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@gentoo.org>

2 files changed, 221 insertions, 0 deletions

diff --git a/sci-biology/fsl/Manifest b/sci-biology/fsl/Manifest
index 868861b84..80c5aa7b8 100644
--- a/sci-biology/fsl/Manifest
+++ b/sci-biology/fsl/Manifest
@@ -1,2 +1,3 @@
 DIST fsl-6.0.2.tar.gz 2505331864 BLAKE2B 0fbc23c788e0960e41a895f8eddd346e8facfae448c637eca18d39b142f8aabd9531427ce4ff97c634fdc5d16a74163947c7bade219a8900722815321144b41e SHA512 fe308393076c51c50b086f9bf7ff5ddebcf8b1284128e734b9d9e501019917ceba7c0ee5cd5aa1ed44452bcd042ad72653c1a8693f94eab9b83a80fe508a56ca
 DIST fsl-6.0.4.tar.gz 2507673220 BLAKE2B 21e7437f8a3fde03ec6711b8022ee203ae159c07b5a3b998f37db768205d3335ffe9b28ad05b859e6bde4916933ea58e4e188012f147648f00fd6e6253ce1a12 SHA512 c65edcf5728920752e6dceea440dc2b528d007b7e4f56390a3d7eed91b1014457544563f699cae77f62c44cdfbdfcc5031265a5fd619fe0ecb99cad5653080d3
+DIST fsl-6.0.5.tar.gz 2509109593 BLAKE2B d1e5efbb6b73e2b40e7147dc4958584e057311084d2064335aae1c0a36cfab5e12061f3fac4f54118d840e66620b7e64a5dc4c32c0e0e3e6233c25cc3b48e6fd SHA512 e5124ae640f51002692de6ad9fdc3aec0e3caffc94dd18c16fadba686fa2a9bf37c7752e67affca53d9859cbab3e2e62ca28ef43c754c464bab5e182e55b02a1
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
+}