diff options
-rw-r--r-- | sci-biology/cutg/ChangeLog | 8 | ||||
-rw-r--r-- | sci-biology/cutg/cutg-160.ebuild | 16 | ||||
-rw-r--r-- | sci-biology/emboss/ChangeLog | 11 | ||||
-rw-r--r-- | sci-biology/emboss/emboss-6.1.0-r1.ebuild | 110 | ||||
-rw-r--r-- | sci-biology/meme/ChangeLog | 8 | ||||
-rw-r--r-- | sci-biology/meme/meme-4.3.0-r1.ebuild | 64 | ||||
-rw-r--r-- | sci-biology/primer3/ChangeLog | 11 | ||||
-rw-r--r-- | sci-biology/primer3/primer3-1.1.4-r1.ebuild | 40 |
8 files changed, 254 insertions, 14 deletions
diff --git a/sci-biology/cutg/ChangeLog b/sci-biology/cutg/ChangeLog index ae22f5ed03b5..e0662433f996 100644 --- a/sci-biology/cutg/ChangeLog +++ b/sci-biology/cutg/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-biology/cutg -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/ChangeLog,v 1.52 2009/09/01 20:54:10 ribosome Exp $ +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/ChangeLog,v 1.53 2010/03/07 20:50:00 jlec Exp $ + + 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> cutg-160.ebuild: + Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, + keyworded as in overlay 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: Giving up maintainership of this package. diff --git a/sci-biology/cutg/cutg-160.ebuild b/sci-biology/cutg/cutg-160.ebuild index 15525aa7685b..5dba4a6b4c31 100644 --- a/sci-biology/cutg/cutg-160.ebuild +++ b/sci-biology/cutg/cutg-160.ebuild @@ -1,6 +1,8 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2010 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/cutg-160.ebuild,v 1.2 2009/08/31 21:13:02 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/cutg-160.ebuild,v 1.3 2010/03/07 20:50:00 jlec Exp $ + +EAPI="3" DESCRIPTION="Codon usage tables calculated from GenBank" LICENSE="public-domain" @@ -11,7 +13,7 @@ SLOT="0" # Minimal build keeps only the indexed files (if applicable) and the # documentation. The non-indexed database is not installed. IUSE="emboss minimal" -KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86" +KEYWORDS="amd64 ~ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" DEPEND="emboss? ( sci-biology/emboss )" RDEPEND="${DEPEND}" @@ -29,17 +31,17 @@ src_compile() { src_install() { if ! use minimal; then - mkdir -p "${D}"usr/share/${PN} - mv *.codon *.spsum "${D}"/usr/share/${PN} || die \ + mkdir -p "${ED}"usr/share/${PN} + mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \ "Installing raw CUTG database failed." fi dodoc README CODON_LABEL SPSUM_LABEL || die \ "Failed to install documentation." if use emboss; then - mkdir -p "${D}"/usr/share/EMBOSS/data/CODONS + mkdir -p "${ED}"/usr/share/EMBOSS/data/CODONS cd CODONS for file in *; do - mv ${file} "${D}"/usr/share/EMBOSS/data/CODONS || die \ + mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS || die \ "Installing the EMBOSS-indexed database failed." done fi diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog index 4ca45c3a1162..de2ba5b04b60 100644 --- a/sci-biology/emboss/ChangeLog +++ b/sci-biology/emboss/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/emboss -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.54 2009/09/01 21:57:55 ribosome Exp $ +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.55 2010/03/07 20:58:42 jlec Exp $ + +*emboss-6.1.0-r1 (07 Mar 2010) + + 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +emboss-6.1.0-r1.ebuild: + Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, + keyworded as in overlay 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: Giving up maintainership of this package. diff --git a/sci-biology/emboss/emboss-6.1.0-r1.ebuild b/sci-biology/emboss/emboss-6.1.0-r1.ebuild new file mode 100644 index 000000000000..485e5d25ddcd --- /dev/null +++ b/sci-biology/emboss/emboss-6.1.0-r1.ebuild @@ -0,0 +1,110 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/emboss-6.1.0-r1.ebuild,v 1.1 2010/03/07 20:58:42 jlec Exp $ + +EAPI="3" + +inherit eutils + +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 ~amd64-linux ~x86-linux ~ppc-macos" +IUSE="X png minimal" + +DEPEND="X? ( x11-libs/libXt ) + png? ( + sys-libs/zlib + media-libs/libpng + media-libs/gd + ) + !minimal? ( + sci-biology/primer3 + sci-biology/clustalw + )" + +RDEPEND="${DEPEND}" + +PDEPEND="!minimal? ( + sci-biology/aaindex + sci-biology/cutg + sci-biology/prints + sci-biology/prosite + >=sci-biology/rebase-707 + sci-biology/transfac + )" + +S="${WORKDIR}/EMBOSS-${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch + + local link_string="-lX11"; + if use png; then + link_string="${link_string} -lgd -lpng" + fi + sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \ + || die "Failed to patch ajax Makefile" +} + +src_configure() { + EXTRA_CONF="--includedir=${ED}/usr/include/emboss" + ! use X && EXTRA_CONF="${EXTRA_CONF} --without-x" + ! use png && EXTRA_CONF="${EXTRA_CONF} --without-pngdriver" + + econf ${EXTRA_CONF} || die + # Do not install the JEMBOSS component (the --without-java configure option + # does not work). JEMBOSS will eventually be available as a separate package. + sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \ + Makefile || die +} + +src_install() { + einstall || die "Failed to install program files." + + dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \ + || die "Failed to install documentation." + newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \ + || die "Failed to install Gentoo readme file." + + # Install env file for setting libplplot and acd files path. + cat <<- EOF > 22emboss + # plplot libs dir + PLPLOT_LIB="${EPREFIX}/usr/share/EMBOSS/" + # ACD files location + EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" + EOF + doenvd 22emboss || die "Failed to install environment file." + + # Symlink preinstalled docs to "/usr/share/doc". + dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${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/${PF}/html || die + + # Remove frestdist documentation conflicting with the EMBASSY philypnew + # package. + rm "${ED}"/usr/share/EMBOSS/doc/programs/text/frestdist.txt || \ + die "Failed to remove duplicated documentation." + + # Remove useless dummy files from the image. + rm "${ED}"/usr/share/EMBOSS/data/{AAINDEX,PRINTS,PROSITE,REBASE}/dummyfile \ + || die "Failed to remove dummy files." + + # Move the provided codon files to a different directory. This will avoid + # user confusion and file collisions on case-insensitive file systems (see + # bug #115446). This change is documented in "README.Gentoo". + mv "${ED}"/usr/share/EMBOSS/data/CODONS \ + "${ED}"/usr/share/EMBOSS/data/CODONS.orig || \ + die "Failed to move CODON directory." + + # Move the provided restriction enzyme prototypes file to a different name. + # This avoids file collisions with versions of rebase that install their + # own enzyme prototypes file (see bug #118832). + mv "${ED}"/usr/share/EMBOSS/data/embossre.equ \ + "${ED}"/usr/share/EMBOSS/data/embossre.equ.orig || \ + die "Failed to move enzyme equivalence file." +} diff --git a/sci-biology/meme/ChangeLog b/sci-biology/meme/ChangeLog index eead4aac10cd..e136263f8321 100644 --- a/sci-biology/meme/ChangeLog +++ b/sci-biology/meme/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/meme # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.13 2010/01/03 14:12:59 pacho Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/ChangeLog,v 1.14 2010/03/07 20:56:03 jlec Exp $ + +*meme-4.3.0-r1 (07 Mar 2010) + + 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> +meme-4.3.0-r1.ebuild: + Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, + keyworded as in overlay 03 Jan 2010; Pacho Ramos <pacho@gentoo.org> meme-4.3.0.ebuild: amd64 stable, bug 298760 diff --git a/sci-biology/meme/meme-4.3.0-r1.ebuild b/sci-biology/meme/meme-4.3.0-r1.ebuild new file mode 100644 index 000000000000..2b8bc777833a --- /dev/null +++ b/sci-biology/meme/meme-4.3.0-r1.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/meme/meme-4.3.0-r1.ebuild,v 1.1 2010/03/07 20:56:03 jlec Exp $ + +EAPI="3" + +inherit autotools eutils + +DESCRIPTION="The MEME/MAST system - Motif discovery and search" +HOMEPAGE="http://meme.sdsc.edu/meme" +SRC_URI="http://meme.nbcr.net/downloads/${PN}_${PV}.tar.gz" +LICENSE="meme" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" + +IUSE="mpi" + +DEPEND="dev-libs/libxml2 + dev-libs/libxslt + app-shells/tcsh + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${PN}_${PV}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-4.0.0-Makefile.am.patch + eautoreconf +} + +src_configure() { + MY_PREFIX="${EROOT}opt/meme" + USE_DISABLE_MPI=""; if ! use mpi; then USE_DISABLE_MPI="--enable-serial"; fi + econf --prefix=$MY_PREFIX --sysconfdir=${MY_PREFIX}/etc \ + --with-logs="${EROOT}var/log/meme" \ + $USE_DISABLE_MPI + # $(use_enable openmp) +} + +#pkg_setup() { + # generate meme group to restrict logging to /var/log/meme +# enewgroup meme +#} + +src_install() { + emake install DESTDIR="${D}" || die "Failed to install program files." + echo "PATH=${EPREFIX}/opt/${PN}/bin" > 99${PN} + doenvd 99${PN} || die + # allow logging only for members of meme group + # diropts -m 0770 -g meme -o root + diropts -m ugo+rwxt -o root + keepdir /var/log/meme +} + +#pkg_postinst() { +# einfo 'Log files are produced in the "/var/log/meme" directory. Users' +# einfo 'need to be part of the meme group to use this facility.' +#} + +src_test() { + # bug #297070 + emake -j1 test || die "Regression tests failed." +} diff --git a/sci-biology/primer3/ChangeLog b/sci-biology/primer3/ChangeLog index da40f6f2ea79..f70008b4d463 100644 --- a/sci-biology/primer3/ChangeLog +++ b/sci-biology/primer3/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-biology/primer3 -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.21 2009/09/01 16:07:03 ribosome Exp $ +# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/ChangeLog,v 1.22 2010/03/07 20:53:15 jlec Exp $ + +*primer3-1.1.4-r1 (07 Mar 2010) + + 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> + +primer3-1.1.4-r1.ebuild: + Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, + keyworded as in overlay 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> primer3-1.1.4.ebuild: Stabilised on x86 and amd64. diff --git a/sci-biology/primer3/primer3-1.1.4-r1.ebuild b/sci-biology/primer3/primer3-1.1.4-r1.ebuild new file mode 100644 index 000000000000..65e39e19f6f5 --- /dev/null +++ b/sci-biology/primer3/primer3-1.1.4-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/primer3/primer3-1.1.4-r1.ebuild,v 1.1 2010/03/07 20:53:15 jlec Exp $ + +EAPI="3" + +DESCRIPTION="Design primers for PCR reactions." +HOMEPAGE="http://primer3.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +LICENSE="whitehead" + +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris" +IUSE="" + +DEPEND="dev-lang/perl" + +RDEPEND="" + +S="${WORKDIR}/src" + +src_prepare() { + [[ ${CHOST} == *-darwin* ]] && \ + sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile +} + +src_compile() { + emake -e || die +} + +src_test () { + make primer_test || die +} + +src_install () { + dobin long_seq_tm_test ntdpal oligotm primer3_core || die \ + "Could not install program." + dodoc ../{how-to-cite.txt,README.txt,example} || die \ + "Could not install documentation." +} |