sci-biology/mafft: Version Bump

Package-Manager: portage-2.2.0_alpha173/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

5 files changed, 288 insertions, 17 deletions

diff --git a/sci-biology/mafft/ChangeLog b/sci-biology/mafft/ChangeLog
index 2449852694fc..9c0792768c95 100644
--- a/sci-biology/mafft/ChangeLog
+++ b/sci-biology/mafft/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/mafft
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.9 2011/11/21 15:30:19 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.10 2013/04/29 10:05:58 jlec Exp $
+
+*mafft-7.037 (29 Apr 2013)
+
+  29 Apr 2013; Justin Lecher <jlec@gentoo.org> +mafft-7.037.ebuild,
+  +files/mafft-7.037-respect.patch, metadata.xml:
+  Version Bump
 
   21 Nov 2011; Justin Lecher <jlec@gentoo.org> mafft-6.811.ebuild:
   keyworded for ~x86-macos ~x64-macos, tested by Johan Hattne #390123
diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
index 67c0b6a6ddd9..2b5091573e26 100644
--- a/sci-biology/mafft/Manifest
+++ b/sci-biology/mafft/Manifest
@@ -1,20 +1,23 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA512
 
-AUX 6.811-respect.patch 6327 RMD160 03c7abe1a03a161698cfdad2f271cbf8d5308bc0 SHA1 be7eea3fcdb65b3bccd4d900cf53b8a41610482f SHA256 3d527220ce3fb90e4fa2dd2f41bca1f2684bb03f0de94313d7aea432b955e37c
-AUX mafft-6.240-mktemp.patch 6497 RMD160 ffa5d5889315614fd065e72425b1db3e8272f7b2 SHA1 5584719991e7b5c7d014c8cb1b59391f71f24668 SHA256 783f6f5678781dff1fafece92f37688698052fe1e0bfa13850443a0f8cc91533
-DIST mafft-6.240-src.tgz 657197 RMD160 1cb77af7a5a6b9ab818560d9626e746fb7a3b839 SHA1 8fc05350d9dcf8a9f56bdeed20790a4e1f21ceba SHA256 d0183ab1d6a5e0d1132b95cb917fedb3b6dc16c38d3fde35d7140ecdca555e8f
-DIST mafft-6.707-without-extensions-src.tgz 455884 RMD160 6676133b9f50c2037f13f50ea86e9543022028ce SHA1 1dd955255e5572b8c4a0b23c65cea832383b6a97 SHA256 08789aa9351128e32b0003cb524668c3f2e35aec7ea9f834047f0780851989a0
-DIST mafft-6.811-without-extensions-src.tgz 500063 RMD160 1b26aeb742df3bf8ed3849907ca966b1ebd41ebc SHA1 09bc404c1d39609373989faffe9e04b043c2355e SHA256 a99b57444787b2e910b0b56a5cc8c69949dc987b7ff12995650a1dd0be065c43
-EBUILD mafft-6.240-r1.ebuild 1004 RMD160 b81d375d94b48681a9b08b54d8562b83c2f439ec SHA1 8bcd0b62a3c92b7fcb332496af8d8042324d45ac SHA256 70cb92f9d6a0a9e6dab1e5bae147191ffbe54c4517df9d2efd859cceb6df41e6
-EBUILD mafft-6.707.ebuild 998 RMD160 333ac5159c103cd02417919e95696d34ee23ebce SHA1 9aa1a78f1411f6410ed8dc3bdc6e3b5e926fc5da SHA256 ca548edebc7b720371b27b456d63c806141c2d6337d1436cd973b6c5261581bc
-EBUILD mafft-6.811.ebuild 1166 RMD160 37118a38ec2afa735179dd3b4e990bf8ea911825 SHA1 b5823a955f959059963a9b6c25a18525c35e6649 SHA256 a83f99b61abe2933ec68b7f0bc65708c36670b658dc225e470a693817e73fdfa
-MISC ChangeLog 1996 RMD160 7986e8ccce0ea233832140533cd88eda0c11a562 SHA1 77dc0b3ac61821bedd6ab44bee22467f990c4f26 SHA256 f985fca95b402372f3027aee84008db8d5db594a904effc3adde78ab2be02d25
-MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
+AUX 6.811-respect.patch 6327 SHA256 3d527220ce3fb90e4fa2dd2f41bca1f2684bb03f0de94313d7aea432b955e37c SHA512 0e7e829cc95fcf218fbdf9763983ee6d6ecfb6153201c302fb18ef05818ee19b3b7852c1f85162d2eb2055869033f759cdb3fdbc98cfe4d30ee3607148290e6c WHIRLPOOL ae5c596613dab72df381f849cff927a44dd7f1d9281564fa51f019f38e7435175293674390418f19bbd7305fe4a4748db87abd83cc49a67954ae2a05a6747efb
+AUX mafft-6.240-mktemp.patch 6497 SHA256 783f6f5678781dff1fafece92f37688698052fe1e0bfa13850443a0f8cc91533 SHA512 ade9d0f296a70324f4847763d03585b29cea6bd4a81fa04868eb92df56da40f9df0877f9b310de925c257baaac50208ca17f406639a87cd10c2c83361463b571 WHIRLPOOL af88a170882c110e44026f3402a8d1192264865e1f028725eb1d4d3e94bf7793c4190c53437d1e29e3a57d29e4e08cf8c10db517641f2c809c862a300a27ef0e
+AUX mafft-7.037-respect.patch 7463 SHA256 eeedc574ad5977661ea879eefaa1c4b4d428384f25af891c1fcef16e6bfc6293 SHA512 ba706bc83b1c249c08fa7e39d6b80df42be058ea2e68baf1028125dcad289764ead3a6269e557bffc62da87a7ac2ff9856a602e20ca5eae052060d44b431994b WHIRLPOOL cf340ae92dec7ac35099706e5f2a31ac123b341391d2ebe25d4050fc470bbc295ab51c26612c4cc6c659abfba48c355df170b5352b2a6b6a04e8eeca6f453bb5
+DIST mafft-6.240-src.tgz 657197 SHA256 d0183ab1d6a5e0d1132b95cb917fedb3b6dc16c38d3fde35d7140ecdca555e8f
+DIST mafft-6.707-without-extensions-src.tgz 455884 SHA256 08789aa9351128e32b0003cb524668c3f2e35aec7ea9f834047f0780851989a0
+DIST mafft-6.811-without-extensions-src.tgz 500063 SHA256 a99b57444787b2e910b0b56a5cc8c69949dc987b7ff12995650a1dd0be065c43 SHA512 c50296209e09e0c4dfe4cf68956c470970462497c0ddb5a1af51f075e83ea84ab3c271c7651ac44018375a41f119619b0263f9d4c155364d647ee9571a18f940 WHIRLPOOL 3b1c3fe990e78dfc971f49e6db77e6c166ab8ba599a0cb6ce979c22294cad0110e14089faa9cfc5648f9e0c21528d70e344518508e52ef005df72e7a36ca867a
+DIST mafft-7.037-without-extensions-src.tgz 371344 SHA256 9c4688e55d8f47202ea8fd100753970dfe7c8c349f855f54bf5af4a90ee9d9dd SHA512 c32cf15a7ef935c5f78ce2d6472eba062e14ed5d49fcc3dff86f293223dfb79183fecef7e519b3116a16076f0f1f32d88233c0e85f64fbffeef2ad9cd06c9740 WHIRLPOOL 950049ad719f0ee6eb4abb7578a87752ac8c2dc419089c49122f929841918d79e5fb995b7ac324fb88617d8a4b8daa4ce8c9fce4c5b7fb4a2bd95c37e12fdfa7
+EBUILD mafft-6.240-r1.ebuild 1004 SHA256 70cb92f9d6a0a9e6dab1e5bae147191ffbe54c4517df9d2efd859cceb6df41e6 SHA512 40ddd365b68b82446ba3931525ad1d1d91a1e442af2d0e8efa20448b69b3d79b0fb8c24adffadd5cbd2e1e10ff32643af7eb6058a53a9b28bfbaa17f97f1ca2f WHIRLPOOL d2d0a212d863f125bd866de9003c05ad3f5a92434550cd75567ce572cc50c25d12bbb18019040be2f6a686d28ce609e27537038198f678eb60186a80a06a7fe1
+EBUILD mafft-6.707.ebuild 998 SHA256 ca548edebc7b720371b27b456d63c806141c2d6337d1436cd973b6c5261581bc SHA512 b8067e0e56d0bec8a2f2af3d11d03cd92db1432f1c1b6bfe680ee7d9958a537b3f6f60219c813b74c753d7d7f353495164c947fe953f9113997aedd03a2ca8f6 WHIRLPOOL a0781c7b82d4fb07837ff00526cc748c4102492166449b6b0274381a42f364236efbce58c46561fdf120a81c0d4bd0a7b94a761034c6c2ec6128a1ae1858070d
+EBUILD mafft-6.811.ebuild 1166 SHA256 a83f99b61abe2933ec68b7f0bc65708c36670b658dc225e470a693817e73fdfa SHA512 ab298b855b637f183f7f5869fe528cca32e9dfda5fe978fe7d6e189141aed5a1cfcbf0cd803cda98b747c35d8366376d03ec548ef8db0f41780b550a774bc86f WHIRLPOOL f1bbe9eceb8d495b1cfad1069c7531b3c528934d456b225583c36ef357dcbfe5b8b941315c20a98d1675cf46b1b1916ec1eb9c3fb56d0b53e406f861f823b20b
+EBUILD mafft-7.037.ebuild 1179 SHA256 18ada2e1daab714025a758c476fe66961a8800f70de24cef84756293fdd9b224 SHA512 72f8983373b70a0bfa883f0f60eb8622e55cffc0a0bc1106c15c6071b94d1109c0b01c73d4a778733ea314c542d56412a9bbadfe495a3047e6fa6cae26839d80 WHIRLPOOL 5139acbeb83f5dcd7f60a81e44644190265688146a91be7c1010634de4f6edf15366ae7fa6480bad8ae9d1f83255b26390682a0ab68ae20348a09d10a4332016
+MISC ChangeLog 2159 SHA256 0ce2ca8bcc1e6000d2646802405cbb9fd4f05a797d733a35c035547b855d4557 SHA512 b79f28451d43acd13f921da73f5d831e5794da53eafcdb467702c7943bdfdc54d155316b54d4c5630b29a05a9b63d27de2ddc0f9e4d99b26579ead25696eedfd WHIRLPOOL bca9877a487b1fca3a04db58a60f9fb643858ff9911d75ec915da8340a14773603bb229198706d4b5ddde8c92d74f4b7f7c7c8cf03a4d85bc375efde0965a2db
+MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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+Version: GnuPG v2.0.19 (GNU/Linux)
 
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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-7.037.ebuild b/sci-biology/mafft/mafft-7.037.ebuild
new file mode 100644
index 000000000000..00cf1a80f4e9
--- /dev/null
+++ b/sci-biology/mafft/mafft-7.037.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.037.ebuild,v 1.1 2013/04/29 10:05:58 jlec Exp $
+
+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 ~x64-macos ~x86-macos"
+IUSE="threads"
+
+S="${WORKDIR}"/${P}${EXTENSIONS}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-respect.patch
+	use threads && append-flags -Denablemultithread
+	sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile
+	sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed"
+}
+
+src_compile() {
+	pushd core
+	emake \
+		ENABLE_MULTITHREAD=1 \
+		PREFIX="${EPREFIX}"/usr \
+		CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" \
+		|| die "make failed"
+	popd
+}
+
+src_install() {
+	pushd core
+	emake PREFIX="${ED}usr" install || die "install failed"
+	popd
+	dodoc readme || die
+}
diff --git a/sci-biology/mafft/metadata.xml b/sci-biology/mafft/metadata.xml
index 34294c65ca04..f17a827e3101 100644
--- a/sci-biology/mafft/metadata.xml
+++ b/sci-biology/mafft/metadata.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci-biology</herd>
+  <herd>sci-biology</herd>
 </pkgmetadata>