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Diffstat (limited to 'sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild')
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild329
1 files changed, 0 insertions, 329 deletions
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
deleted file mode 100644
index a618abbd6..000000000
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ /dev/null
@@ -1,329 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-inherit eutils flag-o-matic multilib toolchain-funcs
-
-MY_TAG="Jun_15_2010"
-MY_Y="${MY_TAG/*_/}"
-MY_PV="9_0_0"
-MY_P="ncbi_cxx--${MY_PV}"
-#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz
-
-DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
-HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit"
-SRC_URI="
- ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz"
-# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz"
-
-# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
-# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
-
-LICENSE="public-domain"
-SLOT="0"
-IUSE="
- debug static-libs static threads pch
- test wxwidgets odbc
- berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
- glut gnutls hdf5 icu lzo jpeg mesa mysql muparser opengl pcre png python
- sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X"
-#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-KEYWORDS=""
-
-# sys-libs/db should be compiled with USE=cxx
-DEPEND="
- berkdb? ( sys-libs/db:4.3[cxx] )
- boost? ( dev-libs/boost )
- curl? ( net-misc/curl )
- sqlite? ( dev-db/sqlite )
- sqlite3? ( dev-db/sqlite:3 )
- mysql? ( virtual/mysql )
- gnutls? ( net-libs/gnutls )
- fltk? ( x11-libs/fltk )
- opengl? ( virtual/opengl )
- mesa? ( media-libs/mesa[osmesa]
- media-libs/glew
- )
- glut? ( media-libs/freeglut )
- freetype? ( media-libs/freetype )
- fastcgi? ( www-apache/mod_fastcgi )
- python? ( dev-lang/python )
- cppunit? ( dev-util/cppunit )
- icu? ( dev-libs/icu )
- expat? ( dev-libs/expat )
- sablotron? ( app-text/sablotron )
- xml? ( dev-libs/libxml2 )
- xslt? ( dev-libs/libxslt )
- xerces? ( dev-libs/xerces-c )
- xalan? ( dev-libs/xalan-c )
- muparser? ( dev-cpp/muParser )
- hdf5? ( sci-libs/hdf5 )
- gif? ( media-libs/giflib )
- jpeg? ( virtual/jpeg )
- png? ( media-libs/libpng )
- tiff? ( media-libs/tiff )
- xpm? ( x11-libs/libXpm )
- lzo? ( dev-libs/lzo )
- app-arch/bzip2
- dev-libs/libpcre"
-# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge
-# Intentionally omitted USE flags:
-# ftds? ( dev-db/freetds ) # useless, no real apps use it outside NCBI
-
-
-# seems muParser is required, also glew is required. configure exitss otherwise
-
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-src_prepare() {
-# filter-ldflags -Wl,--as-needed
-# append-ldflags -Wl,--no-undefined
-# sed -i -e 's/-print-file-name=libstdc++.a//' \
-# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
-# src/build-system/configure || die
-# epatch \
-# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \
-# "${FILESDIR}"/curl-types.patch \
-# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \
-# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \
-# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \
-# "${FILESDIR}"/report_project_settings_configure.ac.patch \
-# "${FILESDIR}"/report_project_settings_configure.patch \
-# "${FILESDIR}"/make_install.patch
-
-# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch
-
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \
-# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \
-# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch
-
-# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}"
-
- local PATCHES=(
- "${FILESDIR}"/${P}-conf-opts.patch
- "${FILESDIR}"/${P}-as-needed.patch
- "${FILESDIR}"/${P}-fix-creaders-linking.patch
- "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch
- "${FILESDIR}"/${P}-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
- "${FILESDIR}"/${P}-remove-LZO-definition-upstream.patch
- )
- epatch ${PATCHES[@]}
-
- tc-export CXX CC
-
-# cd src/build-system || die
-# eaclocal -I.
-# eautoconf
-}
-
-src_configure() {
- local myconf=()
- #--without-optimization turn off optimization flags in non-debug mode
- #--with-profiling build profiled versions of libs and apps
- #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR)
- #--with-plugin-auto-load always enable the plugin manager by default
- #--with-bundles build bundles in addition to dylibs on Mac OS X
- #--with-bin-release build executables suitable for public release
- # no dll and such
- #--with-64 compile to 64-bit code
- #--with-universal build universal binaries on Mac OS X
- #--with-universal=CPUs build universal binaries targeting the given CPUs
- #--without-exe do not build executables
- #--with-relative-runpath=P specify an executable-relative DLL search path
- #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH
- #--with-limited-linker don't attempt to build especially large projects
- #--with-extra-action= script to call after the configuration is complete
- #--with-autodep automatic generation of dependencies (GNU make)
- #--with-fake-root=DIR appear to have been built under DIR
- #--with-build-root-sfx=X add a user-specified suffix to the build dir name
- #--without-execopy do not copy built executables to the BIN area
- #--with-lib-rebuilds ensure that apps use up-to-date libraries
- #--with-lib-rebuilds=ask ask whether to update each app's libraries
- #--without-deactivation keep old copies of libraries that no longer build
- #--without-makefile-auto-update do not auto-update generated makefiles
- #--with-projects=FILE build projects listed in FILE by default
- #--without-flat-makefile do not generate an all-encompassing flat makefile
- #--with-configure-dialog allow interactive flat makefile project selection
- #--with-saved-settings=F load configuration settings from the file F
- #--with-check-tools=... use the specified tools for testing
- #--with-ncbi-public ensure compatibility for all in-house platforms
- #--with-sybase-local=DIR use local SYBASE install (DIR is optional)
- #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0)
- #--without-sp do not use SP libraries
- #--without-orbacus do not use ORBacus CORBA libraries
- #--with-orbacus=DIR use ORBacus installation in DIR
- #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR)
- #--with-sablot=DIR use Sablotron installation in DIR
- #--without-sablot, do not use Sablotron
- #--with-oechem=DIR use OpenEye OEChem installation in DIR
- #--without-oechem do not use OEChem
- #--with-sge=DIR use Sun Grid Engine installation in DIR
- #--without-sge do not use Sun Grid Engine
- #--with-magic=DIR use libmagic installation in DIR
- #--without-magic do not use libmagic
- #--without-local-lbsm turn off support for IPC with locally running LBSMD
- #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt
- #--without-connext do not build non-public CONNECT library extensions
- #--without-serial do not build the serialization library and tools
- #--without-objects do not generate/build serializeable objects from ASNs
- #--without-dbapi do not build database connectivity libraries
- #--without-app do not build standalone applications like ID1_FETCH
- #--without-gui do not build most graphical projects
- #--without-algo do not build CPU-intensive algorithms
- #--without-internal do not build internal projects
- #--with-gbench ensure that Genome Workbench can be built
- #--without-gbench do not build Genome Workbench
- myconf+=(
- --with-dll
- --with-lfs
- --with-build-root="${S}"_build
- --without-suffix
- --without-hostspec
- --without-version
- --with-bincopy
- --without-strip
- --without-ccache
- --without-distcc
-# --with-ncbi-c
- --without-ctools
-# --with-sss
-# --with-sssutils
-# --with-sssdb
-# --with-included-sss
- --with-z="${EPREFIX}/usr"
- --with-bz2="${EPREFIX}/usr"
- --with-muparser="${EPREFIX}/usr"
- --without-sybase
- --with-autodep
-
-# due to \*-fix-undef-reference-to-GenBankReaders_Register_Id1.patch
-# ./configure ... --with-flat-makefile
-# cd .../build
-# make -f Makefile.flat
-#
- --with-flat-makefile
-# --with-3psw=std:netopt favor standard (system) builds of the above pkgs
-
-
-# Note: only care about gnutls, nothing actually uses openssl except a forgotten configure test
- $(use_with debug)
- $(use_with debug max-debug)
- $(use_with debug symbols)
- $(use_with static-libs static)
- $(use_with static static-exe)
- $(use_with threads mt)
- $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/ncbi_cxx")
- $(use_with test check)
- $(use_with pch)
- $(use_with lzo lzo "${EPREFIX}/usr")
- $(use_with pcre pcre "${EPREFIX}/usr")
- $(use_with gnutls gnutls "${EPREFIX}/usr")
- $(use_with mysql mysql "${EPREFIX}/usr")
- $(use_with fltk fltk "${EPREFIX}/usr")
- $(use_with opengl opengl "${EPREFIX}/usr")
- $(use_with mesa mesa "${EPREFIX}/usr")
- $(use_with opengl glut "${EPREFIX}/usr")
- $(use_with opengl glew "${EPREFIX}/usr")
- $(use_with opengl glew-mx)
- $(use_with wxwidgets wxwidgets "${EPREFIX}/usr")
- $(use_with wxwidgets wxwidgets-ucs)
- $(use_with freetype freetype "${EPREFIX}/usr")
- $(use_with fastcgi fastcgi "${EPREFIX}/usr")
- $(use_with berkdb bdb "${EPREFIX}/usr")
- $(use_with odbc odbc "${EPREFIX}/usr")
- $(use_with python python "${EPREFIX}/usr")
- $(use_with boost boost "${EPREFIX}/usr")
- $(use_with sqlite sqlite3 "${EPREFIX}/usr")
- $(use_with icu icu "${EPREFIX}/usr")
- $(use_with expat expat "${EPREFIX}/usr")
- $(use_with xml libxml "${EPREFIX}/usr")
- $(use_with xml libxslt "${EPREFIX}/usr")
- $(use_with xerces xerces "${EPREFIX}/usr")
- $(use_with hdf5 hdf5 "${EPREFIX}/usr")
- $(use_with xalan xalan "${EPREFIX}/usr")
-# $(use_with gif gif "${EPREFIX}/usr")
- $(use_with jpeg jpeg "${EPREFIX}/usr")
- $(use_with tiff tiff "${EPREFIX}/usr")
- $(use_with png png "${EPREFIX}/usr")
- $(use_with xpm xpm "${EPREFIX}/usr")
- $(use_with curl curl "${EPREFIX}/usr")
-# $(use_with X x "${EPREFIX}/usr")
- $(use_with X x)
- )
-
- # http://www.ncbi.nlm.nih.gov/books/NBK7167/
- use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt )
-
- # TODO
- # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure
- # otherwise your -O2 will be dropped in some subdirectories and repalced by e.g. -O9
-
- einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}"
-
-# bash \
-# ./src/build-system/configure \
-# cd src/build-system || die
- econf \
- --srcdir="${S}" \
- --prefix="${EPREFIX}/usr" \
- --libdir=/usr/lib64 \
- ${myconf} LDFLAGS="-Wl,-rpath-link,${S}_build/lib -Wl,--no-as-needed" \
- ${myconf[@]} || die
-#--without-debug \
-# --with-bin-release \
-# --with-bincopy \
-# --without-static \
-# --with-dll \
-# --with-mt \
-# --with-openmp \
-# --with-lfs \
-# --prefix="${ED}"/usr \
-# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
-# ${myconf} LDFLAGS="-Wl,--no-as-needed" \
-# || die
-# econf ${myconf[@]}
-}
-
-src_compile() {
- # all_r would ignore the --with-projects contents and build more
- # emake all_r -C GCC*-Release*/build || die
- # all_p with compile only selected/required components
-# cd "${S}"_build &&\
-
- # disabling this because we need to take the flat Makefile route
- # emake all_p -C "${S}"_build/build
-
- # take the flat Makefile route
- emake -f Makefile.flat -C "${S}"_build/build
-
-
-# emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?"
-}
-
-src_install() {
- rm -rvf "${S}"_build/lib/ncbi || die
- emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}"
-
-# dobin "${S}"_build/bin/*
-# dolib.so "${S}"_build/lib/*so*
-# dolib.a "${S}"_build/lib/*.a
-# doheader "${S}"_build/inc/*
-
- # File collisions with sci-biology/ncbi-tools
- rm -f "${ED}"/usr/bin/{asn2asn,rpsblast,test_regexp}
- mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop2
-
- echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
- doenvd "${S}/99${PN}"
-}
-
-pkg_postinst() {
- einfo 'Please run "source /etc/profile" before using this package in the current shell.'
- einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/'
-}