Initial import, thanks to Jose Maria Fernandez Gonzalez

Package-Manager: portage-2.2_rc62/cvs/Linux x86_64

5 files changed, 125 insertions, 0 deletions

diff --git a/sci-biology/fasta/ChangeLog b/sci-biology/fasta/ChangeLog
new file mode 100644
index 000000000000..d4a9b4db6903
--- /dev/null
+++ b/sci-biology/fasta/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/fasta
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasta/ChangeLog,v 1.1 2010/02/06 20:00:24 jlec Exp $
+
+*fasta-35.4.10 (06 Feb 2010)
+
+  06 Feb 2010; Justin Lecher (jlec) <jlec@gentoo.org>
+  +files/35.4.10-ldflags.patch, +fasta-35.4.10.ebuild, +metadata.xml:
+  Initial import, thanks to Jose Maria Fernandez Gonzalez
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
new file mode 100644
index 000000000000..0e429489c435
--- /dev/null
+++ b/sci-biology/fasta/Manifest
@@ -0,0 +1,15 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
+AUX 35.4.10-ldflags.patch 1036 RMD160 49cfa8e067824012b46086e6878699dcadf2938e SHA1 1013030756dfadf0ef9d04305e4500701c9a3561 SHA256 21b6c290ca565c50376da61cd980f21f7a96598ea5da046294321d8d6be5d5fe
+DIST fasta-35.4.10.tar.gz 618971 RMD160 6dc98a555f88cdf1d5033c50cdb37371f868acc8 SHA1 0595d369d7a4a9a9e35d57a77703616c6c9b7d14 SHA256 60616963093784d2e41ff9c125d68d7a43bbe411cdef8dc37ce922b4c3aec758
+EBUILD fasta-35.4.10.ebuild 1373 RMD160 757fa95726b19fee03b95391092fc7c809e24962 SHA1 82b61d1a4eba48f67ceca4e3dc8d6e5f5abfe494 SHA256 b84d4d0a4c0c05984e1b3e297ca58727cb869be057d6f0d8ce047f3124a7110c
+MISC ChangeLog 417 RMD160 3cdc7a599fa05b0420f2fe2531828dbd413cfc63 SHA1 7f61aab1a63f76ee600e26837e62191ad908ab91 SHA256 c30a0a83aaa49fc107532650be900e058476334ae52e680e7bd06f77e6f54ed7
+MISC metadata.xml 382 RMD160 75d40acc3b5a8fb8ea656817aa204cc524ef7059 SHA1 7c7a5b42930a24b3fb2609716b7238ba3193e18d SHA256 2d9cc9ccec1bcd41294ff75ff29b4b449868a1dc2cd763ac28ee946a90611185
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAkttyl4ACgkQgAnW8HDreRbHaACeJtFPuP016fO4xk3o1HrTQLQ+
+m7sAniRoddgIkSN7o5rmW8Gb6gEaXwvC
+=zdmO
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/fasta/fasta-35.4.10.ebuild b/sci-biology/fasta/fasta-35.4.10.ebuild
new file mode 100644
index 000000000000..697352dd93a6
--- /dev/null
+++ b/sci-biology/fasta/fasta-35.4.10.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasta/fasta-35.4.10.ebuild,v 1.1 2010/02/06 20:00:24 jlec Exp $
+
+EAPI="2"
+
+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}3/${P}.tar.gz"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="debug icc sse2"
+
+DEPEND="
+	icc? ( dev-lang/icc )
+	test? ( app-shells/tcsh )"
+RDEPEND=""
+
+src_prepare() {
+	CC_ALT=
+	CFLAGS_ALT=
+	ALT=
+
+	use debug && append-flags -DDEBUG
+
+	if use icc ; then
+		CC_ALT=icc
+		ALT="${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
+		use icc || append-flags -ffast-math
+	fi
+
+	export CC_ALT="${CC_ALT}"
+	export ALT="${ALT}"
+
+	epatch "${FILESDIR}"/${PV}-ldflags.patch
+}
+
+src_compile() {
+	cd src
+	emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all || die
+}
+
+src_install() {
+	dobin bin/* || die
+	doman doc/{prss3.1,fasta35.1,pvcomp.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} || die
+	dodoc  FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} || die
+}
diff --git a/sci-biology/fasta/files/35.4.10-ldflags.patch b/sci-biology/fasta/files/35.4.10-ldflags.patch
new file mode 100644
index 000000000000..c3b7a9b56904
--- /dev/null
+++ b/sci-biology/fasta/files/35.4.10-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/make/Makefile.pcom b/make/Makefile.pcom
+index a808667..405be95 100644
+--- a/make/Makefile.pcom
++++ b/make/Makefile.pcom
+@@ -274,16 +274,16 @@ 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
+ 
+ res_stats : res_stats.o scale_se.o
+-	$(CC) -DUNIX -o $(BIN)/res_stats res_stats.o scale_se.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/res_stats res_stats.o scale_se.o -lm
diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml
new file mode 100644
index 000000000000..7bf7a49aa862
--- /dev/null
+++ b/sci-biology/fasta/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-biology</herd>
+	<maintainer>
+		<email>je_fro@gentoo.org</email>
+		<name>Jeff Gardner</name>
+	</maintainer>
+	<longdescription lang="en">
+	</longdescription>
+	<use>
+		<flag name='icc'>Use intel compiler instead of gcc</flag>
+	</use>
+</pkgmetadata>
+