# ChangeLog for sci-biology/ncbi-tools
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.77 2010/03/29 09:45:07 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.78 2010/06/24 20:41:40 jlec Exp $
+
+ 24 Jun 2010; Justin Lecher <jlec@gentoo.org> -ncbi-tools-20060507.ebuild,
+ -ncbi-tools-20061015-r1.ebuild, -ncbi-tools-20070826.ebuild,
+ -ncbi-tools-20090301.ebuild:
+ Cleaned old version
29 Mar 2010; Pacho Ramos <pacho@gentoo.org> ncbi-tools-20090809.ebuild:
amd64 stable, bug 298779
AUX ncbi-tools-extra_vib.patch 1393 RMD160 05e2dcf17b6af9475625eb0aa0be6bc96071a923 SHA1 bb92aeada6786d4573f9ad98e3d50b4a4201ba10 SHA256 b7639937d59c8bd636c6b02a65a4469d188645b9a10fffd0c8680fb861a7a8e1
AUX ncbi-tools-lop.patch 701 RMD160 1b9d8d196b1d4f27b090e616c9ac03cb9b4e6a09 SHA1 be28d340be72b9840342b407d95dc2a558e39de9 SHA256 9e5c57e944d23920f196f36912933653c236998729f69f28be8b55964865dfbc
AUX ncbirc 33 RMD160 3bfa36288b608b4e29252ad1972bb8c06cded3e1 SHA1 eb14976d464f4fa0e14085c8dd58886b0c684a56 SHA256 8687909c83658049cbad656b6d99c8e6143365286e2fa981fbdddc87b178ab8e
-DIST mpiblast-20060625.tar.gz 165096 RMD160 22a9bda3ea63076c1411f8c361c7bbf84213e215 SHA1 e0acdde2770973b752396a6ba1a99b47ea4ddcde SHA256 49eb549196b306d6c152b12522ff2ca08163f4d3a2582118790c88c327c15097
-DIST ncbi-tools-20060507.tar.gz 15396356 RMD160 56114d25ace0338d1ef5c8c2a3cc36ce740a12e3 SHA1 64269236b09fba29d4afe0cd8a3ac6a47fee5218 SHA256 b3cac971d552b2ad86ee7d82e77e6a425b98b33a7b6f1c77062aff133e34d129
-DIST ncbi-tools-20061015.tar.gz 15772715 RMD160 034124b92d4320be31b2bacbb0966270cbfa63b3 SHA1 4e7990e9fed1cc507d10a1b5285e51dc183d318a SHA256 0833f4b4f0389f75cdc0754329b3b8c1420c5b9abd7f3d8e352b4c134b3446de
-DIST ncbi-tools-20070826.tar.gz 17076175 RMD160 00daadd503bf729c15ada0008e305492a076fe15 SHA1 5e61f4f73ef52d145d0df86bb00f03f2db833ee9 SHA256 58be3bb76c4a112217c414fd5d05de58a893cfd6ace3856629616a97a61ee4c8
DIST ncbi-tools-20080302.tar.gz 17294669 RMD160 e269bcadc9e498163252e348a314bab8d0ece8f6 SHA1 d91a66bafac62dd07cc2e524874492388e5a780d SHA256 93a30ec0a6e408858c6364039a4eb240d9fadaf8ce670a14151e03c5169a12c1
DIST ncbi-tools-20090809.tar.gz 64646971 RMD160 a1482a252647b2ea878ac9b08093cfd48bfaa82a SHA1 9727c13d94cc06cfe2f70148fa6bc5dfe011af50 SHA256 0c874961baf1bbfde9c209cc65fdcc5fe07f6f644b69674a89703b6726b66b15
DIST ncbi-tools-sdk-doc.tar.bz2 263568 RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b SHA1 6fd259b1fc75684db43bd817fc4720e92f56e81c SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2
-DIST ncbi.tar.gz 64548732 RMD160 fc15c1e6ab68a6b45fb70f17e88905fee68240c0 SHA1 89cfde43423ffcec9588fa9295a875ee22967c63 SHA256 631ffcd37e65a9482b075b795beb3eb02a022f415e8fd9ed3844e80eb8b772df
-EBUILD ncbi-tools-20060507.ebuild 6428 RMD160 244feb61ad1dbb37090e5940526f0fc5a67390bf SHA1 298d7e6a207ee394438cb998a2886c8fc7077eeb SHA256 c9ef92fb8c4b8ac18d2fd654b57e2e090f1a6feffe33c5ee0049e617ec838215
-EBUILD ncbi-tools-20061015-r1.ebuild 6516 RMD160 71ce04a50d4112108796258757fb10d82b481ef9 SHA1 ac688ece6074201fc535e1a5c2d396311079b55a SHA256 77ad207082d5ec9ba5a9ef562e0639b9ef9d4382ba969f889143ed120425500d
-EBUILD ncbi-tools-20070826.ebuild 7143 RMD160 4c276b590925dfd3d31e354a2942db4e502adcd9 SHA1 f6a50ad5f18b56490f542fd8ba641142df202b4f SHA256 34d6b65d94e7ce07a21aa691618dbabaa0e20655b86ab01f98f1681ed3e675aa
EBUILD ncbi-tools-20080302.ebuild 7142 RMD160 e3075bab7683b75cf57d6d05649d439a4c97889a SHA1 cbf189eb91175135b765d532eed3569a1b254900 SHA256 c68218365e73bb1cc38bf7e7003d52789e39bd23e5a77a6ed94a75441cff5b33
-EBUILD ncbi-tools-20090301.ebuild 6144 RMD160 0251429f54617b235813f815347e1e75bb2ac5a7 SHA1 7d5eb45821fbb49e8540a3c1cbd5ac4ee49d6c5e SHA256 a51f35b5ab07e2b24088f3d5e0075acc57bf257514fd9d0697126c88eb59091b
EBUILD ncbi-tools-20090809-r1.ebuild 6369 RMD160 53e310cb8c26e3c558ce5b05e1983cdff8ecfd1b SHA1 a6cc52cedd9c150d3357c302d41fbea9632146d1 SHA256 25fb0726fd7c7a31622037dea83f14af0dbb640eb61a66c5ebd11d8a8f8289a1
EBUILD ncbi-tools-20090809-r2.ebuild 6408 RMD160 25d7b53e5f3981d42a6debb3c8c942161757e705 SHA1 f78e56fad65e993c634e429b3c4aed146a5aa616 SHA256 ff41f9b663414314d0418d8eededc3a8fb59d31cde7d0e927114eff3c4161d1f
EBUILD ncbi-tools-20090809.ebuild 6126 RMD160 e26c8ebfd87e22517b735b4dff8b448bd1600c6a SHA1 d965066318a5376a4beb4165c16a01f2dd678943 SHA256 9cf86f497256a35108c7779a02b433bde2532ada28584cbf56a8d1b40c548e0b
-MISC ChangeLog 15646 RMD160 3541a5197816acb86079d3b16bd651e9b6ea1e54 SHA1 2ef5b0cf3ed2ebfca0ce11cbcd58b3a4f4ad4176 SHA256 1fe4a9024f1e237fa16354922bb8cb8dcc778ea5309c743f346ef095238b3eae
+MISC ChangeLog 15838 RMD160 27310e1db7d7c37bbb3775c65cef8389380a6adc SHA1 bf9359b4f5934e46c6e7a4cddb95ea3d5a2094ae SHA256 c9f7e2fa2f1e747f5034cfe6c8e67f41369201f73e31d8d8858aab0874576469
MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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+++ /dev/null
-# 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-20060507.ebuild,v 1.12 2008/06/27 10:23:37 ulm 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-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
- mpi? ( virtual/mpi )
- X? ( x11-libs/openmotif )"
-
-DEPEND="${RDEPEND}
- sys-devel/pmake"
-
-S="${WORKDIR}/ncbi"
-
-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}-asn2all.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() {
- 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."
- dobin "${S}"/build/asn2all || die "Failed to install binaries."
- dolib "${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."
-}
+++ /dev/null
-# 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-20061015-r1.ebuild,v 1.3 2008/06/27 10:23:37 ulm 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-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
- mpi? ( virtual/mpi )
- X? ( x11-libs/openmotif )"
-
-DEPEND="${RDEPEND}
- sys-devel/pmake"
-
-S="${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."
-}
+++ /dev/null
-# 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-20070826.ebuild,v 1.7 2008/06/27 10:23:37 ulm 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
- X? ( x11-libs/openmotif )"
-
-DEPEND="${RDEPEND}
- sys-devel/pmake"
-
-# mpi? ( virtual/mpi )
-
-S="${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."
-}
+++ /dev/null
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20090301.ebuild,v 1.5 2009/09/22 14:29:57 maekke Exp $
-
-EAPI="1"
-
-inherit flag-o-matic toolchain-funcs eutils
-
-DESCRIPTION="Development toolkit and applications for computational biology"
-LICENSE="public-domain"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
-
-#SRC_URI="mirror://gentoo/${P}.tar.gz"
-SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PV}/ncbi.tar.gz"
-
-SLOT="0"
-KEYWORDS="~alpha amd64 ~ppc64 x86"
-
-# IUSE=mpi deprecated, use sci-biology/mpiblast separately
-IUSE="doc X"
-
-RDEPEND="app-shells/tcsh
- dev-lang/perl
- media-libs/libpng
- X? ( x11-libs/openmotif )"
-
-DEPEND="${RDEPEND}"
-
-S="${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 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 = $(tc-getCC)/" linux.ncbi.mk || die
-
- # We use dynamic libraries
- sed -i -e "s/-Wl,-Bstatic//" *linux*.ncbi.mk || die
-}
-
-src_compile() {
- export EXTRA_VIB
- cd "${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
-}
-
-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."
-
- # TODO: wwwblast with webapps
- #insinto /usr/share/ncbi/lib/cgi
- #doins ${S}/cgi/*
- #insinto /usr/share/ncbi/lib/real
- #doins ${S}/real/*
-
- # Basic documentation
- dodoc "${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 "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
-
- # Developer documentation
- if use doc; then
- # Demo programs
- mkdir "${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."
-}
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