167 lines
4.4 KiB
Bash
167 lines
4.4 KiB
Bash
# Copyright 1999-2020 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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inherit flag-o-matic toolchain-funcs prefix
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DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
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HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
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SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
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LICENSE="FSL BSD-2 newmat"
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SLOT="0"
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KEYWORDS="~amd64"
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IUSE=""
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DEPEND="
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dev-libs/boost
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dev-python/fslpy
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media-gfx/graphviz
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media-libs/gd
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media-libs/glu
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media-libs/libpng:0=
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sci-libs/ciftilib
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sci-libs/nlopt
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sys-libs/zlib
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dev-lang/tcl:0=
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dev-lang/tk:0=
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>=virtual/lapack-3.8
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>=virtual/blas-3.8
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"
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RDEPEND="${DEPEND}"
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S=${WORKDIR}/${PN}
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UPSTREAM_FSLDIR="/usr/share/fsl"
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PATCHES=(
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"${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch
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"${FILESDIR}/${PN}"-6.0.2-setup.patch
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"${FILESDIR}/${PN}"-6.0.2-template.patch
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"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
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"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
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"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
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"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
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"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
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"${FILESDIR}/${PN}"-5.0.9-headers.patch
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"${FILESDIR}/${PN}"-6.0.2-fsldir_redux.patch
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)
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src_prepare(){
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default
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sed -i \
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-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
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-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
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-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
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config/buildSettings.mk || die
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eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
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etc/js/label-div.html
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# Disable mist-clean the hard way for now.
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rm -rf src/mist-clean
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makefilelist=$(find src/ -name Makefile)
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sed -i \
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-e "s:-I\${INC_BOOST}::" \
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-e "s:-I\${INC_ZLIB}::" \
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-e "s:-I\${INC_GD}::" \
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-e "s:-I\${INC_PNG}::" \
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-e "s:-L\${LIB_GD}::" \
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-e "s:-L\${LIB_PNG}::" \
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-e "s:-L\${LIB_ZLIB}::" \
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${makefilelist} || die
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sed -e "s:\${FSLDIR}/bin/::g" \
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-e "s:\$FSLDIR/bin/::g" \
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-i $(grep -rl "\${FSLDIR}/bin" src/*) \
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-i $(grep -rl "\$FSLDIR/bin" src/*) \
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$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
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$(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
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sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
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-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
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-i $(grep -rl "\$FSLDIR/data" src/*) \
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$(grep -rl "\${FSLDIR}/data" src/*) || die
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sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
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-e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
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-i $(grep -rl "\$FSLDIR/doc" src/*) \
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$(grep -rl "\${FSLDIR}/doc" src/*) || die
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sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
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-i $(grep -rl "/usr/share/fsl/doc" src/*) || die
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sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
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-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
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-i $(grep -rlI "\$FSLDIR/etc" *) \
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-i $(grep -rlI "\${FSLDIR}/etc" *) || die
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# Use generic blas/lapack rather than openblas
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sed -e "s:-lopenblas:-llapack -lblas:g" \
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-i $(grep -rlI lopenblas *) || die
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# script wanting to have access to flsversion at buildtime
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sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
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-i ${makefilelist} || die
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}
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src_compile() {
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export FSLDIR=${WORKDIR}/${PN}
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export FSLCONDIR=${WORKDIR}/${PN}/config
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export FSLMACHTYPE=generic
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export USERLDFLAGS="${LDFLAGS}"
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export USERCFLAGS="${CFLAGS}"
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export USERCXXFLAGS="${CXXFLAGS}"
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export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
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export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
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./build || die
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}
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src_install() {
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sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
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$(grep -lI "\${FSLDIR}/tcl" bin/*) \
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$(grep -l "\${FSLDIR}/tcl" tcl/*) || die
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sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
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$(grep -l "\$FSLDIR/tcl" tcl/*) || die
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dobin bin/*
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insinto /usr/share/${PN}
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doins -r data
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dodoc -r doc/. refdoc
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insinto /usr/libexec/fsl
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doins -r tcl/*
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insinto /etc/fslconf
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doins etc/fslconf/fsl.sh
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insinto /etc
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doins etc/fslversion
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doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
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#the following is needed for FSL and depending programs to be able
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#to find its files, since FSL uses an uncommon installation path:
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#https://github.com/gentoo-science/sci/pull/612#r60289295
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dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
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dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
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dosym ../../bin ${UPSTREAM_FSLDIR}/bin
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doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
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mv "${ED}"/usr/bin/{,fsl_}cluster || die
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}
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pkg_postinst() {
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echo
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einfo "Please run the following commands if you"
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einfo "intend to use fsl from an existing shell:"
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einfo "env-update && source /etc/profile"
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echo
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}
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