Updated package app-sci/emboss

12 files changed, 111 insertions, 174 deletions

diff --git a/app-sci/emboss/ChangeLog b/app-sci/emboss/ChangeLog
index 61c31ad58e83..95aec1737421 100644
--- a/app-sci/emboss/ChangeLog
+++ b/app-sci/emboss/ChangeLog
@@ -1,6 +1,19 @@
 # ChangeLog for app-sci/emboss
 # Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/ChangeLog,v 1.9 2004/06/24 21:57:40 agriffis Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/ChangeLog,v 1.10 2004/07/15 02:06:20 ribosome Exp $
+
+  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:
diff --git a/app-sci/emboss/Manifest b/app-sci/emboss/Manifest
index 8978e5efa264..2de7d6998adc 100644
--- a/app-sci/emboss/Manifest
+++ b/app-sci/emboss/Manifest
@@ -1,22 +1,7 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
-MD5 622eb23718e8d96a4c19f0b9ba7a838f ChangeLog 1236
-MD5 962ddde274b3c68aa058d87635e91691 emboss-2.7.1.ebuild 1204
-MD5 65b761fd4940716d5e143b85020d696f emboss-2.8.0.ebuild 1146
-MD5 8c623e53daafa025137077c6b65815bd metadata.xml 156
-MD5 adb6b19caeae014710e371ce79ce5153 emboss-2.8.0-r1.ebuild 1405
-MD5 d4836dcee22f76b65e5c06d7aae74c30 emboss-2.8.0-r2.ebuild 1423
-MD5 cdf8dfd33e803ec4429d2ecfc2931b39 files/22emboss 120
-MD5 e0cdf72a0fd91e172b9a2831546e7a41 files/digest-emboss-2.7.1 66
-MD5 048d6642b77660671ad5c64cdc351df6 files/digest-emboss-2.8.0 66
-MD5 048d6642b77660671ad5c64cdc351df6 files/digest-emboss-2.8.0-r1 66
-MD5 ef2dfa3d13837026f59c0cf5f04f67c5 files/22emboss-r1 110
+MD5 7c123e17854b7ea6afdb0db6cbb0a611 emboss-2.8.0-r2.ebuild 1422
+MD5 f37e96bcaf37a2775370a9c875fc7eb7 ChangeLog 2044
+MD5 6051afb1f26bf343082490327784b958 metadata.xml 1013
+MD5 6df12f4b1a53fd29595f1543331abc34 emboss-2.8.0-r3.ebuild 2033
 MD5 048d6642b77660671ad5c64cdc351df6 files/digest-emboss-2.8.0-r2 66
------BEGIN PGP SIGNATURE-----
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-
-iD8DBQFA4vUTHTu7gpaalycRAmu6AJ0dq+Ex9Gc1TWomKauVb983e5K6qwCfSGTj
-vb03p+12fPcJfjjYkMphvvI=
-=yaND
------END PGP SIGNATURE-----
+MD5 048d6642b77660671ad5c64cdc351df6 files/digest-emboss-2.8.0-r3 66
+MD5 ef2dfa3d13837026f59c0cf5f04f67c5 files/22emboss-r1 110
diff --git a/app-sci/emboss/emboss-2.7.1.ebuild b/app-sci/emboss/emboss-2.7.1.ebuild
deleted file mode 100644
index 985daa6d6800..000000000000
--- a/app-sci/emboss/emboss-2.7.1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/emboss-2.7.1.ebuild,v 1.7 2004/06/30 17:14:33 vapier Exp $
-
-DESCRIPTION="The European Molecular Biology Open Software Suite: EMBOSS is a package of high-quality FREE Open Source software for sequence analysis"
-HOMEPAGE="http://www.emboss.org/"
-SRC_URI="ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
-
-LICENSE="GPL-2 LGPL-2"
-SLOT="0"
-KEYWORDS="x86"
-IUSE="png X"
-
-DEPEND="X? ( virtual/x11 )
-	png? ( >=sys-libs/zlib-1.1.4
-	>=media-libs/libpng-1.2.4
-	>=media-libs/gd-1.8.4 )"
-
-S=${WORKDIR}/EMBOSS-${PV}
-
-src_install() {
-	einstall || die
-
-	# env file
-	dodir /etc/env.d
-	insinto /etc/env.d
-	doins ${FILESDIR}/22emboss
-
-	#install files...
-	dodoc AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS LICENSE README THANKS NEWS ONEWS PROBLEMS
-
-	# symlink preinstalled docs to /usr/share...
-	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${P}/manuals
-	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${P}/programs
-	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${P}/tutorials
-
-
-}
-
-src_compile() {
-
-	econf || die
-	emake || die
-}
-
diff --git a/app-sci/emboss/emboss-2.8.0-r1.ebuild b/app-sci/emboss/emboss-2.8.0-r1.ebuild
deleted file mode 100644
index 7737d6b2f7ec..000000000000
--- a/app-sci/emboss/emboss-2.8.0-r1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/emboss-2.8.0-r1.ebuild,v 1.4 2004/06/30 17:14:33 vapier Exp $
-
-DESCRIPTION="The European Molecular Biology Open Software Suite: EMBOSS is a package of high-quality FREE Open Source software for sequence analysis"
-HOMEPAGE="http://www.emboss.org/"
-SRC_URI="ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
-
-LICENSE="GPL-2 LGPL-2"
-SLOT="0"
-KEYWORDS="~x86"
-IUSE="X png"
-
-DEPEND="X? ( virtual/x11
-	png? ( >=sys-libs/zlib-1.1.4
-		>=media-libs/libpng-1.2.4
-		>=media-libs/gd-1.8.4 )
-	)"
-
-S=${WORKDIR}/EMBOSS-${PV}
-
-src_compile() {
-
-	local myconf
-	if ! use X
-	then
-		myconf="--without-x --without-pngdriver"
-	else
-		if ! use png
-		then
-			myconf="${myconf} --without-pngdriver"
-		fi
-	fi
-
-
-	ewarn "myconf: ${myconf}"
-
-	econf ${myconf} || die
-	emake || die
-
-}
-
-src_install() {
-	einstall || die
-
-	# env file
-	dodir /etc/env.d
-	insinto /etc/env.d
-	doins ${FILESDIR}/22emboss
-
-	#install files...
-	dodoc AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS LICENSE README THANKS NEWS ONEWS PROBLEMS
-
-	# symlink preinstalled docs to /usr/share...
-	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${P}/manuals
-	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${P}/programs
-	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${P}/tutorials
-
-
-}
diff --git a/app-sci/emboss/emboss-2.8.0-r2.ebuild b/app-sci/emboss/emboss-2.8.0-r2.ebuild
index 8a2c3c53603d..064aaf9e678f 100644
--- a/app-sci/emboss/emboss-2.8.0-r2.ebuild
+++ b/app-sci/emboss/emboss-2.8.0-r2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2004 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/emboss-2.8.0-r2.ebuild,v 1.5 2004/06/30 17:14:33 vapier Exp $
+# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/emboss-2.8.0-r2.ebuild,v 1.6 2004/07/15 02:06:20 ribosome Exp $
 
 DESCRIPTION="The European Molecular Biology Open Software Suite: EMBOSS is a package of high-quality FREE Open Source software for sequence analysis"
 HOMEPAGE="http://www.emboss.org/"
@@ -8,7 +8,7 @@ SRC_URI="ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
 
 LICENSE="GPL-2 LGPL-2"
 SLOT="0"
-KEYWORDS="~x86 ~ppc"
+KEYWORDS="x86 ~ppc"
 IUSE="X png"
 
 DEPEND="X? ( virtual/x11
diff --git a/app-sci/emboss/emboss-2.8.0-r3.ebuild b/app-sci/emboss/emboss-2.8.0-r3.ebuild
new file mode 100644
index 000000000000..8dc704d73c43
--- /dev/null
+++ b/app-sci/emboss/emboss-2.8.0-r3.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/emboss-2.8.0-r3.ebuild,v 1.1 2004/07/15 02:06:20 ribosome Exp $
+
+DESCRIPTION="The European Molecular Biology Open Software Suite: a sequence analysis package."
+HOMEPAGE="http://www.emboss.org/"
+SRC_URI="ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
+LICENSE="GPL-2 LGPL-2"
+
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="X png icc no-biodata"
+
+RDEPEND="X? ( virtual/x11 )
+	png? (
+		sys-libs/zlib
+		media-libs/libpng
+		>=media-libs/gd-1.8
+	)
+	app-sci/primer3
+	app-sci/clustalw"
+
+PDEPEND="!no-biodata? (
+		app-sci/aaindex
+		app-sci/cutg
+		app-sci/prints
+		app-sci/prosite
+		app-sci/rebase
+		app-sci/transfac
+	)"
+
+DEPEND="icc? ( dev-lang/icc )
+	${RDEPEND}"
+
+S=${WORKDIR}/EMBOSS-${PV}
+
+src_compile() {
+	if use icc; then
+		CC=/opt/intel/compiler80/bin/icc
+		CXX=/opt/intel/compiler80/bin/icc
+	fi
+	local EXTRA_CONF
+	! use X && EXTRA_CONF="${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 COPYING ChangeLog FAQ INSTALL LICENSE README THANKS NEWS
+
+	# Install env file for setting libplplot and acd files path.
+	insinto /etc/env.d
+	newins ${FILESDIR}/22emboss-r1 22emboss
+
+	# Include files necessary for EMBASSY packages and EMBOSS development.
+	insinto /usr/include/${PN}
+	doins plplot/*.h
+	doins ajax/*.h
+	doins nucleus/*.h
+
+	# 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/app-sci/emboss/emboss-2.8.0.ebuild b/app-sci/emboss/emboss-2.8.0.ebuild
deleted file mode 100644
index 7d4374b29f1f..000000000000
--- a/app-sci/emboss/emboss-2.8.0.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/emboss/emboss-2.8.0.ebuild,v 1.6 2004/06/30 17:14:33 vapier Exp $
-
-DESCRIPTION="The European Molecular Biology Open Software Suite: EMBOSS is a package of high-quality FREE Open Source software for sequence analysis"
-HOMEPAGE="http://www.emboss.org/"
-SRC_URI="ftp://ftp.uk.embnet.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
-
-LICENSE="GPL-2 LGPL-2"
-SLOT="0"
-KEYWORDS="x86"
-IUSE="png"
-
-DEPEND="virtual/x11
-	png? ( >=sys-libs/zlib-1.1.4
-	>=media-libs/libpng-1.2.4
-	>=media-libs/gd-1.8.4 )"
-
-S=${WORKDIR}/EMBOSS-${PV}
-
-src_install() {
-	einstall || die
-
-	# env file
-	dodir /etc/env.d
-	insinto /etc/env.d
-	doins ${FILESDIR}/22emboss
-
-	#install files...
-	dodoc AUTHORS COMPAT COPYING ChangeLog FAQ INSTALL KNOWN_BUGS LICENSE README THANKS NEWS ONEWS PROBLEMS
-
-	# symlink preinstalled docs to /usr/share...
-	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${P}/manuals
-	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${P}/programs
-	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${P}/tutorials
-
-
-}
diff --git a/app-sci/emboss/files/22emboss b/app-sci/emboss/files/22emboss
deleted file mode 100644
index b6f8e3f0e873..000000000000
--- a/app-sci/emboss/files/22emboss
+++ /dev/null
@@ -1,4 +0,0 @@
-# plplot libs dir
-PLPLOT_LIB="/usr/share/EMBOSS/plplot/lib"
-# ACD files location
-EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
diff --git a/app-sci/emboss/files/digest-emboss-2.7.1 b/app-sci/emboss/files/digest-emboss-2.7.1
deleted file mode 100644
index 772f8cd2c0e6..000000000000
--- a/app-sci/emboss/files/digest-emboss-2.7.1
+++ /dev/null
@@ -1 +0,0 @@
-MD5 7d86aa7101070513b640b265698e8e38 EMBOSS-2.7.1.tar.gz 13394297
diff --git a/app-sci/emboss/files/digest-emboss-2.8.0-r1 b/app-sci/emboss/files/digest-emboss-2.8.0-r1
deleted file mode 100644
index 80470321af64..000000000000
--- a/app-sci/emboss/files/digest-emboss-2.8.0-r1
+++ /dev/null
@@ -1 +0,0 @@
-MD5 5692e52632546dfe4103b51dd1eaa3c3 EMBOSS-2.8.0.tar.gz 14024961
diff --git a/app-sci/emboss/files/digest-emboss-2.8.0 b/app-sci/emboss/files/digest-emboss-2.8.0-r3
index 80470321af64..80470321af64 100644
--- a/app-sci/emboss/files/digest-emboss-2.8.0
+++ b/app-sci/emboss/files/digest-emboss-2.8.0-r3
diff --git a/app-sci/emboss/metadata.xml b/app-sci/emboss/metadata.xml
index b229aec85b8f..ff86b6a3a444 100644
--- a/app-sci/emboss/metadata.xml
+++ b/app-sci/emboss/metadata.xml
@@ -1,5 +1,22 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
+	<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>