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

6 files changed, 169 insertions, 0 deletions

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
new file mode 100644
index 000000000000..b13e15f441be
--- /dev/null
+++ b/sci-biology/emboss/ChangeLog
@@ -0,0 +1,79 @@
+# ChangeLog for app-sci/emboss
+# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.1 2004/12/23 22:51:48 ribosome Exp $
+
+*emboss-2.9.0 (23 Dec 2004)
+
+  23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/22emboss-r1, +emboss-2.9.0.ebuild:
+  Moved from app-sci/emboss to sci-biology/emboss.
+
+  31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild,
+  -emboss-2.8.0-r3.ebuild:
+  Removed old version. Added 2.9.0 to x86.
+
+  10 Aug 2004; Olivier Fisette <ribosome@gentoo.org>
+  emboss-2.8.0-r3.ebuild:
+  Added to x86.
+  emboss-2.8.0-r2.ebuild:
+  Removed obsolete ebuild.
+
+  21 Jul 2004; David Holm <dholm@gentoo.org> emboss-2.9.0.ebuild:
+  Added to ~ppc.
+
+  20 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
+  emboss-2.8.0-r3.ebuild, emboss-2.9.0.ebuild:
+  Removed icc support since no patching is needed.
+
+  19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild:
+  Version bump. Changed the configuration and install steps a bit to
+  reflect the fact that header files are now installed automatically.
+
+  14 Jul 2004; Olivier Fisette <ribosome@gentoo.org>
+  emboss-2.8.0-r3.ebuild: Modified configuration step to make the X and png
+  USE flags independent; Added support for icc; Added primer3 and clustalw
+  to the dependencies since some EMBOSS programs won't work without them;
+  Added support for the biological databases aaindex, cutg, prints, prosite,
+  rebase and transfac, which are needed for many EMBOSS programs (the databases
+  are PDEPENDencies since they all must be indexed with an EMBOSS program before
+  use) (this database support is optional); Added header files installation for
+  EMBOSS development.
+  emboss-2.8.0-r2.ebuild: Added to x86.
+  emboss-2.8.0-r1.ebuild, emboss-2.8.0.ebuild, emboss-2.7.1.ebuild: Removed files.
+  metadata.xml: Added long description; Set myself as maintainer.
+
+  02 Jun 2004; Aron Griffis <agriffis@gentoo.org> emboss-2.8.0-r1.ebuild,
+  emboss-2.8.0-r2.ebuild:
+  Fix use invocation
+
+  12 May 2004; David Holm <dholm@gentoo.org> emboss-2.8.0-r2.ebuild:
+  Added to ~ppc.
+
+*emboss-2.8.0-r2 (11 May 2004)
+
+  11 May 2004; Patrick Kursawe <phosphan@gentoo.org> emboss-2.8.0-r2.ebuild,
+  files/22emboss-r1:
+  Adjusted value of PLPLOT_LIB, see bug #50176
+
+*emboss-2.8.0-r1 (30 Jan 2004)
+
+  30 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0-r1.ebuild:
+  Modified to use X and png properly for servers
+
+  28 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0.ebuild:
+  Modified 2.8.0 ebuild to require X not just USE it.
+
+*emboss-2.8.0 (13 Dec 2003)
+
+  13 Dec 2003; Stephen Diener <sediener@gentoo.org> emboss-2.7.1.ebuild,
+  emboss-2.8.0.ebuild:
+  Version bump...
+
+  20 Oct 2003; George Shapovalov <george@gentoo.org> metdata.xml :
+  added metadata.xml, marked ebuild stable
+
+*emboss-2.7.1 (03 Sep 2003)
+
+  03 Sep 2003; <sediener@gentoo.org> emboss-2.7.1.ebuild:
+  Initial ebuild
+
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
new file mode 100644
index 000000000000..87e3b32a9144
--- /dev/null
+++ b/sci-biology/emboss/Manifest
@@ -0,0 +1,5 @@
+MD5 02e17352ecec7dabbaa1aab84769e746 emboss-2.9.0.ebuild 1779
+MD5 1b0826c48804a608a2bb548e7c27dc93 ChangeLog 2789
+MD5 6051afb1f26bf343082490327784b958 metadata.xml 1013
+MD5 68e42b6377bb0887a0aeac76cf530854 files/digest-emboss-2.9.0 66
+MD5 ef2dfa3d13837026f59c0cf5f04f67c5 files/22emboss-r1 110
diff --git a/sci-biology/emboss/emboss-2.9.0.ebuild b/sci-biology/emboss/emboss-2.9.0.ebuild
new file mode 100644
index 000000000000..08d96f4ae1d2
--- /dev/null
+++ b/sci-biology/emboss/emboss-2.9.0.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-2.9.0.ebuild,v 1.1 2004/12/23 22:51:48 ribosome Exp $
+
+DESCRIPTION="The European Molecular Biology Open Software Suite: a sequence analysis package."
+HOMEPAGE="http://emboss.sourceforge.net/"
+SRC_URI="ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
+LICENSE="GPL-2 LGPL-2"
+
+SLOT="0"
+KEYWORDS="x86 ~ppc"
+IUSE="X png no-biodata"
+
+DEPEND="X? ( virtual/x11 )
+	png? (
+		sys-libs/zlib
+		media-libs/libpng
+		>=media-libs/gd-1.8
+	)
+	sci-biology/primer3
+	sci-biology/clustalw"
+
+PDEPEND="!no-biodata? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/prints
+		sci-biology/prosite
+		sci-biology/rebase
+		sci-biology/transfac
+	)"
+
+S=${WORKDIR}/EMBOSS-${PV}
+
+src_compile() {
+	EXTRA_CONF="--includedir=${D}/usr/include/emboss"
+	! use X && EXTRA_CONF="${EXTRA_CONF} --without-x"
+	! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver"
+
+	econf ${EXTRA_CONF} || die
+	# Do not install the JEMBOSS component (the --without-java configure option
+	# does not work). JEMBOSS will be available as a separate package.
+	sed -i -e 's/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/' Makefile
+	emake || die
+}
+
+src_install() {
+	einstall || die
+	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS
+
+	# Install env file for setting libplplot and acd files path.
+	insinto /etc/env.d
+	newins ${FILESDIR}/22emboss-r1 22emboss
+
+	# Symlink preinstalled docs to /usr/share/doc.
+	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals
+	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs
+	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials
+}
diff --git a/sci-biology/emboss/files/22emboss-r1 b/sci-biology/emboss/files/22emboss-r1
new file mode 100644
index 000000000000..177643ced11f
--- /dev/null
+++ b/sci-biology/emboss/files/22emboss-r1
@@ -0,0 +1,4 @@
+# plplot libs dir
+PLPLOT_LIB="/usr/share/EMBOSS/"
+# ACD files location
+EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
diff --git a/sci-biology/emboss/files/digest-emboss-2.9.0 b/sci-biology/emboss/files/digest-emboss-2.9.0
new file mode 100644
index 000000000000..ab9c2bc595ca
--- /dev/null
+++ b/sci-biology/emboss/files/digest-emboss-2.9.0
@@ -0,0 +1 @@
+MD5 c6facfd1750e88a0c8b7bb7ac826d472 EMBOSS-2.9.0.tar.gz 14479274
diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml
new file mode 100644
index 000000000000..ff86b6a3a444
--- /dev/null
+++ b/sci-biology/emboss/metadata.xml
@@ -0,0 +1,22 @@
+<?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>
+		EMBOSS is "The European Molecular Biology Open Software Suite".
+		EMBOSS is a free Open Source software analysis package specially
+		developed for the needs of the molecular biology (e.g. EMBnet) user
+		community. The software automatically copes with data in a variety
+		of formats and even allows transparent retrieval of sequence data
+		from the web. Also, as extensive libraries are provided with the
+		package, it is a platform to allow other scientists to develop and
+		release software in true open source spirit. EMBOSS also integrates
+		a range of currently available packages and tools for sequence
+		analysis into a seamless whole. EMBOSS breaks the historical trend
+		towards commercial software packages.
+	</longdescription>
+</pkgmetadata>