168 lines
4.4 KiB
Bash
168 lines
4.4 KiB
Bash
# Copyright 1999-2021 Gentoo Authors
|
|
# Distributed under the terms of the GNU General Public License v2
|
|
|
|
EAPI=7
|
|
|
|
inherit flag-o-matic toolchain-funcs prefix
|
|
|
|
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
|
|
HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
|
|
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
|
|
|
|
LICENSE="FSL BSD-2 newmat"
|
|
SLOT="0"
|
|
KEYWORDS="~amd64"
|
|
IUSE=""
|
|
|
|
DEPEND="
|
|
dev-libs/boost
|
|
<dev-python/fslpy-3
|
|
media-gfx/graphviz
|
|
media-libs/gd
|
|
media-libs/glu
|
|
media-libs/libpng:0=
|
|
sci-libs/ciftilib
|
|
sci-libs/nlopt
|
|
sys-libs/zlib
|
|
dev-lang/tcl:0=
|
|
dev-lang/tk:0=
|
|
>=virtual/lapack-3.8
|
|
>=virtual/blas-3.8
|
|
"
|
|
RDEPEND="${DEPEND}"
|
|
|
|
S=${WORKDIR}/${PN}
|
|
UPSTREAM_FSLDIR="/usr/share/fsl"
|
|
|
|
PATCHES=(
|
|
"${FILESDIR}/${PN}"-6.0.2-gcc10_include.patch
|
|
"${FILESDIR}/${PN}"-6.0.2-setup.patch
|
|
"${FILESDIR}/${PN}"-6.0.2-template.patch
|
|
"${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
|
|
"${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
|
|
"${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
|
|
"${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
|
|
"${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
|
|
"${FILESDIR}/${PN}"-5.0.9-headers.patch
|
|
"${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p1.patch
|
|
"${FILESDIR}/${PN}"-6.0.2-fsldir_redux-p2.patch
|
|
)
|
|
|
|
src_prepare(){
|
|
default
|
|
|
|
sed -i \
|
|
-e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
|
|
-e "s:@@GENTOO_CC@@:$(tc-getCC):" \
|
|
-e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
|
|
config/buildSettings.mk || die
|
|
|
|
eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
|
|
etc/js/label-div.html
|
|
|
|
# Disable mist-clean the hard way for now.
|
|
rm -rf src/mist-clean
|
|
|
|
makefilelist=$(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 -e "s:\${FSLDIR}/bin/::g" \
|
|
-e "s:\$FSLDIR/bin/::g" \
|
|
-i $(grep -rl "\${FSLDIR}/bin" src/*) \
|
|
-i $(grep -rl "\$FSLDIR/bin" src/*) \
|
|
$(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
|
|
$(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
|
|
|
|
sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
|
|
-e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
|
|
-i $(grep -rl "\$FSLDIR/data" src/*) \
|
|
$(grep -rl "\${FSLDIR}/data" src/*) || die
|
|
|
|
sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
|
|
-e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
|
|
-i $(grep -rl "\$FSLDIR/doc" src/*) \
|
|
$(grep -rl "\${FSLDIR}/doc" src/*) || die
|
|
|
|
sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
|
|
-i $(grep -rl "/usr/share/fsl/doc" src/*) || die
|
|
|
|
sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
|
|
-e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
|
|
-i $(grep -rlI "\$FSLDIR/etc" *) \
|
|
-i $(grep -rlI "\${FSLDIR}/etc" *) || die
|
|
|
|
# Use generic blas/lapack rather than openblas
|
|
sed -e "s:-lopenblas:-llapack -lblas:g" \
|
|
-i $(grep -rlI lopenblas *) || die
|
|
|
|
# script wanting to have access to flsversion at buildtime
|
|
sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
|
|
-i ${makefilelist} || die
|
|
}
|
|
|
|
src_compile() {
|
|
export FSLDIR=${WORKDIR}/${PN}
|
|
export FSLCONDIR=${WORKDIR}/${PN}/config
|
|
export FSLMACHTYPE=generic
|
|
|
|
export USERLDFLAGS="${LDFLAGS}"
|
|
export USERCFLAGS="${CFLAGS}"
|
|
export USERCXXFLAGS="${CXXFLAGS}"
|
|
|
|
export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
|
|
export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
|
|
|
|
./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
|
|
|
|
#the following is needed for FSL and depending programs to be able
|
|
#to find its files, since FSL uses an uncommon installation path:
|
|
#https://github.com/gentoo-science/sci/pull/612#r60289295
|
|
dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
|
|
dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
|
|
dosym ../../bin ${UPSTREAM_FSLDIR}/bin
|
|
|
|
doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
|
|
mv "${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
|
|
}
|