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-rw-r--r--sci-biology/fasta/ChangeLog10
-rw-r--r--sci-biology/fasta/fasta-36.3.5e.ebuild79
-rw-r--r--sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch74
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