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Diffstat (limited to 'sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild')
-rw-r--r--sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild200
1 files changed, 200 insertions, 0 deletions
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild
new file mode 100644
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+++ b/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild
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+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+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-20060625.tar.gz )"
+
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~ppc ~ppc64 ~sparc ~x86"
+IUSE="doc mpi X"
+
+DEPEND="app-shells/tcsh
+ dev-lang/perl
+ media-libs/libpng
+ sys-devel/pmake
+ mpi? ( virtual/mpi )
+ X? ( virtual/motif )"
+
+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_Dec2005_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 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 Linux.
+ sed -i -e "s/NCBI_CC = gcc/NCBI_CC = $(tc-getCC)/" linux.ncbi.mk || die
+
+ # GNU make 3.81 is confused by those nightmarish Makefiles, so we use pmake
+ # instead. The right solution would be to fix the Makefiles. (Be my guest.)
+ cd "${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 "${S}"/real || die
+
+ if use mpi; then
+ cd "${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."
+}