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# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=6
inherit eutils toolchain-funcs prefix
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}-sources.tar.gz"
LICENSE="FSL BSD-2 newmat"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
COMMON_DEPEND="
dev-libs/boost
media-gfx/graphviz
media-libs/gd
media-libs/glu
media-libs/libpng:0=
sys-libs/zlib
"
DEPEND="${COMMON_DEPEND}"
RDEPEND="${COMMON_DEPEND}
dev-lang/tcl:0=
dev-lang/tk:0=
"
S=${WORKDIR}/${PN}
src_prepare(){
epatch \
"${FILESDIR}/${PN}"-5.0.8-setup.patch \
"${FILESDIR}/${PN}"-5.0.8-headers.patch \
"${FILESDIR}/${PN}"-5.0.8-fsldir_redux.patch
sed -i \
-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
config/generic/systemvars.mk || die
eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
etc/js/label-div.html
makefilelist=$(find src/ -name Makefile)
sed -i \
-e "s:-I\${INC_BOOST}::" \
-e "s:-I\${INC_ZLIB}::" \
-e "s:-I\${INC_GD}::" \
-e "s:-I\${INC_PNG}::" \
-e "s:-L\${LIB_GD}::" \
-e "s:-L\${LIB_PNG}::" \
-e "s:-L\${LIB_ZLIB}::" \
${makefilelist} || die
sed -i "s:\${FSLDIR}/bin/::g" \
$(grep -rl "\${FSLDIR}/bin" src/*) \
$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)
sed -i "s:\$FSLDIR/bin/::g" \
$(grep -rl "\$FSLDIR/bin" src/*) \
$(grep -rl "\$FSLDIR/bin" etc/matlab/*)
sed -i "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
$(grep -rl "\$FSLDIR/data" src/*)
sed -i "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
$(grep -rl "\${FSLDIR}/data" src/*)
sed -i "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
$(grep -rl "\$FSLDIR/etc" src/*)
sed -i "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
$(grep -rl "\${FSLDIR}/etc" src/*)
sed -i "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
$(grep -rl "\$FSLDIR/doc" src/*)
sed -i "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
$(grep -rl "\${FSLDIR}/doc" src/*)
sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \
$(grep -rl "\'\${FSLDIR}\'/doc" src/*)
sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *`
default
}
src_compile() {
export FSLDIR=${WORKDIR}/${PN}
export FSLCONDIR=${WORKDIR}/${PN}/config
export FSLMACHTYPE=generic
export USERLDFLAGS="${LDFLAGS}"
export USERCFLAGS="${CFLAGS}"
export USERCXXFLAGS="${CXXFLAGS}"
./build || die
}
src_install() {
sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
$(grep -lI "\${FSLDIR}/tcl" bin/*) \
$(grep -l "\${FSLDIR}/tcl" tcl/*) || die
sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
$(grep -l "\$FSLDIR/tcl" tcl/*) || die
dobin bin/*
insinto /usr/share/${PN}
doins -r data
dodoc -r doc/. refdoc
insinto /usr/libexec/fsl
doins -r tcl/*
insinto /etc/fslconf
doins etc/fslconf/fsl.sh
insinto /etc
doins etc/fslversion
doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
#if use matlab; then
# doins etc/matlab
#fi
#the following is needed for FSL and depending programs to be able
#to find its files, since FSL uses an uncommon:
#https://github.com/gentoo-science/sci/pull/612#r60289295
dosym /etc /usr/share/fsl/etc
dosym /usr/share/doc/${P} /usr/share/fsl/doc
doenvd "${FILESDIR}"/99fsl
mv "${ED}"/usr/bin/{,fsl_}cluster || die
}
pkg_postinst() {
echo
einfo "Please run the following commands if you"
einfo "intend to use fsl from an existing shell:"
einfo "env-update && source /etc/profile"
echo
}
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