New upstream version.

Package-Manager: portage-2.1.2.9

6 files changed, 149 insertions, 2 deletions

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 8fdcc566c332..9dc703149859 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/emboss
 # Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.42 2007/04/09 23:06:58 je_fro Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.43 2007/07/18 00:55:33 ribosome Exp $
+
+*emboss-5.0.0 (18 Jul 2007)
+
+  18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +emboss-5.0.0.ebuild:
+  New upstream version.
 
   09 Apr 2007; Jeff Gardner <je_fro@gentoo.org> +files/22emboss,
   -files/22emboss-r1, emboss-4.0.0.ebuild:
diff --git a/sci-biology/emboss/emboss-5.0.0.ebuild b/sci-biology/emboss/emboss-5.0.0.ebuild
new file mode 100644
index 000000000000..5d7a83176305
--- /dev/null
+++ b/sci-biology/emboss/emboss-5.0.0.ebuild
@@ -0,0 +1,89 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-5.0.0.ebuild,v 1.1 2007/07/18 00:55:33 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 ~ppc64 ~sparc ~x86"
+IUSE="X png minimal"
+
+DEPEND="X? ( x11-libs/libXt )
+	png? (
+		sys-libs/zlib
+		media-libs/libpng
+		media-libs/gd
+	)
+	!minimal? (
+		sci-biology/primer3
+		sci-biology/clustalw
+	)"
+
+PDEPEND="!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/prints
+		sci-biology/prosite
+		>=sci-biology/rebase-707
+		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 ${EXTRA_CONF} || die
+	# Do not install the JEMBOSS component (the --without-java configure option
+	# does not work). JEMBOSS will eventually be available as a separate package.
+	sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \
+			Makefile || die
+	emake || die
+}
+
+src_install() {
+	einstall || die "Failed to install program files."
+
+	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \
+			|| die "Failed to install documentation."
+	newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \
+			|| die "Failed to install Gentoo readme file."
+
+	# Install env file for setting libplplot and acd files path.
+	cat <<- EOF > 22emboss
+		# plplot libs dir
+		PLPLOT_LIB="/usr/share/EMBOSS/"
+		# ACD files location
+		EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
+	EOF
+	doenvd 22emboss || die "Failed to install environment file."
+
+	# Symlink preinstalled docs to "/usr/share/doc".
+	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${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 avoids file collisions with versions of rebase that 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."
+}
diff --git a/sci-biology/emboss/files/digest-emboss-5.0.0 b/sci-biology/emboss/files/digest-emboss-5.0.0
new file mode 100644
index 000000000000..eccc0f1d9afe
--- /dev/null
+++ b/sci-biology/emboss/files/digest-emboss-5.0.0
@@ -0,0 +1,3 @@
+MD5 be4c895220ad34afd65d450ba7d8e34b EMBOSS-5.0.0.tar.gz 20666560
+RMD160 1bf510c0919d991e4ba67182137448dee49bab4d EMBOSS-5.0.0.tar.gz 20666560
+SHA256 64e6f09b82a719ff26de7f21fdf7d2bd605d2c664384c1c7b48f9d245d5f40ae EMBOSS-5.0.0.tar.gz 20666560
diff --git a/sci-biology/prosite/ChangeLog b/sci-biology/prosite/ChangeLog
index 640456725f0a..595ddd762d3c 100644
--- a/sci-biology/prosite/ChangeLog
+++ b/sci-biology/prosite/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/prosite
 # Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/prosite/ChangeLog,v 1.97 2007/05/22 00:44:50 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/prosite/ChangeLog,v 1.98 2007/07/18 00:58:25 ribosome Exp $
+
+*prosite-20.16 (18 Jul 2007)
+
+  18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +prosite-20.16.ebuild:
+  New upstream version.
 
 *prosite-20.12 (22 May 2007)
 
diff --git a/sci-biology/prosite/files/digest-prosite-20.16 b/sci-biology/prosite/files/digest-prosite-20.16
new file mode 100644
index 000000000000..1205cddb483e
--- /dev/null
+++ b/sci-biology/prosite/files/digest-prosite-20.16
@@ -0,0 +1,3 @@
+MD5 27da0642ed7d4e0ba28be901102a30df prosite-20.16.tar.bz2 5261819
+RMD160 2fba63783b6694afb28b9b5c8f7f096d51582708 prosite-20.16.tar.bz2 5261819
+SHA256 35d03c4ca41da28766acebe208b4671e6a0d4e6f3c45c6e2fd0d66a934c4efa8 prosite-20.16.tar.bz2 5261819
diff --git a/sci-biology/prosite/prosite-20.16.ebuild b/sci-biology/prosite/prosite-20.16.ebuild
new file mode 100644
index 000000000000..b21512d292c5
--- /dev/null
+++ b/sci-biology/prosite/prosite-20.16.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/prosite/prosite-20.16.ebuild,v 1.1 2007/07/18 00:58:25 ribosome Exp $
+
+DESCRIPTION="A protein families and domains database"
+LICENSE="swiss-prot"
+HOMEPAGE="http://ca.expasy.org/prosite"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86"
+
+DEPEND="emboss? ( >=sci-biology/emboss-3.0.0 )"
+
+src_compile() {
+	if use emboss; then
+		mkdir PROSITE
+		echo
+		einfo "Indexing PROSITE for usage with EMBOSS."
+		EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die \
+			"Indexing PROSITE failed."
+		echo
+	fi
+}
+
+src_install() {
+	if ! use minimal; then
+		insinto /usr/share/${PN}
+		doins *.{doc,dat,lis} || die "Installing raw database failed."
+	fi
+	dodoc *.txt || die "Documentation installation failed."
+	dohtml *.htm || die "HTML documentation installation failed."
+	insinto /usr/share/doc/${PF}
+	doins *.pdf || die "PDF documentation installation failed."
+	if use emboss; then
+		insinto /usr/share/EMBOSS/data/PROSITE
+		doins PROSITE/* || die "Installing EMBOSS data files failed."
+	fi
+}