New upstream version.

Package-Manager: portage-2.2_rc40/cvs/Linux x86_64

3 files changed, 115 insertions, 2 deletions

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index 2e0b86153478..3f09f3698d56 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/emboss
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.51 2009/09/01 18:18:17 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.52 2009/09/01 19:26:04 ribosome Exp $
+
+*emboss-6.1.0 (01 Sep 2009)
+
+  01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +emboss-6.1.0.ebuild:
+  New upstream version.
 
   01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.0.1.ebuild:
   Stabilised on x86 and amd64.
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index ea14851dbbca..3d8eb3284d3f 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -4,7 +4,9 @@ AUX emboss-5.0.0-as-needed.patch 1751 RMD160 f43faab31a3d5afb4b73704ba597de57866
 AUX emboss-README.Gentoo-1 1474 RMD160 a116b4516cd0d8e0b28734bf1e51f1e0833737c4 SHA1 ec23610137ebddc3fc15976757d2cdebd741f9ec SHA256 e97558bbc8296f2e9395080061e494b282303ed69e1d6eb45554846617b47abd
 DIST EMBOSS-4.0.0.tar.gz 17651607 RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 SHA1 784c729f2d2e746339a90048277c9e4f052e036a SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231
 DIST EMBOSS-6.0.1.tar.gz 20204153 RMD160 c97673670a110b51a6c1d1a0305451c44cd7b504 SHA1 ea6fa6e1e4222bc57e748a4d674d72d9b03475dd SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
+DIST EMBOSS-6.1.0.tar.gz 21968220 RMD160 2eb01da419464ccbc53a95407df0243d00be8720 SHA1 2f2a48d7aa66a8852c1dd531cfe061b024521c33 SHA256 033d205c108e10e314b1ca61ec026a4a7fec2780e8781da67b0e16825b63af41
 EBUILD emboss-4.0.0.ebuild 3016 RMD160 58843ed818c0b377160a24890f6a423b037dada4 SHA1 0c0c3940a92023f3a12b04b1e18b52d4ffda3112 SHA256 87799af4224869fde9ef40fd9944fc5559af935f7a324aadd2acce98a2dd9e3d
 EBUILD emboss-6.0.1.ebuild 3479 RMD160 ad0392ebaa1a6ec78c65c8f7f037879fc459f1a8 SHA1 67402d66d7e605d8e89686642f6991d3a3c6b2a0 SHA256 0810a2d3cde0f42c0ab59fa93b70edfeaefc7ed22762eb98c827e054603e819b
-MISC ChangeLog 8968 RMD160 37ea2c9169f62fc491ea7b269e1bd7489be5f68f SHA1 a7c029669a93a660e8fc673a128c25c4ae4e4a94 SHA256 e0623664ae0890e3c6b7e64376e9dfbb4c7ce9bb54c0fbf487198d8e2237ba1e
+EBUILD emboss-6.1.0.ebuild 3471 RMD160 a4b498e6bfb101fd8ab3e750261db9a78626d434 SHA1 f712c1121bc661589869122f709b321fec3c3dcd SHA256 e09a5359bddf52bfefd97d11ac86e81a7e87502dd8591a2ae55445af90c9b59c
+MISC ChangeLog 9097 RMD160 1d5f76c5efd38204bc8371084d2bb364268ef5aa SHA1 99b2b707d082f5018bf88aed69d3de421b544a5a SHA256 9995724bb7c00c536c46fd0203ddceac9e1485c3554efc33a2aa96a0697d9176
 MISC metadata.xml 1021 RMD160 ee767f436af5f815ecb9526df9063438dab8eb14 SHA1 eff46db435f88e0b457ce2a38e5ff786ae6324e1 SHA256 0c5af548d0483d41a3344695cb04acaf0974fb56b70bc1e2ec0a9749ecbc45a0
diff --git a/sci-biology/emboss/emboss-6.1.0.ebuild b/sci-biology/emboss/emboss-6.1.0.ebuild
new file mode 100644
index 000000000000..27ba2c556559
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.1.0.ebuild
@@ -0,0 +1,106 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.1.0.ebuild,v 1.1 2009/09/01 19:26:04 ribosome Exp $
+
+inherit eutils
+
+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
+	)"
+
+RDEPEND="${DEPEND}"
+
+PDEPEND="!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/prints
+		sci-biology/prosite
+		>=sci-biology/rebase-707
+		sci-biology/transfac
+	)"
+
+S="${WORKDIR}/EMBOSS-${PV}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch
+
+	local link_string="-lX11";
+	if use png; then
+		link_string="${link_string} -lgd -lpng"
+	fi
+	sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
+		|| die "Failed to patch ajax Makefile"
+}
+
+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."
+}