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author | 2006-07-21 14:45:20 +0000 | |
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committer | 2006-07-21 14:45:20 +0000 | |
commit | 10634d473bd08d984d420eb2be693ec577fbc976 (patch) | |
tree | df09091b7d5fa2ed7b982b3d08ed50d49141ae39 /sci-biology/emboss | |
parent | Add java-ant-2. (diff) | |
download | gentoo-2-10634d473bd08d984d420eb2be693ec577fbc976.tar.gz gentoo-2-10634d473bd08d984d420eb2be693ec577fbc976.tar.bz2 gentoo-2-10634d473bd08d984d420eb2be693ec577fbc976.zip |
New upstream version
(Portage version: 2.1-r1)
Diffstat (limited to 'sci-biology/emboss')
-rw-r--r-- | sci-biology/emboss/ChangeLog | 8 | ||||
-rw-r--r-- | sci-biology/emboss/emboss-4.0.0.ebuild | 84 | ||||
-rw-r--r-- | sci-biology/emboss/files/digest-emboss-4.0.0 | 3 |
3 files changed, 94 insertions, 1 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/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 |