| # 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-4.0.0.ebuild,v 1.12 2009/08/31 21:41:26 ribosome Exp $ |
| |
| EAPI=1 |
| |
| 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-1.8 |
| ) |
| !minimal? ( |
| sci-biology/primer3 |
| sci-biology/clustalw:1 |
| ) |
| !<dev-util/pscan-20000721-r1" |
| |
| RDEPEND="${DEPEND}" |
| |
| PDEPEND="!minimal? ( |
| sci-biology/aaindex |
| sci-biology/cutg |
| sci-biology/prints |
| >=sci-biology/prosite-19.7 |
| >=sci-biology/rebase-601-r1 |
| sci-biology/transfac |
| )" |
| |
| S="${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. |
| doenvd "${FILESDIR}"/22emboss || die "Failed to install environment file." |
| |
| # Symlink preinstalled docs to /usr/share/doc. |
| dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${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." |
| } |