diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
---|---|---|
committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/mafft |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/mafft')
-rw-r--r-- | sci-biology/mafft/Manifest | 10 | ||||
-rw-r--r-- | sci-biology/mafft/files/mafft-7.037-respect.patch | 217 | ||||
-rw-r--r-- | sci-biology/mafft/mafft-7.050.ebuild | 60 | ||||
-rw-r--r-- | sci-biology/mafft/mafft-7.215.ebuild | 64 | ||||
-rw-r--r-- | sci-biology/mafft/mafft-7.305.ebuild | 68 | ||||
-rw-r--r-- | sci-biology/mafft/metadata.xml | 8 |
6 files changed, 427 insertions, 0 deletions
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest new file mode 100644 index 000000000000..fead05e00a48 --- /dev/null +++ b/sci-biology/mafft/Manifest @@ -0,0 +1,10 @@ +AUX mafft-7.037-respect.patch 7463 SHA256 eeedc574ad5977661ea879eefaa1c4b4d428384f25af891c1fcef16e6bfc6293 SHA512 ba706bc83b1c249c08fa7e39d6b80df42be058ea2e68baf1028125dcad289764ead3a6269e557bffc62da87a7ac2ff9856a602e20ca5eae052060d44b431994b WHIRLPOOL cf340ae92dec7ac35099706e5f2a31ac123b341391d2ebe25d4050fc470bbc295ab51c26612c4cc6c659abfba48c355df170b5352b2a6b6a04e8eeca6f453bb5 +DIST mafft-7.050-without-extensions-src.tgz 380375 SHA256 29ddb276bfca24f5815acc41f1e640a705bb12c9d29b7c74902ebca68cece7bc SHA512 ffddedcd03f37241b1493a62bf843eb23caa04089bd0182006aa7669f74de27204d324817e22fec1cb4ae11c4c226db5b725d03ba9f73b30a71ca3d38368d73e WHIRLPOOL d46d7d4dfe453bfb54b9e418308772fb063bffce1d6d45d92262bee45504301daff9a6e57ecde41912a6c11852bb64510fb5ba6df04c7e79dc671e7a31444d49 +DIST mafft-7.215-without-extensions-src.tgz 393239 SHA256 22099e42274ef0078302d7cb87180880ee5fd64ef15fdcafd8c95d0018191408 SHA512 1a44b968e2f9ac9db5d17487163a38a7138dc784e63b3aa4082ff6a16c8e168edd09948e2cf182bc7a466802d4a07bdd7ab23386e251df13520acdfb69ebdada WHIRLPOOL de43ba4107e3c1149d5ce47085bacc996393a7ef73535777439b7024eea1dce5f28c1b3c7e518f644345b7b5ea5e70fccbcaba18f16ecb9a6f5f5c31a6b5dca4 +DIST mafft-7.305-without-extensions-src.tgz 458448 SHA256 194503ee6dc9826f5098ac0fd9283034dfee8a1be1287def437f5854dea9317e SHA512 2aa351dd9b329024f183642cd98287239d12a00a2a65937e072560cba54925bed1fab19fafc734d9a5048ff85151560193ddb0796e0d7510d921fafc4553ebb9 WHIRLPOOL 85e9cda397853692f737a4e74159e67e0303076c28d94b85d4039ffe17b72c9d852a8af85941eaaa0fd73e0f1cbdbfe5b6a68e8ad5464506fbb38969f137a1b1 +EBUILD mafft-7.050.ebuild 1794 SHA256 6d828e21936ff4da139a9428b14650f8fa85d659c14b26b890b5490bede7169d SHA512 b908836f2024be4a6315333a84708379e5f4213b179b4c104365f4d0c5878f90602548e9a38d3f11330513f15522094c34aa5cd0e6bc60250c68d18a9d2dd09f WHIRLPOOL c58a2d20101258f53e6e894d0110c3d68e568d9252e21da9e87b98a303ab2df34ed15d44afcd6b7b0265b40bf77922a867bebfcdc3cbd2890cab4c170504226d +EBUILD mafft-7.215.ebuild 1974 SHA256 f05b0c0fd4e7a3bd1a4c34d8c253318fc965e28c48506014a920396b3b81a4f9 SHA512 787a8bf04c3a5d894328331a5908aeb1c1b0850602d145345965cb740beef75be90bf464a9b8519fb93c691253c05665e62a099b72b39ca7081685755c2c1a8b WHIRLPOOL 81b03148e8aaf3c565dc7a3920db9dc21fddd774ce3ad26b310f53624a6d636c92f3b9eb3b09a552c364bfcc8e89f91402f2ecc957470c12717f52e9849fb0d0 +EBUILD mafft-7.305.ebuild 2013 SHA256 e5f702e020d36a3f6707888857234bccf9f3f80f60a22f86d4d90d46d46e262c SHA512 557a10cb6c9dd0690b7d4979661780597dbcfa110df924250d2b9e6a3943a6f0876c73e803e99c5733fa223c79760fc9e37ef45879a75b2b934452cb86c1615b WHIRLPOOL 24d123737d357d67378d6dcd4ca286ca7825a00f4fed965a6cefa45c9810b64fc1d0bf071ebed444cbe1ba0df72e67d827feb1c5a24b003d0237fc49dc5f4d15 +MISC ChangeLog 2703 SHA256 130559f8cd746a02e79bfc373bfd03cf6791727f16b4fa10d24163766d089e50 SHA512 f37f0113b13582265330bb0ce4894213b0a432c20c79f9238d12cb5e3f700e2e00372f74b23dfd6fc8150044562b34e8a19f7f716b61112be85d06308b1c854f WHIRLPOOL 7ac705e03de52f67b07cc4259ff3f7ae5d0ae14940f136b9187e6732cd6de33a3d97e99e02a0e0b68fdae7be93c447c2d1032a613eafc44708e2970dda17c355 +MISC ChangeLog-2015 3896 SHA256 ab05832fb272023664f91ee73d5ab266e21ff0f102fd6e82bd624398b2b87dfe SHA512 9aac609a3d28937b353955fc9e586d0f302e0df7c03c22f4224b03f369916fd2b6f02cc42bd23d8d738f843222d3cf39b2847cd95e821443bcc1e515b17d5d05 WHIRLPOOL 2a24f13c56b2c90930a7604346e168b286c941b97319478bfca4f5c7afc72a9d63f6e01fc27dc404468feaa6ec9b34943a32c14908f2903b606d884fc300491a +MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13 diff --git a/sci-biology/mafft/files/mafft-7.037-respect.patch b/sci-biology/mafft/files/mafft-7.037-respect.patch new file mode 100644 index 000000000000..6fba7153622d --- /dev/null +++ b/sci-biology/mafft/files/mafft-7.037-respect.patch @@ -0,0 +1,217 @@ + core/Makefile | 100 +++++++++++++++++++++++++++++----------------------------- + 1 file changed, 50 insertions(+), 50 deletions(-) + +diff --git a/core/Makefile b/core/Makefile +index 9acebb3..3838a45 100644 +--- a/core/Makefile ++++ b/core/Makefile +@@ -145,151 +145,151 @@ mltaln.h : functions.h + touch mltaln.h + + version : version.c mltaln.h +- $(CC) -o $@ version.c $(MYCFLAGS) ++ $(CC) $(LDFLAGS) -o $@ version.c $(MYCFLAGS) + + tbfast : $(OBJTBFAST) +- $(CC) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(MYCFLAGS) $(LIBS) + + addsingle : $(OBJADDSINGLE) +- $(CC) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJADDSINGLE) $(MYCFLAGS) $(LIBS) + + tbfast2 : $(OBJTBFAST2) +- $(CC) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(MYCFLAGS) $(LIBS) + + disttbfast : $(OBJDISTTBFAST) +- $(CC) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(MYCFLAGS) $(LIBS) + + makedirectionlist : $(OBJMAKEDIRECTIONLIST) +- $(CC) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMAKEDIRECTIONLIST) $(MYCFLAGS) $(LIBS) + + splittbfast : $(OBJSPLITTBFAST) +- $(CC) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(MYCFLAGS) $(LIBS) + + splitfromaln : $(OBJSPLITFROMALN) +- $(CC) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(MYCFLAGS) $(LIBS) + + splittbfast2 : $(OBJSPLITTBFAST2) +- $(CC) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(MYCFLAGS) $(LIBS) + + dummy : $(OBJDUMMY) +- $(CC) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(MYCFLAGS) $(LIBS) + + setcore : $(OBJSETCORE) +- $(CC) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(MYCFLAGS) $(LIBS) + + countlen : $(OBJCOUNTLEN) +- $(CC) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(MYCFLAGS) $(LIBS) + + seq2regtable : $(OBJSEQ2REGTABLE) +- $(CC) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(MYCFLAGS) $(LIBS) + + regtable2seq : $(OBJREGTABLE2SEQ) +- $(CC) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(MYCFLAGS) $(LIBS) + + setdirection : $(OBJSETDIRECTION) +- $(CC) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSETDIRECTION) $(MYCFLAGS) $(LIBS) + + replaceu : $(OBJREPLACEU) +- $(CC) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJREPLACEU) $(MYCFLAGS) $(LIBS) + + restoreu : $(OBJRESTOREU) +- $(CC) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRESTOREU) $(MYCFLAGS) $(LIBS) + + f2cl : $(OBJF2CL) +- $(CC) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(MYCFLAGS) $(LIBS) + + mccaskillwrap : $(OBJMCCASKILLWRAP) +- $(CC) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(MYCFLAGS) $(LIBS) + + contrafoldwrap : $(OBJCONTRAFOLDWRAP) +- $(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(MYCFLAGS) $(LIBS) + + pairlocalalign : $(OBJPAIRLOCALALIGN) +- $(CC) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(MYCFLAGS) $(LIBS) + + pairash : $(OBJPAIRASH) +- $(CC) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(MYCFLAGS) $(LIBS) + + rnatest : $(OBJRNATEST) +- $(CC) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(MYCFLAGS) $(LIBS) + + pair2hat3s : $(OBJPAIR2HAT3S) +- $(CC) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(MYCFLAGS) $(LIBS) + + multi2hat3s : $(OBJMULTI2HAT3S) +- $(CC) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(MYCFLAGS) $(LIBS) + + getlag : $(OBJGETLAG) +- $(CC) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(MYCFLAGS) $(LIBS) + + tditr : $(OBJTDITR) +- $(CC) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(MYCFLAGS) $(LIBS) + + dvtditr : $(OBJDVTDITR) +- $(CC) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(MYCFLAGS) $(LIBS) + + mafft-profile : $(OBJGALN) +- $(CC) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(MYCFLAGS) $(LIBS) + + gapfill : $(OBJGAPFILL) +- $(CC) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(MYCFLAGS) $(LIBS) + + dndfast4 : $(OBJDNDFAST4) +- $(CC) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(MYCFLAGS) $(LIBS) + + dndfast5 : $(OBJDNDFAST5) +- $(CC) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(MYCFLAGS) $(LIBS) + + dndfast6 : $(OBJDNDFAST6) +- $(CC) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(MYCFLAGS) $(LIBS) + + dndfast7 : $(OBJDNDFAST7) +- $(CC) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(MYCFLAGS) $(LIBS) + + dndblast : $(OBJDNDBLAST) +- $(CC) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(MYCFLAGS) $(LIBS) + + dndfast3 : $(OBJDNDFAST3) +- $(CC) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(MYCFLAGS) $(LIBS) + + triplet : $(OBJTRIPLET) +- $(CC) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(MYCFLAGS) $(LIBS) + + triplet3 : $(OBJTRIPLET3) +- $(CC) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(MYCFLAGS) $(LIBS) + + sextet3 : $(OBJSEXTET3) +- $(CC) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(MYCFLAGS) $(LIBS) + + sextet4 : $(OBJSEXTET4) +- $(CC) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(MYCFLAGS) $(LIBS) + + sextet5 : $(OBJSEXTET5) +- $(CC) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(MYCFLAGS) $(LIBS) + + mafft-distance : $(OBJDISTANCE) +- $(CC) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(MYCFLAGS) $(LIBS) + + triplet5 : $(OBJTRIPLET5) +- $(CC) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(MYCFLAGS) $(LIBS) + + triplet6 : $(OBJTRIPLET6) +- $(CC) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(MYCFLAGS) $(LIBS) + + octet4 : $(OBJOCTET4) +- $(CC) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(MYCFLAGS) $(LIBS) + + dndpre : $(OBJDNDPRE) +- $(CC) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(MYCFLAGS) $(LIBS) + + dndpre2 : $(OBJDNDPRESCORE) +- $(CC) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(MYCFLAGS) $(LIBS) + + score : $(OBJSCORE) +- $(CC) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(MYCFLAGS) $(LIBS) + + genMtx : $(OBJGENMTX) +- $(CC) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) ++ $(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(MYCFLAGS) $(LIBS) + + gapfill.o : gapfill.c $(HEADER) + $(CC) $(MYCFLAGS) -c gapfill.c +@@ -525,7 +525,7 @@ install : all + chmod 755 $(SCRIPTS) + $(INSTALL) $(SCRIPTS) $(BINDIR) + chmod 755 $(PROGS) +- $(INSTALL) -s $(PROGS) $(LIBDIR) ++ $(INSTALL) $(PROGS) $(LIBDIR) + $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR) + + ( cd $(BINDIR); \ diff --git a/sci-biology/mafft/mafft-7.050.ebuild b/sci-biology/mafft/mafft-7.050.ebuild new file mode 100644 index 000000000000..685d78005c73 --- /dev/null +++ b/sci-biology/mafft/mafft-7.050.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic multilib toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" +SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="threads" + +S="${WORKDIR}"/${P}${EXTENSIONS} + +src_prepare() { + epatch "${FILESDIR}"/${PN}-7.037-respect.patch + use threads && append-cppflags -Denablemultithread + sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die + sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" +} + +src_compile() { + pushd core > /dev/null || die + emake \ + $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" + popd > /dev/null || die +} + +src_test() { + export MAFFT_BINARIES="${S}"/core + cd test || die + bash ../core/mafft sample > test.fftns2 || die + bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die + bash ../core/mafft --globalpair sample > test.gins1 || die + bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die + bash ../core/mafft --localpair sample > test.lins1 || die + bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die + + diff test.fftns2 sample.fftns2 || die + diff test.fftnsi sample.fftnsi || die + diff test.gins1 sample.gins1 || die + diff test.ginsi sample.ginsi || die + diff test.lins1 sample.lins1 || die +} + +src_install() { + pushd core + emake PREFIX="${ED}usr" install + popd + dodoc readme +} diff --git a/sci-biology/mafft/mafft-7.215.ebuild b/sci-biology/mafft/mafft-7.215.ebuild new file mode 100644 index 000000000000..21761f1378e4 --- /dev/null +++ b/sci-biology/mafft/mafft-7.215.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit eutils flag-o-matic multilib toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" +SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="threads" + +S="${WORKDIR}"/${P}${EXTENSIONS} + +src_prepare() { +# epatch "${FILESDIR}"/${PN}-7.037-respect.patch + use threads && append-cppflags -Denablemultithread +# sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die + sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" + sed \ + -e 's:$(LDFLAGS)::g' \ + -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \ + -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \ + -e '/INSTALL/s: -s : :g' \ + -i core/Makefile || die +} + +src_compile() { + cd core || die + emake \ + $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS} -Wno-unused-result" +} + +src_test() { + export MAFFT_BINARIES="${S}"/core + cd test || die + bash ../core/mafft sample > test.fftns2 || die + bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die + bash ../core/mafft --globalpair sample > test.gins1 || die + bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die + bash ../core/mafft --localpair sample > test.lins1 || die + bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die + + diff test.fftns2 sample.fftns2 || die + diff test.fftnsi sample.fftnsi || die + diff test.gins1 sample.gins1 || die + diff test.ginsi sample.ginsi || die + diff test.lins1 sample.lins1 || die +} + +src_install() { + dodoc readme + cd core || die + emake PREFIX="${ED}usr" install +} diff --git a/sci-biology/mafft/mafft-7.305.ebuild b/sci-biology/mafft/mafft-7.305.ebuild new file mode 100644 index 000000000000..92925d8342b2 --- /dev/null +++ b/sci-biology/mafft/mafft-7.305.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit flag-o-matic toolchain-funcs + +EXTENSIONS="-without-extensions" + +DESCRIPTION="Multiple sequence alignments using a variety of algorithms" +HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" +SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" +IUSE="threads" + +S="${WORKDIR}/${P}${EXTENSIONS}" + +src_prepare() { + default + + append-cflags -Wno-unused-result + use threads && append-cppflags -Denablemultithread + + sed \ + -e 's/(PREFIX)\/man/(PREFIX)\/share\/man/' \ + -e 's:$(LDFLAGS)::g' \ + -e 's:$(CC) -o $@:$(CC) $(LDFLAGS) -o $@:g' \ + -e 's:$(CC) -shared -o $@:$(CC) $(LDFLAGS) -shared -o $@:g' \ + -e '/INSTALL/s: -s : :g' \ + -i core/Makefile || die +} + +src_compile() { + cd core || die + emake \ + $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ + PREFIX="${EPREFIX}"/usr \ + CC="$(tc-getCC)" \ + CFLAGS="${CFLAGS}" +} + +src_test() { + export MAFFT_BINARIES="${S}"/core + cd test || die + bash ../core/mafft sample > test.fftns2 || die "Tests failed" + bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die "Tests failed" + bash ../core/mafft --globalpair sample > test.gins1 || die "Tests failed" + bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die "Tests failed" + bash ../core/mafft --localpair sample > test.lins1 || die "Tests failed" + bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die "Tests failed" + + diff test.fftns2 sample.fftns2 || die "Tests failed" + diff test.fftnsi sample.fftnsi || die "Tests failed" + diff test.gins1 sample.gins1 || die "Tests failed" + diff test.ginsi sample.ginsi || die "Tests failed" + diff test.lins1 sample.lins1 || die "Tests failed" +} + +src_install() { + DOCS=( readme ) + einstalldocs + + cd core || die + emake PREFIX="${ED%/}/usr" install +} diff --git a/sci-biology/mafft/metadata.xml b/sci-biology/mafft/metadata.xml new file mode 100644 index 000000000000..959160fe46b1 --- /dev/null +++ b/sci-biology/mafft/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> |