sci-biology/fasta: Version BUmp

(Portage version: 2.2.0_alpha174/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916)

3 files changed, 161 insertions, 2 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/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