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# Contributor: cornholio <vigo.the.unholy.carpathian@gmail.com>
pkgname=fsl
pkgver=5.0.9
pkgrel=1
pkgdesc="A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data"
arch=("i686" "x86_64")
url="http://www.fmrib.ox.ac.uk/fsl/"
license=(custom)
depends=()
makedepends=()
optdepends=("fslview")
md5sums=('5e38052b268dbc0fc09114615eff85c9')
source=("http://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-sources.tar.gz")
build() {
export FSLDIR="${srcdir}/fsl"
. "${FSLDIR}/etc/fslconf/fsl.sh"
export FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
if [ ! -e "${FSLDIR}/config/${FSLMACHTYPE}" ]; then
cp -rv "${FSLDIR}/config/linux_64-gcc4.4" "${FSLDIR}/config/${FSLMACHTYPE}"
fi
if test "$CARCH" == i686; then
sed -i "s^-m64^^g" "${FSLDIR}/config/${FSLMACHTYPE}/systemvars.mk"
fi
sed -i 's^#include <vector>^#include <vector>\n#include <stdlib.h>^g' "${FSLDIR}/src/utils/opttst.cc"
sed -i "s^//#include <cmath>^#include <cmath>^g" "${FSLDIR}/src/fslsurface/fslsurface_structs.h"
cd "${FSLDIR}"
./build
}
package() {
rm -rf "${srcdir}/fsl/extras/src"
mkdir -p "${pkgdir}/usr/bin"
mkdir -p "${pkgdir}/opt/fsl"
cp "${srcdir}/fsl/bin/"* "${pkgdir}/usr/bin/"
cp -r "${srcdir}/fsl/data" "${pkgdir}/opt/fsl/"
cp -r "${srcdir}/fsl/doc" "${pkgdir}/opt/fsl/"
cp -r "${srcdir}/fsl/etc" "${pkgdir}/opt/fsl/"
cp -r "${srcdir}/fsl/extras" "${pkgdir}/opt/fsl/"
cp -r "${srcdir}/fsl/include" "${pkgdir}/opt/fsl/"
cp -r "${srcdir}/fsl/lib" "${pkgdir}/opt/fsl/"
cp -r "${srcdir}/fsl/refdoc" "${pkgdir}/opt/fsl/"
cp -r "${srcdir}/fsl/tcl" "${pkgdir}/opt/fsl/"
mkdir -p "${pkgdir}/etc/profile.d"
echo 'FSLDIR=/opt/fsl' > "${pkgdir}/etc/profile.d/fsl.sh"
echo '. ${FSLDIR}/etc/fslconf/fsl.sh' >> "${pkgdir}/etc/profile.d/fsl.sh"
echo 'export FSLDIR' >> "${pkgdir}/etc/profile.d/fsl.sh"
mkdir -p "${pkgdir}/usr/share/licenses/fsl"
grep -v \< "${srcdir}/fsl/doc/fsl/licence.html" | cat -s > "${pkgdir}/usr/share/licenses/fsl/LICENSE"
find "${pkgdir}" -type f -exec chmod 644 {} \;
find "${pkgdir}" -type d -exec chmod 755 {} \;
find "${pkgdir}/usr/bin" -exec chmod 755 {} \;
find "${pkgdir}/opt/fsl/etc/fslconf" -exec chmod 755 {} \;
find "${pkgdir}/opt/fsl/extras/bin" -exec chmod 755 {} \;
chmod 755 "${pkgdir}/etc/profile.d/fsl.sh"
ln -s /usr/bin "${pkgdir}/opt/fsl/bin"
}
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