Initial import.

(Portage version: 2.0.51.19)

7 files changed, 131 insertions, 0 deletions

diff --git a/sci-biology/wise/ChangeLog b/sci-biology/wise/ChangeLog
new file mode 100644
index 000000000000..303ea98d0454
--- /dev/null
+++ b/sci-biology/wise/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/wise
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/ChangeLog,v 1.1 2005/03/06 17:11:21 ribosome Exp $
+
+*wise-2.2.0 (06 Mar 2005)
+
+  06 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/wise-api.tex.patch, +files/wise-env, +wise-2.2.0.ebuild:
+  Initial import.
+
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
new file mode 100644
index 000000000000..0ad5fdbcde9a
--- /dev/null
+++ b/sci-biology/wise/Manifest
@@ -0,0 +1,4 @@
+MD5 23a3fc2fd3ca9159648f077e0485b662 wise-2.2.0.ebuild 1658
+MD5 dfe3a28949733a00d7126ed491e8b3f2 files/digest-wise-2.2.0 62
+MD5 6c1b047599122f062a65ad125739936b files/wise-api.tex.patch 2234
+MD5 7321fc88d375cef4db1411e6e6c867ab files/wise-env 40
diff --git a/sci-biology/wise/files/digest-wise-2.2.0 b/sci-biology/wise/files/digest-wise-2.2.0
new file mode 100644
index 000000000000..ad9dcdce97a3
--- /dev/null
+++ b/sci-biology/wise/files/digest-wise-2.2.0
@@ -0,0 +1 @@
+MD5 0584240f77885e37528e99e64535ab60 wise2.2.0.tar.gz 2108151
diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch
new file mode 100644
index 000000000000..827ce4cdfa7a
--- /dev/null
+++ b/sci-biology/wise/files/wise-api.tex.patch
@@ -0,0 +1,38 @@
+--- api.tex.old	2005-03-06 11:31:59.862760952 -0500
++++ api.tex	2005-03-06 11:42:31.375756384 -0500
+@@ -204,7 +204,7 @@
+ \item Build two Sequence objects, from a file or strings (\ref{object_Sequence})
+ \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins
+ \item Read in the comparison matrix using CompMat (\ref{object_CompMat})
+-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap})
++\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap})
+ \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay})
+ \end{itemize}
+ 
+@@ -213,7 +213,7 @@
+ \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence})
+ \item Make a protein database from the single protein object (\ref{object_ProteinDB})
+ \item Make a protein database from a single fasta file (\ref{object_ProteinDB})
+-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap})
++\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap})
+ \item Show the Hscore object using a show function (\ref{object_Hscore})
+ \item Retrieve individual protein objects from the database by taking out the
+ DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object
+@@ -232,7 +232,7 @@
+ \item Read in a codon table (\ref{object_CodonTable})
+ \item Make a random DNA model (\ref{object_RandomModelDNA})
+ \item Make an algorithm type (\ref{module_gwrap})
+-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap})
++\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap})
+ \item Run the actual algorithm (\ref{module_gwrap})
+ \item show the alignment using genedisplay (\ref{module_gwrap})
+ \end{itemize}
+@@ -5055,7 +5055,7 @@
+ Member functions of RandomModel
+ 
+ \section{sequence\_codon}
+-\label{module_sequence\_codon}
++\label{module_sequence_codon}
+ This module only contains factory methods
+ 
+ \subsection{sequence\_codon factory methods}
diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env
new file mode 100644
index 000000000000..3f781c80833b
--- /dev/null
+++ b/sci-biology/wise/files/wise-env
@@ -0,0 +1 @@
+WISECONFIGDIR="/usr/share/wise/wisecfg"
diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml
new file mode 100644
index 000000000000..e9391a41a838
--- /dev/null
+++ b/sci-biology/wise/metadata.xml
@@ -0,0 +1,9 @@
+<?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>
+</pkgmetadata>
diff --git a/sci-biology/wise/wise-2.2.0.ebuild b/sci-biology/wise/wise-2.2.0.ebuild
new file mode 100644
index 000000000000..33f8e3bc43c5
--- /dev/null
+++ b/sci-biology/wise/wise-2.2.0.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.2.0.ebuild,v 1.1 2005/03/06 17:11:21 ribosome Exp $
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Intelligent algorithms for DNA searches"
+LICENSE="BSD"
+HOMEPAGE="http://www.ebi.ac.uk/Wise2/"
+SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}2/${PN}${PV}.tar.gz"
+
+SLOT="0"
+IUSE=""
+KEYWORDS="~x86"
+
+RDEPEND="=sci-biology/hmmer-2.3.2-r1"
+
+DEPEND="${RDEPEND}
+	app-shells/tcsh
+	dev-lang/perl
+	virtual/tetex"
+
+S=${WORKDIR}/${PN}${PV}
+
+src_unpack() {
+	unpack ${A}
+	cd ${S}/src
+#	if use threads; then
+#		append-flags "-DPTHREAD"
+#		sed -e "s/#EXTRALIBS = -lpthread/EXTRALIBS = -lpthread/" -i makefile || die
+#	fi
+	sed -e "s/CC = cc/CC = $(tc-getCC)/" \
+		-e "s/CFLAGS = -c -O/CFLAGS = -c ${CFLAGS}/" \
+		-i makefile || die
+	cd ${S}/docs
+	cat ${S}/src/models/*.tex ${S}/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex
+	cat wise2api.tex temp.tex apiend.tex > api.tex
+	epatch ${FILESDIR}/${PN}-api.tex.patch
+}
+
+src_compile() {
+	cd src
+	make all || die
+	cd ${S}/docs
+	for i in api appendix dynamite wise2 wise3arch; do
+		latex ${i} || die
+		latex ${i} || die
+		dvips ${i}.dvi -o || die
+	done
+}
+
+src_install() {
+	dobin ${S}/src/bin/*
+	dolib ${S}/src/base/libwisebase.a
+	dolib ${S}/src/dynlibsrc/libdyna.a
+	dobin ${S}/src/dynlibsrc/testgendb
+	dolib ${S}/src/models/libmodel.a
+	insinto /usr/share/${PN}
+	doins -r ${S}/wisecfg
+	insinto /usr/share/doc/${PF}
+	doins ${S}/docs/*.ps
+	newenvd ${FILESDIR}/${PN}-env 24wise
+}
+
+src_test() {
+	cd ${S}/src
+	WISECONFIGDIR="${S}/wisecfg" make test || die
+}