commit: ea391932cb773a0305bcb60273dca6b59dfc331f Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Fri Jan 14 20:36:21 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Fri Jan 14 20:36:21 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ea391932
sci-biology/fsl: add version 6.0.5 No keywords, compile fails, need patches Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> sci-biology/fsl/fsl-6.0.5.ebuild | 220 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 220 insertions(+) diff --git a/sci-biology/fsl/fsl-6.0.5.ebuild b/sci-biology/fsl/fsl-6.0.5.ebuild new file mode 100644 index 000000000..c51a9d30e --- /dev/null +++ b/sci-biology/fsl/fsl-6.0.5.ebuild @@ -0,0 +1,220 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cuda 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 -> ${P}.tar.gz" +S="${WORKDIR}/${PN}" + +LICENSE="FSL BSD-2 newmat" +SLOT="0" +KEYWORDS="" +IUSE="cuda" + +DEPEND=" + dev-cpp/libxmlpp:= + dev-cpp/tbb + dev-db/sqlite + dev-libs/boost + dev-libs/libfmt + dev-libs/libxml2 + dev-libs/pugixml + >=dev-python/fslpy-3.7.0 + media-gfx/graphviz + media-libs/gd + media-libs/glu + media-libs/libpng:0= + sci-libs/gsl + sci-libs/ciftilib + sci-libs/fftw + sci-libs/nlopt + sci-libs/vtk + sys-libs/zlib + dev-lang/tcl:0= + dev-lang/tk:0= + >=virtual/lapack-3.8 + >=virtual/blas-3.8 + cuda? ( + || ( + ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* ) + ) + ) + " +RDEPEND="${DEPEND}" + +UPSTREAM_FSLDIR="/usr/share/fsl" + +PATCHES=( +# "${FILESDIR}/${PN}"-6.0.4-gcc10_include.patch + "${FILESDIR}/${PN}"-6.0.4-setup.patch +# "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch +# "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.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}"-6.0.4-flameo_std.patch + "${FILESDIR}/${PN}"-6.0.4-melodic_std.patch + "${FILESDIR}/${PN}"-6.0.4-remove_fslpy_collisions-p1.patch + "${FILESDIR}/${PN}"-6.0.4-remove_fslpy_collisions-p2.patch +# "${FILESDIR}/${PN}"-6.0.4-fdt_cuda.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 $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \ + etc/js/label-div.html + +# # Disable mist the hard way for now. +# rm -r src/mist || die +# +# # Disable ptx2 for now +# rm -r src/ptx2 || die +# + makefilelist=$(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 $(grep -rlI lopenblas *) || die + + # script wanting to have access to fslversion at buildtime + sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \ + -i ${makefilelist} || die + + if use cuda; then + einfo + + gcc_ver=`gcc-fullversion` + einfo "GCC version: ${gcc_ver}" + + cuda_gcc=`cuda_gccdir` + cuda_NVCC_flags=`cuda_gccdir -f` + einfo "CUDA GCC path: ${cuda_gcc}" + einfo " ${cuda_NVCC_flags}" + + CUDA_INSTALLATION="/opt/cuda" + CUDAVER=`cuda_toolkit_version` + + eapply "${FILESDIR}/${PN}-6.0.4-eddy_cuda.patch" + eapply "${FILESDIR}/${PN}-6.0.4-cuda_buildsettings.patch" + + sed -i \ + -e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \ + src/eddy/Makefile || die + + cuda_sanitize + fi +} + +src_compile() { + export FSLDIR=${WORKDIR}/${PN} + export FSLCONDIR=${WORKDIR}/${PN}/config + export FSLMACHTYPE=generic + + # define the default build system to match upstream official standard + # -> individual projects may overwrite the '-std=' flag + export ANSI_CFLAGS="-std=c99" + export ANSI_CXXFLAGS="-std=c++98" + + export USERLDFLAGS="${LDFLAGS}" + export USERCFLAGS="${CFLAGS}" + export USERCPPFLAGS="${CPPFLAGS}" + export USERCXXFLAGS="${CXXFLAGS}" + + export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)" + export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)" + + if use cuda; then + einfo "CUDA_INSTALLATION: ${CUDA_INSTALLATION}" + einfo "CUDAVER: ${CUDAVER}" + fi + + ./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 +}
