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/augustus |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/augustus')
-rw-r--r-- | sci-biology/augustus/Manifest | 6 | ||||
-rw-r--r-- | sci-biology/augustus/augustus-2.5.5.ebuild | 49 | ||||
-rw-r--r-- | sci-biology/augustus/files/augustus-2.5.5-sane-build.patch | 156 | ||||
-rw-r--r-- | sci-biology/augustus/metadata.xml | 8 |
4 files changed, 219 insertions, 0 deletions
diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest new file mode 100644 index 000000000000..ff0fe1247ee3 --- /dev/null +++ b/sci-biology/augustus/Manifest @@ -0,0 +1,6 @@ +AUX augustus-2.5.5-sane-build.patch 5271 SHA256 0e8692203f1cc994398bc639d101b2be915c4747a5d234d0d564cf0ada6e9ebc SHA512 5afe12b51b8ce27ef32e8e66dd72be451022757228b4c86dec938b26870885bee06712438a22801a42944d2def8ae8bf4a2d7fdb82e12455c145abcd6f0c4aa1 WHIRLPOOL f6bde27abe50c567a2a07ef61ce9c8033592261b26a61828eac9f6d6e74b104220a986d9bd57138b74375a747e2b9c619a49e7a6865be4de037a288b7882186b +DIST augustus.2.5.5.tar.gz 70826249 SHA256 2bd97784fa651addf836e2100a7d4106b43e50fe06f13c664001d4625d0eab9a SHA512 33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f WHIRLPOOL 875f56f10251767fb066b5e21b0c2361c952d5cc44daa811658be8119957ffa34fd4552fde7e17384d5bc916aee5ef91982ded3999d0077cf3834d5fc20e7f1a +EBUILD augustus-2.5.5.ebuild 1010 SHA256 033f5e2e2b896c957d5d8967453e0b1b96f678f29868c8b5eb851eecbd8df0c1 SHA512 6cf6076dd9c1c957302f5ec65867b9055a29e4a893f925bc18cb96cc7c57509e65497013e574a33dbe718f0aeb4a25422078874cf0b85603b30ca40abe81527f WHIRLPOOL 2bb05518431d7bdd3668ec1d6a2b176c2ef1dfcb7d64795ff8cc3cbc17de24b92673f85070f0fd456010a5be31660366863240d105cf2280c2cceafea2df3e7a +MISC ChangeLog 2473 SHA256 2c4273e98146a8dc38d829552338065b456a56e357159e132118fdf965ede5d8 SHA512 062913083dad8dac702b249e13c9ca47dd724251bc87ee8544b2e22e5a8dab6e85359a285da508d039187907df52ed34ba6f9c99550d9517f7b07425278dc5ef WHIRLPOOL dc3e0173575eeb291afb2e72623c1e13919f3c9b6ecf2bf25fd59d2e98114b55b146cd36e1b7d5facbdd8c72125911d0812309e7b83ff06cdbcb250e0f88db49 +MISC ChangeLog-2015 2694 SHA256 e16526a6f364e77aee894fdebdf37d30122ab4160720c02958d7f5da49a5d431 SHA512 6c32e0eca978ac36d1eeaca4bb8319ea279789709a09ebe00dcd3af6e581c877d1f09a6391e3c92fc0d616354bb7c6661c961a13d2256f7df5a14f8c3874d5c7 WHIRLPOOL e01995e98d2882ce11571bb9c9990de20d80d1fe22a126f295fde66b36fbedd2f5c3e3dfa00d898c2c59a3c5799018c6729a459cbb697f9ddbda24f6a5a3c4f6 +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild b/sci-biology/augustus/augustus-2.5.5.ebuild new file mode 100644 index 000000000000..ff4dfd6cc7e0 --- /dev/null +++ b/sci-biology/augustus/augustus-2.5.5.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=4 + +inherit eutils toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="http://augustus.gobics.de/" +SRC_URI="http://augustus.gobics.de/binaries/${PN}.${PV}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="amd64 x86" +IUSE="examples" + +S="${WORKDIR}/${PN}.${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${P}-sane-build.patch + tc-export CC CXX +} + +src_compile() { + emake clean && emake +} + +src_install() { + dobin bin/* +# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign} + + exeinto /usr/libexec/${PN} + doexe scripts/*.p* + insinto /usr/libexec/${PN} + doins scripts/*.conf + + insinto /usr/share/${PN} + doins -r config + + echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + + dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt} + + if use examples; then + insinto /usr/share/${PN}/ + doins -r docs/tutorial examples + fi +} diff --git a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch new file mode 100644 index 000000000000..39cd0762b1c1 --- /dev/null +++ b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch @@ -0,0 +1,156 @@ + Makefile | 8 +++--- + scripts/Makefile | 6 +++- + scripts/aln2wig/Makefile | 8 +++--- + scripts/compileSpliceCands/Makefile | 6 ++-- + src/Makefile | 43 ++++++++++++++++++---------------- + 5 files changed, 38 insertions(+), 33 deletions(-) + +diff --git a/Makefile b/Makefile +index e23a667..64610c8 100644 +--- a/Makefile ++++ b/Makefile +@@ -3,9 +3,9 @@ + # + + all: +- cd src && ${MAKE} +- cd scripts && ${MAKE} ++ $(MAKE) -C src ++ $(MAKE) -C scripts + + clean: +- cd src && ${MAKE} clean +- cd scripts && ${MAKE} clean ++ $(MAKE) -C src clean ++ $(MAKE) -C scripts clean +diff --git a/scripts/Makefile b/scripts/Makefile +index 6d4dd67..ab6a885 100644 +--- a/scripts/Makefile ++++ b/scripts/Makefile +@@ -1,5 +1,7 @@ + all : +- cd aln2wig && ${MAKE} ++ $(MAKE) -C aln2wig ++ $(MAKE) -C compileSpliceCands + + clean : +- cd aln2wig && ${MAKE} clean ++ $(MAKE) -C aln2wig clean ++ $(MAKE) -C compileSpliceCands +diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile +index 64d09f5..9752980 100644 +--- a/scripts/aln2wig/Makefile ++++ b/scripts/aln2wig/Makefile +@@ -1,10 +1,10 @@ +-CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb ++CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic + + psl2wig : aln2wig.o +- gcc $(CFLAGS) -o aln2wig aln2wig.o; +- cp aln2wig ../../bin ++ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o; ++ cp aln2wig ../../bin/ + psl2wig.o : aln2wig.c +- gcc $(CFLAGS) -c aln2wig.c ++ $(CC) $(CFLAGS) -c aln2wig.c + + all : psl2wig + +diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile +index cddada5..8079791 100644 +--- a/scripts/compileSpliceCands/Makefile ++++ b/scripts/compileSpliceCands/Makefile +@@ -1,8 +1,8 @@ + compileSpliceCands : compileSpliceCands.o list.h list.o +- gcc -o compileSpliceCands compileSpliceCands.o list.o; +-# cp compileSpliceCands ../../bin ++ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o; ++ cp compileSpliceCands ../../bin/ + compileSpliceCands.o : compileSpliceCands.c +- gcc -Wall -pedantic -ansi -c compileSpliceCands.c ++ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c + + all : compileSpliceCands + +diff --git a/src/Makefile b/src/Makefile +index 71795b6..732b953 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -6,8 +6,8 @@ + # a strict signed-only usage strategy to avoid mistakes since we are not warned about this. + # - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh) + # +-CC = g++ +-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static ++CXX ?= g++ ++CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static + INCLS = -I../include -I. + LIBS = # -lcwd + OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \ +@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte + PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign + INFO = cflags + +-all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info ++all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin + + .SUFFIXES: + .SUFFIXES: .cc .o .so + + .cc.o: +- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS) ++ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS) + +-augustus: augustus.cc $(OBJS) $(DUMOBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++bin: $(PROGR) ++ cp $(PROGR) ../bin/ ++ ++augustus: augustus.o $(OBJS) $(DUMOBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp augustus ../bin/ + +-etraining: etraining.cc $(TOBJS) $(OBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++etraining: etraining.o $(TOBJS) $(OBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp etraining ../bin/ + +-evaluate: evaluate.cc $(OBJS) $(DUMOBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++evaluate: evaluate.o $(OBJS) $(DUMOBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-consensusFinder: consensusFinder.cc consensus.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++consensusFinder: consensusFinder.o consensus.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-curve2hints: curve2hints.cc exon_seg.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++curve2hints: curve2hints.o exon_seg.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \ ++fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \ + types.o properties.o geneticcode.o pp_profile.o lldouble.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp fastBlockSearch ../bin/ + +-prepareAlign: pp_prepare_align.cc +- $(CC) $(CFLAGS) -o $@ $^ ++prepareAlign: pp_prepare_align.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ + cp prepareAlign ../bin/ + + info: +- echo "$(CFLAGS)" > $(INFO) ++ echo "$(CXXFLAGS)" > $(INFO) + + clean: +- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ++ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/* + + tidy: clean + rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO) diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/augustus/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> |