Moved from app-sci/clustalx to sci-biology/clustalx.

5 files changed, 94 insertions, 0 deletions

diff --git a/sci-biology/clustalx/ChangeLog b/sci-biology/clustalx/ChangeLog
new file mode 100644
index 000000000000..d8149d85df25
--- /dev/null
+++ b/sci-biology/clustalx/ChangeLog
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+# ChangeLog for app-sci/clustalx
+# Copyright 1999-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalx/ChangeLog,v 1.1 2004/12/23 21:31:04 ribosome Exp $
+
+*clustalx-1.83 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +clustalx-1.83.ebuild:
+  Moved from app-sci/clustalx to sci-biology/clustalx.
+
+  22 Nov 2004; Karol Wojtaszek <sekretarz@gentoo.org> clustalx-1.83.ebuild:
+  Added to ~amd64, bug #72084
+
+  18 Nov 2004; Michael Sterrett <mr_bones_@gentoo.org> clustalx-1.83.ebuild:
+  needs stable app-sci/ncbi-tools first
+
+  17 Nov 2004; Olivier Fisette <ribosome@gentoo.org> clustalx-1.83.ebuild:
+  Added to x86. Use toolchain-funcs rather than the gcc eclass.
+
+  14 Oct 2004; Olivier Fisette <ribosome@gentoo.org> clustalx-1.83.ebuild:
+  Use gcc.eclass rather than ${CC}.
+
+*clustalx-1.83 (06 Oct 2004)
+
+  06 Oct 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +clustalx-1.83.ebuild:
+  Initial import.
+
diff --git a/sci-biology/clustalx/Manifest b/sci-biology/clustalx/Manifest
new file mode 100644
index 000000000000..84f965bc69e3
--- /dev/null
+++ b/sci-biology/clustalx/Manifest
@@ -0,0 +1,4 @@
+MD5 85d7c090d64f675746361e68fce19490 ChangeLog 827
+MD5 272b5b012593acd07a7a60b8b64e6761 metadata.xml 509
+MD5 a6bdceb4558eaaa860058204ff1448f2 clustalx-1.83.ebuild 1358
+MD5 800c4da737d4fb9af3d8ffb7f6f44892 files/digest-clustalx-1.83 68
diff --git a/sci-biology/clustalx/clustalx-1.83.ebuild b/sci-biology/clustalx/clustalx-1.83.ebuild
new file mode 100644
index 000000000000..0ea286492f03
--- /dev/null
+++ b/sci-biology/clustalx/clustalx-1.83.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalx/clustalx-1.83.ebuild,v 1.1 2004/12/23 21:31:04 ribosome Exp $
+
+inherit toolchain-funcs
+
+DESCRIPTION="Graphical interface for the ClustalW multiple alignment program"
+HOMEPAGE="http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/"
+SRC_URI="ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/clustalx1.83.sun.tar.gz"
+LICENSE="public-domain"
+
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+DEPEND="sci-biology/ncbi-tools
+	sci-biology/clustalw
+	virtual/x11"
+
+S="${WORKDIR}/${PN}${PV}.sun"
+
+src_unpack() {
+	unpack ${A}
+	cd ${S}
+	cp makefile.linux makefile
+	sed -i -e "s/CC	= cc/CC	= $(tc-getCC)/" makefile
+	sed -i -e "s/CFLAGS  = -c -O/CFLAGS  = -c ${CFLAGS}/" makefile
+	sed -i -e "s/LFLAGS	= -O -lm/LFLAGS	= -lm ${CFLAGS}/" makefile
+	sed -i -e "s%-I/usr/bio/src/ncbi/include%-I/usr/include/ncbi%" makefile
+	sed -i -e "s%-L/usr/bio/src/ncbi/lib -L/usr/ccs/lib -L/usr/X11R6/lib%-L/usr/lib -L/usr/X11R6/lib%" makefile
+	sed -i -e "s%clustalx_help%/usr/share/doc/${PF}/clustalx_help%" clustalx.c
+	sed -i -e "s%clustalw.doc%../clustalw.doc%" clustalx.html
+}
+
+src_compile() {
+	make || die
+}
+
+src_install() {
+	dobin clustalx
+
+	dodoc README_X
+	dohtml clustalx.html
+
+	insinto /usr/share/doc/${PF}
+	doins clustalx_help clustalw.doc
+}
diff --git a/sci-biology/clustalx/files/digest-clustalx-1.83 b/sci-biology/clustalx/files/digest-clustalx-1.83
new file mode 100644
index 000000000000..9d0832e69fb6
--- /dev/null
+++ b/sci-biology/clustalx/files/digest-clustalx-1.83
@@ -0,0 +1 @@
+MD5 732538fe5fea04f4d5dd665e84c3b9ab clustalx1.83.sun.tar.gz 860205
diff --git a/sci-biology/clustalx/metadata.xml b/sci-biology/clustalx/metadata.xml
new file mode 100644
index 000000000000..8ce831f76510
--- /dev/null
+++ b/sci-biology/clustalx/metadata.xml
@@ -0,0 +1,14 @@
+<?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>
+		Clustal X is a graphical interface for the ClustalW multiple sequence
+		alignment program. It provides an integrated environment for performing
+		multiple sequence and profile alignments and analysing the results.
+	</longdescription>
+</pkgmetadata>