diff options
Diffstat (limited to 'sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild')
-rw-r--r-- | sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild | 200 |
1 files changed, 0 insertions, 200 deletions
diff --git a/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild deleted file mode 100644 index e60875c..0000000 --- a/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild +++ /dev/null @@ -1,200 +0,0 @@ -# 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." -} |