proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

6 files changed, 542 insertions, 0 deletions

diff --git a/sci-biology/mafft/Manifest b/sci-biology/mafft/Manifest
new file mode 100644
index 000000000000..0f4b923df331
--- /dev/null
+++ b/sci-biology/mafft/Manifest
@@ -0,0 +1,2 @@
+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
diff --git a/sci-biology/mafft/files/6.811-respect.patch b/sci-biology/mafft/files/6.811-respect.patch
new file mode 100644
index 000000000000..ebfb2c7be7b8
--- /dev/null
+++ b/sci-biology/mafft/files/6.811-respect.patch
@@ -0,0 +1,192 @@
+diff --git a/core/Makefile b/core/Makefile
+index 8bb8baf..cf28559 100644
+--- a/core/Makefile
++++ b/core/Makefile
+@@ -1,5 +1,5 @@
+ PREFIX = /usr/local
+-LIBDIR = $(PREFIX)/lib/mafft
++LIBDIR = $(PREFIX)/GENTOOLIBDIR/mafft
+ BINDIR = $(PREFIX)/bin
+ MANDIR = $(PREFIX)/man/man1
+ 
+@@ -127,136 +127,136 @@ mltaln.h : functions.h
+ 	touch mltaln.h
+ 
+ ord : $(OBJORD)
+-	$(CC) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJORD) $(CFLAGS) $(LIBS)
+ 
+ tbfast : $(OBJTBFAST)
+-	$(CC) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTBFAST) $(CFLAGS) $(LIBS)
+ 
+ tbfast2 : $(OBJTBFAST2)
+-	$(CC) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTBFAST2) $(CFLAGS) $(LIBS)
+ 
+ disttbfast : $(OBJDISTTBFAST)
+-	$(CC) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDISTTBFAST) $(CFLAGS) $(LIBS)
+ 
+ splittbfast : $(OBJSPLITTBFAST)
+-	$(CC) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST) $(CFLAGS) $(LIBS)
+ 
+ splitfromaln : $(OBJSPLITFROMALN)
+-	$(CC) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSPLITFROMALN) $(CFLAGS) $(LIBS)
+ 
+ splittbfast2 : $(OBJSPLITTBFAST2)
+-	$(CC) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSPLITTBFAST2) $(CFLAGS) $(LIBS)
+ 
+ dummy : $(OBJDUMMY)
+-	$(CC) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDUMMY) $(CFLAGS) $(LIBS)
+ 
+ setcore : $(OBJSETCORE)
+-	$(CC) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSETCORE) $(CFLAGS) $(LIBS)
+ 
+ countlen : $(OBJCOUNTLEN)
+-	$(CC) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJCOUNTLEN) $(CFLAGS) $(LIBS)
+ 
+ seq2regtable : $(OBJSEQ2REGTABLE)
+-	$(CC) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEQ2REGTABLE) $(CFLAGS) $(LIBS)
+ 
+ regtable2seq : $(OBJREGTABLE2SEQ)
+-	$(CC) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJREGTABLE2SEQ) $(CFLAGS) $(LIBS)
+ 
+ f2cl : $(OBJF2CL)
+-	$(CC) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJF2CL) $(CFLAGS) $(LIBS)
+ 
+ mccaskillwrap : $(OBJMCCASKILLWRAP)
+-	$(CC) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJMCCASKILLWRAP) $(CFLAGS) $(LIBS)
+ 
+ contrafoldwrap : $(OBJCONTRAFOLDWRAP)
+-	$(CC) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJCONTRAFOLDWRAP) $(CFLAGS) $(LIBS)
+ 
+ pairlocalalign : $(OBJPAIRLOCALALIGN)
+-	$(CC) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJPAIRLOCALALIGN) $(CFLAGS) $(LIBS)
+ 
+ pairash : $(OBJPAIRASH)
+-	$(CC) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJPAIRASH) $(CFLAGS) $(LIBS)
+ 
+ rnatest : $(OBJRNATEST)
+-	$(CC) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJRNATEST) $(CFLAGS) $(LIBS)
+ 
+ pair2hat3s : $(OBJPAIR2HAT3S)
+-	$(CC) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJPAIR2HAT3S) $(CFLAGS) $(LIBS)
+ 
+ multi2hat3s : $(OBJMULTI2HAT3S)
+-	$(CC) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJMULTI2HAT3S) $(CFLAGS) $(LIBS)
+ 
+ getlag : $(OBJGETLAG)
+-	$(CC) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGETLAG) $(CFLAGS) $(LIBS)
+ 
+ tditr : $(OBJTDITR)
+-	$(CC) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTDITR) $(CFLAGS) $(LIBS)
+ 
+ dvtditr : $(OBJDVTDITR)
+-	$(CC) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDVTDITR) $(CFLAGS) $(LIBS)
+ 
+ mafft-profile : $(OBJGALN)
+-	$(CC) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGALN) $(CFLAGS) $(LIBS)
+ 
+ gapfill : $(OBJGAPFILL)
+-	$(CC) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGAPFILL) $(CFLAGS) $(LIBS)
+ 
+ dndfast4 : $(OBJDNDFAST4)
+-	$(CC) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST4) $(CFLAGS) $(LIBS)
+ 
+ dndfast5 : $(OBJDNDFAST5)
+-	$(CC) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST5) $(CFLAGS) $(LIBS)
+ 
+ dndfast6 : $(OBJDNDFAST6)
+-	$(CC) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST6) $(CFLAGS) $(LIBS)
+ 
+ dndfast7 : $(OBJDNDFAST7)
+-	$(CC) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST7) $(CFLAGS) $(LIBS)
+ 
+ dndblast : $(OBJDNDBLAST)
+-	$(CC) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDBLAST) $(CFLAGS) $(LIBS)
+ 
+ dndfast3 : $(OBJDNDFAST3)
+-	$(CC) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDFAST3) $(CFLAGS) $(LIBS)
+ 
+ triplet : $(OBJTRIPLET)
+-	$(CC) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET) $(CFLAGS) $(LIBS)
+ 
+ triplet3 : $(OBJTRIPLET3)
+-	$(CC) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET3) $(CFLAGS) $(LIBS)
+ 
+ sextet3 : $(OBJSEXTET3)
+-	$(CC) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEXTET3) $(CFLAGS) $(LIBS)
+ 
+ sextet4 : $(OBJSEXTET4)
+-	$(CC) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEXTET4) $(CFLAGS) $(LIBS)
+ 
+ sextet5 : $(OBJSEXTET5)
+-	$(CC) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSEXTET5) $(CFLAGS) $(LIBS)
+ 
+ mafft-distance : $(OBJDISTANCE)
+-	$(CC) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDISTANCE) $(CFLAGS) $(LIBS)
+ 
+ triplet5 : $(OBJTRIPLET5)
+-	$(CC) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET5) $(CFLAGS) $(LIBS)
+ 
+ triplet6 : $(OBJTRIPLET6)
+-	$(CC) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJTRIPLET6) $(CFLAGS) $(LIBS)
+ 
+ octet4 : $(OBJOCTET4)
+-	$(CC) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJOCTET4) $(CFLAGS) $(LIBS)
+ 
+ dndpre : $(OBJDNDPRE)
+-	$(CC) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDPRE) $(CFLAGS) $(LIBS)
+ 
+ dndpre2 : $(OBJDNDPRESCORE)
+-	$(CC) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJDNDPRESCORE) $(CFLAGS) $(LIBS)
+ 
+ score : $(OBJSCORE)
+-	$(CC) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJSCORE) $(CFLAGS) $(LIBS)
+ 
+ genMtx : $(OBJGENMTX)
+-	$(CC) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
++	$(CC) $(LDFLAGS) -o $@ $(OBJGENMTX) $(CFLAGS) $(LIBS)
+ 
+ gapfill.o : gapfill.c $(HEADER)
+ 	$(CC) $(CFLAGS) -c gapfill.c
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..d064e73b8089
--- /dev/null
+++ b/sci-biology/mafft/mafft-7.050.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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..b76c0e60839a
--- /dev/null
+++ b/sci-biology/mafft/mafft-7.215.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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/metadata.xml b/sci-biology/mafft/metadata.xml
new file mode 100644
index 000000000000..f17a827e3101
--- /dev/null
+++ b/sci-biology/mafft/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>