sci-biology/afni: env variable for AFNI data

Signed-off-by: Horea Christian <chr@chymera.eu>

2 files changed, 125 insertions, 0 deletions

diff --git a/sci-biology/afni/afni-24.0.08-r2.ebuild b/sci-biology/afni/afni-24.0.08-r2.ebuild
new file mode 100644
index 000000000..270100c0b
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08-r2.ebuild
@@ -0,0 +1,124 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
+SRC_URI="
+	https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+	https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+	https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+	"
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	dev-build/ninja
+	dev-libs/expat
+	dev-libs/glib:2
+	dev-libs/libf2c
+	media-libs/freeglut
+	media-libs/glu
+	media-libs/netpbm
+	media-libs/qhull
+	media-video/mpeg-tools
+	sci-biology/afni-datasets
+	sci-libs/gsl
+	sci-libs/gts
+	sys-devel/llvm:*
+	sys-libs/libomp
+	virtual/jpeg-compat:62
+	x11-libs/libGLw
+	x11-libs/libXft
+	x11-libs/libXi
+	x11-libs/libXmu
+	x11-libs/libXpm
+	x11-libs/libXt
+	x11-libs/motif[-static-libs]
+	"
+DEPEND="
+	${RDEPEND}
+	app-shells/tcsh
+	"
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+	#tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+	tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+	tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+	cmake_src_prepare
+	default
+	}
+
+src_configure() {
+	if use !whirlgif; then
+		eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
+	fi
+	export CFLAGS="-pthread ${CFLAGS}"
+	export GIT_REPO_VERSION=3.0.1.1
+	local mycmakeargs=(
+		-DLIBDIR=/usr/$(get_libdir)
+		-DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+		-DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+		-DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+		-DCOMP_COREBINARIES=ON
+		-DUSE_SYSTEM_NIFTI=OFF
+		-DUSE_SYSTEM_GIFTI=OFF
+		-DUSE_SYSTEM_XMHTML=OFF
+		-DUSE_SYSTEM_GTS=ON
+		-DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+		-DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+		-DCOMP_GUI=ON
+		-DCOMP_PLUGINS=ON
+		-DUSE_OMP=ON
+		-DCOMP_PYTHON=OFF
+		-DUSE_SYSTEM_F2C=ON
+	)
+	tc-export CC
+	cmake_src_configure
+}
+
+src_compile() {
+	cmake_src_compile
+	pushd src/python_scripts
+		distutils-r1_src_compile
+	popd
+}
+
+src_install() {
+	cmake_src_install
+	pushd src/python_scripts
+		distutils-r1_src_install
+	popd
+	cd "${D}"
+	rm usr/bin/mpeg_encode
+	doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+	echo
+	einfo "Please run the following commands if you"
+	einfo "intend to use afni binaries from an existing shell:"
+	einfo "source /etc/profile"
+	echo
+}
diff --git a/sci-biology/afni/files/97afni b/sci-biology/afni/files/97afni
new file mode 100644
index 000000000..dbf463f47
--- /dev/null
+++ b/sci-biology/afni/files/97afni
@@ -0,0 +1 @@
+export AFNI_ATLAS_PATH=/usr/share/afni-datasets