New upstream version

Package-Manager: portage-2.1-r1

1 files changed, 84 insertions, 0 deletions

diff --git a/sci-biology/emboss/emboss-4.0.0.ebuild b/sci-biology/emboss/emboss-4.0.0.ebuild
new file mode 100644
index 000000000000..fc86b785eff1
--- /dev/null
+++ b/sci-biology/emboss/emboss-4.0.0.ebuild
@@ -0,0 +1,84 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-4.0.0.ebuild,v 1.1 2006/07/21 14:45:20 ribosome Exp $
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+HOMEPAGE="http://emboss.sourceforge.net/"
+SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
+LICENSE="GPL-2 LGPL-2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~ppc-macos ~ppc64 ~x86"
+IUSE="X png minimal"
+
+DEPEND="X? ( || ( x11-libs/libXt virtual/x11 ) )
+	png? (
+		sys-libs/zlib
+		media-libs/libpng
+		>=media-libs/gd-1.8
+	)
+	!minimal? (
+		sci-biology/primer3
+		sci-biology/clustalw
+	)
+	!<dev-util/pscan-20000721-r1"
+
+PDEPEND="!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/prints
+		>=sci-biology/prosite-19.7
+		>=sci-biology/rebase-601-r1
+		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 ${EXTRA_CONF} || die
+	# Do not install the JEMBOSS component (the --without-java configure option
+	# does not work). JEMBOSS will eventually be available as a separate package.
+	sed -i -e 's/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/' \
+			Makefile || die
+	emake || die
+}
+
+src_install() {
+	einstall || die "Failed to install program files."
+
+	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS "${FILESDIR}"/README.Gentoo \
+			|| die "Failed to install documentation."
+
+	# Install env file for setting libplplot and acd files path.
+	insinto /etc/env.d
+	newins ${FILESDIR}/22emboss-r1 22emboss || \
+			die "Failed to install environment file."
+
+	# Symlink preinstalled docs to /usr/share/doc.
+	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die
+	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die
+	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
+	dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die
+
+	# Remove useless dummy files from the image.
+	rm "${D}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \
+			|| die "Failed to remove dummy files."
+
+	# Move the provided codon files to a different directory. This will avoid
+	# user confusion and file collisions on case-insensitive file systems (see
+	# bug #115446). This change is documented in "README.Gentoo".
+	mv "${D}"/usr/share/EMBOSS/data/CODONS \
+			"${D}"/usr/share/EMBOSS/data/CODONS.orig || \
+			die "Failed to move CODON directory."
+
+	# Move the provided restriction enzyme prototypes file to a different name.
+	# This will avoid file collisions with future versions of rebase that will
+	# install their own enzyme prototypes file (see bug #118832).
+	mv "${D}"/usr/share/EMBOSS/data/embossre.equ \
+			"${D}"/usr/share/EMBOSS/data/embossre.equ.orig || \
+			die "Failed to move enzyme equivalence file."
+}