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ribosome 09/09/01 19:26:04 |
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|
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Modified: ChangeLog |
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Added: emboss-6.1.0.ebuild |
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Log: |
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New upstream version. |
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(Portage version: 2.2_rc40/cvs/Linux x86_64) |
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|
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Revision Changes Path |
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1.52 sci-biology/emboss/ChangeLog |
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|
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/emboss/ChangeLog?rev=1.52&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/emboss/ChangeLog?rev=1.52&content-type=text/plain |
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diff : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/emboss/ChangeLog?r1=1.51&r2=1.52 |
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|
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Index: ChangeLog |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v |
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retrieving revision 1.51 |
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retrieving revision 1.52 |
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diff -u -r1.51 -r1.52 |
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--- ChangeLog 1 Sep 2009 18:18:17 -0000 1.51 |
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+++ ChangeLog 1 Sep 2009 19:26:04 -0000 1.52 |
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@@ -1,6 +1,11 @@ |
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# ChangeLog for sci-biology/emboss |
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# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 |
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-# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.51 2009/09/01 18:18:17 ribosome Exp $ |
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+# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.52 2009/09/01 19:26:04 ribosome Exp $ |
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+ |
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+*emboss-6.1.0 (01 Sep 2009) |
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+ |
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+ 01 Sep 2009; Olivier Fisette <ribosome@g.o> +emboss-6.1.0.ebuild: |
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+ New upstream version. |
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|
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01 Sep 2009; Olivier Fisette <ribosome@g.o> emboss-6.0.1.ebuild: |
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Stabilised on x86 and amd64. |
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|
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|
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|
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1.1 sci-biology/emboss/emboss-6.1.0.ebuild |
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|
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file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/emboss/emboss-6.1.0.ebuild?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/emboss/emboss-6.1.0.ebuild?rev=1.1&content-type=text/plain |
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|
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Index: emboss-6.1.0.ebuild |
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=================================================================== |
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# Copyright 1999-2009 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.1.0.ebuild,v 1.1 2009/09/01 19:26:04 ribosome Exp $ |
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|
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inherit eutils |
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|
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DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" |
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HOMEPAGE="http://emboss.sourceforge.net/" |
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SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" |
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LICENSE="GPL-2 LGPL-2" |
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|
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SLOT="0" |
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KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86" |
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IUSE="X png minimal" |
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|
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DEPEND="X? ( x11-libs/libXt ) |
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png? ( |
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sys-libs/zlib |
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media-libs/libpng |
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media-libs/gd |
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) |
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!minimal? ( |
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sci-biology/primer3 |
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sci-biology/clustalw |
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)" |
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|
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RDEPEND="${DEPEND}" |
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|
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PDEPEND="!minimal? ( |
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sci-biology/aaindex |
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sci-biology/cutg |
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sci-biology/prints |
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sci-biology/prosite |
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>=sci-biology/rebase-707 |
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sci-biology/transfac |
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)" |
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|
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S="${WORKDIR}/EMBOSS-${PV}" |
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|
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src_unpack() { |
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unpack ${A} |
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cd "${S}" |
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epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch |
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|
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local link_string="-lX11"; |
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if use png; then |
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link_string="${link_string} -lgd -lpng" |
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fi |
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sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \ |
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|| die "Failed to patch ajax Makefile" |
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} |
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|
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src_compile() { |
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EXTRA_CONF="--includedir=${D}/usr/include/emboss" |
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! use X && EXTRA_CONF="${EXTRA_CONF} --without-x" |
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! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver" |
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|
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econf ${EXTRA_CONF} || die |
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# Do not install the JEMBOSS component (the --without-java configure option |
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# does not work). JEMBOSS will eventually be available as a separate package. |
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sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ |
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Makefile || die |
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emake || die |
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} |
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|
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src_install() { |
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einstall || die "Failed to install program files." |
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|
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dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \ |
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|| die "Failed to install documentation." |
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newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \ |
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|| die "Failed to install Gentoo readme file." |
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|
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# Install env file for setting libplplot and acd files path. |
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cat <<- EOF > 22emboss |
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# plplot libs dir |
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PLPLOT_LIB="/usr/share/EMBOSS/" |
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# ACD files location |
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EMBOSS_ACDROOT="/usr/share/EMBOSS/acd" |
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EOF |
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doenvd 22emboss || die "Failed to install environment file." |
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|
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# Symlink preinstalled docs to "/usr/share/doc". |
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dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die |
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dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die |
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dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die |
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dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die |
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|
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# Remove useless dummy files from the image. |
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rm "${D}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \ |
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|| die "Failed to remove dummy files." |
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|
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# Move the provided codon files to a different directory. This will avoid |
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# user confusion and file collisions on case-insensitive file systems (see |
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# bug #115446). This change is documented in "README.Gentoo". |
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mv "${D}"/usr/share/EMBOSS/data/CODONS \ |
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"${D}"/usr/share/EMBOSS/data/CODONS.orig || \ |
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die "Failed to move CODON directory." |
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|
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# Move the provided restriction enzyme prototypes file to a different name. |
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# This avoids file collisions with versions of rebase that install their |
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# own enzyme prototypes file (see bug #118832). |
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mv "${D}"/usr/share/EMBOSS/data/embossre.equ \ |
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"${D}"/usr/share/EMBOSS/data/embossre.equ.orig || \ |
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die "Failed to move enzyme equivalence file." |
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} |