diff options
| -rw-r--r-- | sci-biology/ncbi-tools/ChangeLog | 7 | ||||
| -rw-r--r-- | sci-biology/ncbi-tools/Manifest | 14 | ||||
| -rw-r--r-- | sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild | 218 |
3 files changed, 227 insertions, 12 deletions
diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog index 8cbe72babd70..d71a45a9227a 100644 --- a/sci-biology/ncbi-tools/ChangeLog +++ b/sci-biology/ncbi-tools/ChangeLog @@ -1,6 +1,11 @@ # ChangeLog for sci-biology/ncbi-tools # Copyright 2000-2008 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.60 2008/04/08 21:35:34 dberkholz Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.61 2008/04/15 01:21:30 je_fro Exp $ + +*ncbi-tools-20080302 (15 Apr 2008) + + 15 Apr 2008; Jeff Gardner <je_fro@gentoo.org> +ncbi-tools-20080302.ebuild: + Latest release from NCBI. 08 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>; Manifest: Fix manifest, connection dropped mid-commit. diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest index 178517f68c8c..e4e9e624a3fd 100644 --- a/sci-biology/ncbi-tools/Manifest +++ b/sci-biology/ncbi-tools/Manifest @@ -1,6 +1,3 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - 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-iD8DBQFH++blXVaO67S1rtsRAtyLAJ9o3xZugvFtxF0IjOS1NgXrLcHQPACfSACq -ew1dOyCE2f2bG0AmOrsF0sY= -=JTrY ------END PGP SIGNATURE----- diff --git a/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild new file mode 100644 index 000000000000..e0b5b49b6a10 --- /dev/null +++ b/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild @@ -0,0 +1,218 @@ +# Copyright 1999-2008 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20080302.ebuild,v 1.1 2008/04/15 01:21:30 je_fro Exp $ + +inherit flag-o-matic toolchain-funcs eutils autotools + +DESCRIPTION="Development toolkit and applications for computational biology" +LICENSE="public-domain" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/" +SRC_URI="mirror://gentoo/${P}.tar.gz + doc? ( mirror://gentoo/${PN}-sdk-doc.tar.bz2 )" + +# mpi? ( mirror://gentoo/mpiblast-20070826.tar.gz ) + +SLOT="0" +KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86" + +# IUSE="doc mpi X" +# mpiblast 1.5.0beta1 doesn't compile as advertised with this ncbi release. +# Currently seeking a fix. + +IUSE="doc X" + +DEPEND="app-shells/tcsh + dev-lang/perl + media-libs/libpng + sys-devel/pmake + X? ( virtual/motif )" + +# mpi? ( virtual/mpi ) + +S="${WORKDIR}/ncbi" + +EXTRA_VIB="asn2all asn2asn" + +pkg_setup() { + echo + ewarn 'Please note that the NCBI toolkit (and especially the X' + ewarn 'applications) are known to have compilation and run-time' + ewarn 'problems when compiled with agressive compilation flags. The' + ewarn '"-O3" flag is filtered by the ebuild on the x86 architecture if' + ewarn 'X support is enabled.' + echo +} + +src_unpack() { + unpack ${A} + cd "${S}" + + epatch "${FILESDIR}"/${PN}-extra_vib.patch + + if use ppc64; then + epatch "${FILESDIR}"/${PN}-lop.patch + fi + +# if use mpi; then +# cd "${WORKDIR}" +# epatch "${WORKDIR}"/mpiblast/ncbi_Mar2007_evalue.patch +# fi + + if ! use X; then + cd "${S}"/make + sed -e "s:\#set HAVE_OGL=0:set HAVE_OGL=0:" \ + -e "s:\#set HAVE_MOTIF=0:set HAVE_MOTIF=0:" \ + -i makedis.csh || die + else + if use x86; then + # X applications segfault on startup on x86 with -O3. + replace-flags '-O3' '-O2' + fi + fi + + # Apply user C flags... + cd "${S}"/platform + # ... on x86... + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O3 -mcpu=pentium4/NCBI_LDFLAGS1 = ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O3 -mcpu=pentium4/NCBI_OPTFLAG = ${CFLAGS}/" \ + -i linux-x86.ncbi.mk || die + # ... on alpha... + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O3 -mieee/NCBI_LDFLAGS1 = -mieee ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O3 -mieee/NCBI_OPTFLAG = -mieee ${CFLAGS}/" \ + -i linux-alpha.ncbi.mk || die + # ... on hppa... + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \ + -i hppalinux.ncbi.mk || die + # ... on ppc... + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O2/NCBI_LDFLAGS1 = ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O2/NCBI_OPTFLAG = ${CFLAGS}/" \ + -i ppclinux.ncbi.mk || die + # ... on generic 64-bit Linux... + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \ + -i linux64.ncbi.mk || die + # ... on generic Linux. + sed -e "s/NCBI_CFLAGS1 = -c/NCBI_CFLAGS1 = -c ${CFLAGS}/" \ + -e "s/NCBI_LDFLAGS1 = -O3/NCBI_LDFLAGS1 = ${CFLAGS}/" \ + -e "s/NCBI_OPTFLAG = -O3/NCBI_OPTFLAG = ${CFLAGS}/" \ + -i linux.ncbi.mk || die + + # Put in our MAKEOPTS (doesn't work). + # sed -e "s:make \$MFLG:make ${MAKEOPTS}:" -i ncbi/make/makedis.csh + + # Set C compiler... + # ... on x86... + sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-x86.ncbi.mk || die + # ... on alpha... + sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux-alpha.ncbi.mk || die + # ... on hppa... + sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" hppalinux.ncbi.mk || die + # ... on ppc... + sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" ppclinux.ncbi.mk || die + # ... on generic 64-bit Linux... + sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux64.ncbi.mk || die + # ... on generic Linux. + sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die + + # We use dynamic libraries + sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die + + # GNU make 3.81 is confused by those nightmarish Makefiles, so we use pmake + # instead. The right solution would be to fix the Makefiles. (Be my guest.) + cd "${S}"/make + sed -i -e "s%CMD='make%CMD='/usr/bin/pmake%" makedis.csh || die \ + "Failed to replace make by pmake." +} + +src_compile() { + export EXTRA_VIB + cd "${WORKDIR}" + ncbi/make/makedis.csh || die + mkdir "${S}"/cgi + mkdir "${S}"/real + mv "${S}"/bin/*.cgi "${S}"/cgi || die + mv "${S}"/bin/*.REAL "${S}"/real || die + +# mpiblast fails to compile... perhaps mpiblast2 contain a fix +# if use mpi; then +# cd "${WORKDIR}"/mpiblast +# AM_OPT="-a" +# eautoreconf +# econf --with-ncbi="${WORKDIR}"/ncbi --with-mpi=/usr || die +# emake || die +# fi +} + +src_install() { + dobin "${S}"/bin/* || die "Failed to install binaries." + for i in ${EXTRA_VIB}; do + dobin "${S}"/build/${i} || die "Failed to install binaries." + done + dolib "${S}"/lib/* || die "Failed to install libraries." + mkdir -p "${D}"/usr/include/ncbi + cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \ + die "Failed to install headers." + +# if use mpi; then +# cd "${WORKDIR}"/mpiblast +# make install DESTDIR="${D}" || die "Failed to install MPI blast." +# fi + + # TODO: Web apps + #insinto /usr/share/ncbi/lib/cgi + #doins ${S}/cgi/* + #insinto /usr/share/ncbi/lib/real + #doins ${S}/real/* + # TODO: Add support for wwwblast. + + # Basic documentation + dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || \ + die "Failed to install basic documentation." + newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \ + die "Failed renaming fa2htgs documentation." + newdoc "${S}"/config/README README.config || \ + die "Failed renaming config documentation." + newdoc "${S}"/network/encrypt/README README.encrypt || \ + die "Failed renaming encrypt documentation." + newdoc "${S}"/network/nsclilib/readme README.nsclilib || \ + die "Failed renaming nsclilib documentation." + newdoc "${S}"/sequin/README README.sequin || \ + die "Failed renaming sequin documentation." + doman "${S}"/doc/man/* || \ + die "Failed to install man pages." + + # Hypertext user documentation + dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \ + die "Failed to install HTML documentation." + insinto /usr/share/doc/${PF}/html/blast + doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation." + + # Developer documentation + if use doc; then + # Hypertext SDK documentation + insinto /usr/share/doc/${PF}/html/sdk + doins "${WORKDIR}"/${PN}-sdk-doc/* || die + + # Demo programs + mkdir "${D}"/usr/share/ncbi + mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die + fi + + # Shared data (similarity matrices and such) and database directory. + insinto /usr/share/ncbi/data + doins "${S}"/data/* || die "Failed to install shared data." + dodir /usr/share/ncbi/formatdb || die + + # Default config file to set the path for shared data. + insinto /etc/ncbi + newins "${FILESDIR}"/ncbirc .ncbirc || die "Failed to install config file." + + # Env file to set the location of the config file and BLAST databases. + newenvd "${FILESDIR}"/21ncbi-r1 21ncbi || die "Failed to install env file." +} |