sci-biology/fasta: Version BUmp

Package-Manager: portage-2.2.0_alpha174/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

4 files changed, 168 insertions, 6 deletions

diff --git a/sci-biology/fasta/ChangeLog b/sci-biology/fasta/ChangeLog
index 9c58ea46a232..8efa7d797262 100644
--- a/sci-biology/fasta/ChangeLog
+++ b/sci-biology/fasta/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/fasta
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasta/ChangeLog,v 1.8 2012/12/10 19:48:44 jlec Exp $
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasta/ChangeLog,v 1.9 2013/05/11 15:39:33 jlec Exp $
+
+*fasta-36.3.5e (11 May 2013)
+
+  11 May 2013; Justin Lecher <jlec@gentoo.org> +fasta-36.3.5e.ebuild,
+  +files/fasta-36.3.5e-ldflags.patch:
+  Version BUmp
 
   10 Dec 2012; Justin Lecher <jlec@gentoo.org> fasta-35.4.10.ebuild,
   metadata.xml:
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index 55930556e5fe..c28268544245 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -2,14 +2,17 @@
 Hash: SHA512
 
 AUX 35.4.10-ldflags.patch 1036 SHA256 21b6c290ca565c50376da61cd980f21f7a96598ea5da046294321d8d6be5d5fe SHA512 8136536c7f9887920a045dbcd04fa9d01dc0a3b22ed0a1771df715e288d6c889d87b0a6d0f52c947b54185f6a5e92fe902316b502074200a13820cac9dfa6594 WHIRLPOOL 35ff6b7fba2b8f16eb51795c48fd1636708155b1ad405be62850def9934a7d7556644ce808360375b4e658098ada81d7d89d2c53eb04f020d4af2aea127c8100
+AUX fasta-36.3.5e-ldflags.patch 2781 SHA256 baaa544d74ec1367875c96945fc5046182b6502be8d5565806b6c4cb81ae819c SHA512 5424bb8385def72ff75701c2da153f697520cbec82f36cbed8de0e98f93d399de660e79da7700ab0ff688fd5388cf9f42a30ccc4359335ae02042bf8cbb3aae7 WHIRLPOOL 1cbb12763b22e4424d953562b7b681ccb6fcbb58df0772a9ad73cb7c28892dae7afd09626fc275371c762eff73f143390b478ff84ad9d1f7f524dce77ff8a4f5
 DIST fasta-35.4.10.tar.gz 618971 SHA256 60616963093784d2e41ff9c125d68d7a43bbe411cdef8dc37ce922b4c3aec758 SHA512 f04268f0eea59cd40985c86597ab68bef40ee28e6ca914a7182c0edfe943ec8fb2a860558f422f210a4c03f3c34f36c677bd3971bc240cb87695826c755f5a47 WHIRLPOOL 87eb008bc507923ceaebe93c5eb2ab367ca184c0fa2304491ba8edf09e5f6eabe16a8823a1b6a11d5157355406157d1c97da9bd1e194dc26709188b995a386ce
+DIST fasta-36.3.5e.tar.gz 943763 SHA256 92f44a0e0e13bcd6782489f2db42044d7109a9071d775fb0435df24288be90c2 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812 WHIRLPOOL 803cee2c7da8487811b6aa9776bfa737ab35c4de2f76887915ab285802a738cb073059f4122379512195bd54ad63db42c61059587b6a2aa34550774e57f9f5fa
 EBUILD fasta-35.4.10.ebuild 1435 SHA256 29715aa9f2596b5ebeaa444b0b11740aca6e26bfbb120146b81a4242d2989f24 SHA512 08a99bf0ebd6ec3c4f13065955533cf27244d19aad7476ac8b09364ce2e7e306f7092b6e22618897a5bb1f2d2fa174fce67f27e4c5305e7d4f4d6d402d9cceb0 WHIRLPOOL d576cd1ccf23b781113a487974f9a37bfc86ec72a20f2344e9b3966141a5c967ecec112dd257a51d6366126b7c5cdcc8c9c03e4671f773360573d0a65f156cef
-MISC ChangeLog 1216 SHA256 ae31345292de5c8204e5ae374e3a6cb8025c04815143762338eaa2c56ea2fe3f SHA512 cca30cd503a98b100d926c0f7a5ba84f3899b071425490ba6dbe9f740461bea3b38f8ee43371fdef072a5b67ca80b3659378da7385e5c8b61b7ffe1178c8b33e WHIRLPOOL 82921ba182082aa34f28dd38e19ef488b46ddea80453a1624f67b55cf92821966f87f500754c92df7572f196ed364796c146bae0268de1fc22c4df00359e6eef
+EBUILD fasta-36.3.5e.ebuild 1708 SHA256 e95cd97e91caf874ac5fb278704c3b87beb3c5e60e55ea4c91c6c457a6db394b SHA512 6acc23f4047cb0ee76afa3b1e3693379bb4cc13ba46ec4b76924f8740227cebea66003788c823382e974eb72e094c909626f4dda0d1501a59fc84b80c6251709 WHIRLPOOL ac8b76ddab8b44d5007fd95c3c39b16e447bb6762797d97367cc0eb1dba81ea9060cfa20fa30320fb33518ba4e86f8bf5118d81dd089eebf310977064bf5f62f
+MISC ChangeLog 1370 SHA256 508578a652c140b03077448aa6ba221ae9ea11e0c43c39fe304490fd17c85135 SHA512 4532ef189bfe7a4642a37ed5b7c96b3b9f1f03b66019c2ad250f5ac2c76c71ba3dec194c01fd2c5036abb73c21f1195d683c9df8a59b3e3eb6d156f06117e660 WHIRLPOOL 0aed404f7ae0782fcbf70c06951dc5d9741de23320185e6e548b6d14fb62dd0a6ecc05c3b9cde43643a94883bdabc3c0b09e37b40e4c3b9d24068f07962959d0
 MISC metadata.xml 314 SHA256 0b3407f27cc0f34c599f9e93093bb2ea5ed80701942f38b327fcf4a71e3593f8 SHA512 c8c9b9bbd59ba0dbae64b994f7c7e7839a5eabdb1eaf1c3b6427271fd3bc048711852b98ee1f041526395ff58c96f4d040c4f2e7c87a8584129991a41a216650 WHIRLPOOL 11286c17eb1013b5fab18034a58dd3c46ae634f17f9c1e89f2783ebc6e39c863c9d864ac303f96e9d4857b1ec2cfdec85741aaf3583ece9fe6846025c456b2ed
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diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild
new file mode 100644
index 000000000000..c49e2c7d5a49
--- /dev/null
+++ b/sci-biology/fasta/fasta-36.3.5e.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasta/fasta-36.3.5e.ebuild,v 1.1 2013/05/11 15:39:33 jlec Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="debug sse2 test"
+
+DEPEND="test? ( app-shells/tcsh )"
+RDEPEND=""
+
+src_prepare() {
+	CC_ALT=
+	CFLAGS_ALT=
+	ALT=
+
+	use debug && append-flags -DDEBUG
+
+	if [[ $(tc-getCC) == *icc* ]]; then
+		CC_ALT=icc
+		ALT="${ALT}_icc"
+	else
+		CC_ALT=$(tc-getCC)
+		use x86 && ALT="32"
+		use amd64 && ALT="64"
+	fi
+
+	if use sse2 ; then
+		ALT="${ALT}_sse2"
+		append-flags -msse2
+		[[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math
+	fi
+
+	export CC_ALT="${CC_ALT}"
+	export ALT="${ALT}"
+
+	epatch "${FILESDIR}"/${P}-ldflags.patch
+
+	sed \
+		-e 's:-ffast-math::g' \
+		-i make/Makefile* || die
+
+}
+
+src_compile() {
+	cd src || die
+	emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
+}
+
+src_test() {
+	cd test || die
+	FASTLIBS="../conf" bash test.sh || die
+}
+
+src_install() {
+	local bin
+	dobin bin/*
+
+	pushd bin > /dev/null || die
+	for bin in *36; do
+		dosym ${bin} /usr/bin/${bin%36} || die
+	done
+	popd
+
+	insinto /usr/share/${PN}
+	doins -r conf/* data seq
+
+	doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
+	dodoc  FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*}
+}
diff --git a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch
new file mode 100644
index 000000000000..a6eeabfdf46c
--- /dev/null
+++ b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch
@@ -0,0 +1,74 @@
+ make/Makefile.pcom   | 8 ++++----
+ make/Makefile.pcom_s | 8 ++++----
+ make/Makefile.pcom_t | 8 ++++----
+ 3 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/make/Makefile.pcom b/make/Makefile.pcom
+index 9c5f801..33fc001 100644
+--- a/make/Makefile.pcom
++++ b/make/Makefile.pcom
+@@ -209,14 +209,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+ 
+ map_db : map_db.c uascii.h ncbl2_head.h
+-	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+ 
+ list_db : list_db.c
+-	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+ 
+ 
+ lav2ps : lav2plt.o lavplt_ps.o
+-	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+ 
+ lav2svg : lav2plt.o lavplt_svg.o
+-	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
+diff --git a/make/Makefile.pcom_s b/make/Makefile.pcom_s
+index dc53001..8a45044 100644
+--- a/make/Makefile.pcom_s
++++ b/make/Makefile.pcom_s
+@@ -143,14 +143,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+ 
+ map_db : map_db.c uascii.h ncbl2_head.h
+-	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+ 
+ list_db : list_db.c
+-	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+ 
+ 
+ lav2ps : lav2plt.o lavplt_ps.o
+-	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+ 
+ lav2svg : lav2plt.o lavplt_svg.o
+-	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
+diff --git a/make/Makefile.pcom_t b/make/Makefile.pcom_t
+index 8a71438..5b08a50 100644
+--- a/make/Makefile.pcom_t
++++ b/make/Makefile.pcom_t
+@@ -164,14 +164,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+ 
+ map_db : map_db.c uascii.h ncbl2_head.h
+-	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+ 
+ list_db : list_db.c
+-	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+ 
+ 
+ lav2ps : lav2plt.o lavplt_ps.o
+-	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+ 
+ lav2svg : lav2plt.o lavplt_svg.o
+-	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm