Initial import.

Package-Manager: portage-2.0.51.18

6 files changed, 79 insertions, 0 deletions

diff --git a/sci-biology/ariadne/ChangeLog b/sci-biology/ariadne/ChangeLog
new file mode 100644
index 000000000000..44e8aee1e25a
--- /dev/null
+++ b/sci-biology/ariadne/ChangeLog
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+# ChangeLog for sci-biology/ariadne
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ariadne/ChangeLog,v 1.1 2005/03/05 21:24:53 ribosome Exp $
+
+*ariadne-1.3 (05 Mar 2005)
+
+  05 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/ariadne-env, +ariadne-1.3.ebuild:
+  Initial import.
+
diff --git a/sci-biology/ariadne/Manifest b/sci-biology/ariadne/Manifest
new file mode 100644
index 000000000000..68dd4d406f8d
--- /dev/null
+++ b/sci-biology/ariadne/Manifest
@@ -0,0 +1,5 @@
+MD5 3eca08caa8cde4d390d78f202da739d0 ariadne-1.3.ebuild 940
+MD5 6e2cf25c0551201747762974675121fe ChangeLog 371
+MD5 feb133611c8c1d9ca6db169db059426a metadata.xml 947
+MD5 2c1e987db0cdcd91873d0e7a4476bbad files/digest-ariadne-1.3 61
+MD5 550f9d19787d675310b812611c92d3e0 files/ariadne-env 30
diff --git a/sci-biology/ariadne/ariadne-1.3.ebuild b/sci-biology/ariadne/ariadne-1.3.ebuild
new file mode 100644
index 000000000000..a1eb2a2130f3
--- /dev/null
+++ b/sci-biology/ariadne/ariadne-1.3.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ariadne/ariadne-1.3.ebuild,v 1.1 2005/03/05 21:24:53 ribosome Exp $
+
+inherit toolchain-funcs
+
+DESCRIPTION="Protein sequences and profiles comparison"
+LICENSE="as-is"
+HOMEPAGE="http://www.well.ox.ac.uk/ariadne/"
+SRC_URI="http://www.well.ox.ac.uk/ariadne/ariadne-1.3.tar.Z"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+DEPEND="virtual/libc
+	sci-biology/ncbi-tools"
+
+S=${WORKDIR}/SRC-${PV}
+
+src_unpack(){
+	unpack ${A}
+	cd ${S}
+	sed -e "s/CC = gcc/CC = $(tc-getCC)/" \
+		-e "s/OPTIMISE = -O2/OPTIMISE = ${CFLAGS}/" \
+		-i Makefile || die
+	sed -e "s/blosum62/BLOSUM62/" -i prospero.c || die
+}
+
+src_compile() {
+	emake || die
+}
+
+src_install() {
+	dobin Linux/{ariadne,prospero}
+	dolib Linux/libseq.a
+	insinto /usr/include/${PN}
+	doins Include/*.h
+	newenvd ${FILESDIR}/${PN}-env 22ariadne
+	dodoc README
+}
diff --git a/sci-biology/ariadne/files/ariadne-env b/sci-biology/ariadne/files/ariadne-env
new file mode 100644
index 000000000000..64c722167af9
--- /dev/null
+++ b/sci-biology/ariadne/files/ariadne-env
@@ -0,0 +1 @@
+BLASTMAT=/usr/share/ncbi/data
diff --git a/sci-biology/ariadne/files/digest-ariadne-1.3 b/sci-biology/ariadne/files/digest-ariadne-1.3
new file mode 100644
index 000000000000..a973c1ce1d54
--- /dev/null
+++ b/sci-biology/ariadne/files/digest-ariadne-1.3
@@ -0,0 +1 @@
+MD5 240dc8b278a02b0fcdf56cd186d9b0ec ariadne-1.3.tar.Z 69427
diff --git a/sci-biology/ariadne/metadata.xml b/sci-biology/ariadne/metadata.xml
new file mode 100644
index 000000000000..01325f9b7108
--- /dev/null
+++ b/sci-biology/ariadne/metadata.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>ribosome@gentoo.org</email>
+		<name>Olivier Fisette</name>
+	</maintainer>
+	<herd>sci</herd>
+	<longdescription>
+		ARIADNE is a package of two programs, ariadne and prospero, that
+		compare protein sequences and profiles using the Smith-Waterman
+		algorithm, and assesses statistical significance using a new accurate
+		formula, described in Mott, 2000, "Accurate Formula for P-values of
+		gapped local sequence and profile alignments" J. Mol Biol. 300:649-659.
+		The sequence/profile comparison algorithms used in ARIADNE are
+		standard, and are probably not the fastest implementations available.
+		The novel part is the method for determining statistical significance,
+		which will give thresholds of significance that are accurate to within
+		5% 95% of the time.
+	</longdescription>
+</pkgmetadata>