bc86017cc1b1 SHA512 9faea51c07ef865eb0dfd9028077ef7a3e42a633ca39dd1a66caf817a35a75236ecda3ed58f9941bd18c925f43a4319e65f1f03510032bfe92f0cae81076dd9d WHIRLPOOL ca23ebcac4ba310cb55e935af13381bf2a93ebfffc65f01912e9bb78d1cacd8705b1f10ed3d5e2c9e89d882ca4b1b7ac9a64dd13fac8f89367de05687b9c1b70 +MISC ChangeLog 2472 SHA256 09afa0cb342126d3541311772971705a0f6f43f43db8e48354fb42cc2203c230 SHA512 d6ab119f62efb6da6d04015fdf0a4d5d7ad8bf664ed22e5908bb50dbe4b73f0e5062100da3175c6715452da03e268f7afc7f8825c5daa7b5c0a2154c555e179e WHIRLPOOL 7187e5733d044e31f78467c17c64badaf8e2d28b870cb8f7632d6d6ddf1962e6abaf110c8692902539cdfb213cc201562167c6ac6d7517f2019c7c5a7abf41ed +MISC ChangeLog-2015 1438 SHA256 139eecbffefb14e67a5ce60286592f4cffc6c854c800c4734d3d6cf317cf711f SHA512 afab9849cf3851d8059bcbb9b451e342a24c5e6c2a780d880c90af3d5ad8dbad293e7a6ae47dba17c2d11166e52f5785336f07a477c72a4603df91c758dacf76 WHIRLPOOL 02a8691b718b35451af167db293045ba823721ef7641223caec20a2c654043a836d908f3233d8dfa3ee9efcdf7445deddd3f56472767701bc414fbce5897d2b0 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch new file mode 100644 index 000000000000..949a4fe3e92d --- /dev/null +++ b/sci-biology/glimmerhmm/files/3.0.1-gentoo.patch @@ -0,0 +1,153 @@ + sources/makefile | 15 +++++-------- + train/makefile | 59 +++++++++++++++++++++++++++++++---------------------- + 2 files changed, 40 insertions(+), 34 deletions(-) + +diff --git a/sources/makefile b/sources/makefile +index f287d71..c560f48 100644 +--- a/sources/makefile ++++ b/sources/makefile +@@ -2,25 +2,22 @@ + + + +-CC=g++ +-CFLAGS=-g +- + all: glimmerhmm + + glimmerhmm: glimmerhmm.o graph.o sites.o tree_util_prob.o util.o +- $(CC) $(CFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm + + glimmerhmm.o: glimmerhmm.c +- $(CC) $(CFLAGS) -c glimmerhmm.c ++ $(CXX) $(CXXFLAGS) -c glimmerhmm.c + + graph.o: graph.c +- $(CC) $(CFLAGS) -c graph.c ++ $(CXX) $(CXXFLAGS) -c graph.c + + sites.o: sites.c +- $(CC) $(CFLAGS) -c sites.c ++ $(CXX) $(CXXFLAGS) -c sites.c + + tree_util_prob.o: tree_util_prob.c +- $(CC) $(CFLAGS) -c tree_util_prob.c ++ $(CXX) $(CXXFLAGS) -c tree_util_prob.c + + util.o: util.c +- $(CC) $(CFLAGS) -c util.c ++ $(CXX) $(CXXFLAGS) -c util.c +diff --git a/train/makefile b/train/makefile +index 2383f18..d5a7107 100644 +--- a/train/makefile ++++ b/train/makefile +@@ -2,9 +2,6 @@ + + # C compiler + +-C = gcc +-CC = g++ +-CFLAGS = -O1 ${SEARCHDIRS} + #CFLAGS = -O3 -g -Wall + LIBS = -lm + +@@ -15,64 +12,76 @@ all: build-icm build-icm-noframe build1 build2 falsecomp findsites karlin sco + + + misc.o: misc.c +- ${C} ${CFLAGS} -c misc.c ++ $(CC) $(CFLAGS) -c misc.c + + build-icm.o: build-icm.c +- ${C} ${CFLAGS} -c build-icm.c ++ $(CC) $(CFLAGS) -c build-icm.c + + build-icm: build-icm.o misc.o +- $(C) -o $@ build-icm.o misc.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm.o misc.o $(LIBS) + + build-icm-noframe.o: build-icm-noframe.c +- ${C} ${CFLAGS} -c build-icm-noframe.c ++ $(CC) $(CFLAGS) -c build-icm-noframe.c + + build-icm-noframe: build-icm-noframe.o misc.o +- $(C) -o $@ build-icm-noframe.o misc.o $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ build-icm-noframe.o misc.o $(LIBS) + + build1: build1.o +- ${CC} build1.c -o build1 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) build1.c -o build1 $(LIBS) + + build2: build2.o +- ${CC} build2.c -o build2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) build2.c -o build2 $(LIBS) + + falsecomp: falsecomp.o +- ${CC} falsecomp.c -o falsecomp $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) falsecomp.c -o falsecomp $(LIBS) + + findsites: findsites.o +- ${CC} findsites.c -o findsites $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) findsites.c -o findsites $(LIBS) + + karlin: karlin.o +- ${CC} karlin.c -o karlin $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) karlin.c -o karlin $(LIBS) + + score: score.o +- ${CC} score.c -o score $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) score.c -o score $(LIBS) + + score2: score2.o +- ${CC} score2.c -o score2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) score2.c -o score2 $(LIBS) + + scoreATG: scoreATG.o +- ${CC} scoreATG.c -o scoreATG $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG.c -o scoreATG $(LIBS) + + scoreATG2: scoreATG2.o +- ${CC} scoreATG2.c -o scoreATG2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreATG2.c -o scoreATG2 $(LIBS) + + scoreSTOP: scoreSTOP.o +- ${CC} scoreSTOP.c -o scoreSTOP $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP.c -o scoreSTOP $(LIBS) + + escoreSTOP2: scoreSTOP2.o +- ${CC} scoreSTOP2.c -o scoreSTOP2 $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) scoreSTOP2.c -o scoreSTOP2 $(LIBS) + +-rfapp: erfapp.o +- ${CC} erfapp.c -o erfapp $(LIBS) ++erfapp: erfapp.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) erfapp.c -o erfapp $(LIBS) + + sites.o: sites.c +- ${CC} ${CFLAGS} -c sites.c ++ $(CXX) $(CXXFLAGS) -c sites.c ++ ++scoreATG.o: scoreATG.c ++ $(CXX) $(CXXFLAGS) -c scoreATG.c ++ ++scoreSTOP.o: scoreSTOP.c ++ $(CXX) $(CXXFLAGS) -c scoreSTOP.c ++ ++scoreSTOP2.o: scoreSTOP2.c ++ $(CXX) $(CXXFLAGS) -c scoreSTOP2.c ++ ++scoreATG2.o: scoreATG2.c ++ $(CXX) $(CXXFLAGS) -c scoreATG2.c + + utils.o: utils.c +- ${CC} ${CFLAGS} -c utils.c ++ $(CXX) $(CXXFLAGS) -c utils.c + + splicescore.o: splicescore.c +- ${CC} ${CFLAGS} -c splicescore.c ++ $(CXX) $(CXXFLAGS) -c splicescore.c + + splicescore: splicescore.o sites.o utils.o +- ${CC} splicescore.o sites.o utils.o -o splicescore $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) splicescore.o sites.o utils.o -o splicescore $(LIBS) diff --git a/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild new file mode 100644 index 000000000000..1d3cf1171d76 --- /dev/null +++ b/sci-biology/glimmerhmm/glimmerhmm-3.0.1-r1.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +MY_P=GlimmerHMM + +DESCRIPTION="A eukaryotic gene finding system from TIGR" +HOMEPAGE="http://www.cbcb.umd.edu/software/GlimmerHMM/" +SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/${MY_P}-${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +IUSE="" +KEYWORDS="amd64 x86" + +src_unpack() { + unpack ${A} + mv GlimmerHMM ${P} +} + +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 "${S}/train/trainGlimmerHMM" || die + + epatch "${FILESDIR}"/${PV}-gentoo.patch + tc-export CC CXX +} + +src_compile() { + emake -C "${S}/sources" + emake -C "${S}/train" +} + +src_install() { + dobin sources/glimmerhmm train/trainGlimmerHMM + + insinto /usr/share/${PN}/lib + doins train/*.pm + insinto /usr/share/${PN}/models + doins -r trained_dir/* + exeinto /usr/libexec/${PN}/training_utils + doexe train/{build{1,2,-icm,-icm-noframe},erfapp,falsecomp,findsites,karlin,score,score{2,ATG,ATG2,STOP,STOP2},splicescore} + + dodoc README.first train/readme.train +} diff --git a/sci-biology/glimmerhmm/metadata.xml b/sci-biology/glimmerhmm/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/glimmerhmm/metadata.xml @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> +</pkgmetadata> |