New upstream version

Package-Manager: portage-2.1-r1

4 files changed, 106 insertions, 5 deletions

diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog
index a0ea73cb44fd..77c5c6ff683d 100644
--- a/sci-biology/emboss/ChangeLog
+++ b/sci-biology/emboss/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/emboss
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.33 2006/04/20 01:09:45 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.34 2006/07/21 14:45:20 ribosome Exp $
+
+*emboss-4.0.0 (21 Jul 2006)
+
+  21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +emboss-4.0.0.ebuild:
+  New upstream version. See change log:
+  "http://emboss.sourceforge.net/developers/changelog.html".
 
   20 Apr 2006; Olivier Fisette <ribosome@gentoo.org> -emboss-3.0.0.ebuild:
   Removed old revision.
diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index f462a5faabe7..f082674fe998 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -7,14 +7,19 @@ MD5 615888722f8d6a0c918f936e0cc1cfcd files/README.Gentoo 1326
 RMD160 bfaa4d7d1218d3bd4ea58d54d000da7f58b6bca6 files/README.Gentoo 1326
 SHA256 33b517b977cc85824847bd6cf4113489a5554fb014f1a6b1d22d6f80c3487e9f files/README.Gentoo 1326
 DIST EMBOSS-3.0.0.tar.gz 16257908
+DIST EMBOSS-4.0.0.tar.gz 17651607 RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 SHA1 784c729f2d2e746339a90048277c9e4f052e036a SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231
 EBUILD emboss-3.0.0-r1.ebuild 2948 RMD160 f11fdb1915a5d2617ec7fac90eac23a28a995d5b SHA1 192b9ffdb0d0d94b2255c4b596d7228ec30a7c5b SHA256 5746e17de8b1b4c0523b4cf04e721312b4890299311393b076d5551e85cf87d7
 MD5 4194379dc2f45d117ac8eba69934c27d emboss-3.0.0-r1.ebuild 2948
 RMD160 f11fdb1915a5d2617ec7fac90eac23a28a995d5b emboss-3.0.0-r1.ebuild 2948
 SHA256 5746e17de8b1b4c0523b4cf04e721312b4890299311393b076d5551e85cf87d7 emboss-3.0.0-r1.ebuild 2948
-MISC ChangeLog 6487 RMD160 6270ccf1b031c83eb29a8453f026023aa591d5c5 SHA1 03d10c702834b247f2c00b5ef79eef62dce9d6f1 SHA256 4841638c868680b3f0c80bfbb48df6b218c453adda140ca6b7f44b42b2db74cd
-MD5 95d37ca94e9f151baa361c99256be065 ChangeLog 6487
-RMD160 6270ccf1b031c83eb29a8453f026023aa591d5c5 ChangeLog 6487
-SHA256 4841638c868680b3f0c80bfbb48df6b218c453adda140ca6b7f44b42b2db74cd ChangeLog 6487
+EBUILD emboss-4.0.0.ebuild 3046 RMD160 6cffbd7fec68b1fd132bf57ca2e9f7e90be75a54 SHA1 355c0b9e2a5fc83c02c53aa0ae98da16a0e2bdab SHA256 c669f4c938048b1bcb050c1fe0fa2f9eb0d4f5be0f26e6ec77f03f057547fc85
+MD5 55d3c62f4ba17e6699033483df42b1fd emboss-4.0.0.ebuild 3046
+RMD160 6cffbd7fec68b1fd132bf57ca2e9f7e90be75a54 emboss-4.0.0.ebuild 3046
+SHA256 c669f4c938048b1bcb050c1fe0fa2f9eb0d4f5be0f26e6ec77f03f057547fc85 emboss-4.0.0.ebuild 3046
+MISC ChangeLog 6693 RMD160 626841069b9be7e497ca1b5100d949d467f3abb9 SHA1 8d205fef046406fd6c86781630fcb7cb175976ea SHA256 853076005d83bbb12ee06b3750b14b09697b2f04b5217227aa24f70022e10945
+MD5 eb6bad94f37e3e1f9ede7f3dfa69f7d6 ChangeLog 6693
+RMD160 626841069b9be7e497ca1b5100d949d467f3abb9 ChangeLog 6693
+SHA256 853076005d83bbb12ee06b3750b14b09697b2f04b5217227aa24f70022e10945 ChangeLog 6693
 MISC metadata.xml 1021 RMD160 ee767f436af5f815ecb9526df9063438dab8eb14 SHA1 eff46db435f88e0b457ce2a38e5ff786ae6324e1 SHA256 0c5af548d0483d41a3344695cb04acaf0974fb56b70bc1e2ec0a9749ecbc45a0
 MD5 ecba11e4d50ee5cc740817f5becffa83 metadata.xml 1021
 RMD160 ee767f436af5f815ecb9526df9063438dab8eb14 metadata.xml 1021
@@ -22,3 +27,6 @@ SHA256 0c5af548d0483d41a3344695cb04acaf0974fb56b70bc1e2ec0a9749ecbc45a0 metadata
 MD5 84fbde044d74a82c084fa22d5d59ae8e files/digest-emboss-3.0.0-r1 66
 RMD160 bacfaf49534b5313c65e3969685f9867550c34b0 files/digest-emboss-3.0.0-r1 66
 SHA256 bdca0dd643312ce9f1a2bbeec7c2098c12ad1427ce475be0d73270a4b4eee891 files/digest-emboss-3.0.0-r1 66
+MD5 868d3a498e023c8ac4cd1ae2504bc8b0 files/digest-emboss-4.0.0 244
+RMD160 9ceca3f11bf27999c9a49c4ae6a438ef8640762f files/digest-emboss-4.0.0 244
+SHA256 4c40525329b260ca9b0ee00d4275b85fd29fc0ea18c51d58dac8534dd19b8179 files/digest-emboss-4.0.0 244
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."
+}
diff --git a/sci-biology/emboss/files/digest-emboss-4.0.0 b/sci-biology/emboss/files/digest-emboss-4.0.0
new file mode 100644
index 000000000000..ffad1f9b9096
--- /dev/null
+++ b/sci-biology/emboss/files/digest-emboss-4.0.0
@@ -0,0 +1,3 @@
+MD5 2ef912cfde4903129f2424d23d6da0d2 EMBOSS-4.0.0.tar.gz 17651607
+RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 EMBOSS-4.0.0.tar.gz 17651607
+SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231 EMBOSS-4.0.0.tar.gz 17651607