reinit the tree, so we can have metadata

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>