diff options
Diffstat (limited to 'PKGBUILD')
| -rwxr-xr-x | PKGBUILD | 55 |
1 files changed, 25 insertions, 30 deletions
@@ -1,41 +1,35 @@ # Maintainer: Tobias Bachmann <tobachmann@gmx.de> # Contributor: fishburn <frankthefishburn@gmail.com> +# Set number of parallel compile jobs, default equals number of CPUs +NJOBS=$(nproc) +NJOBS=8 + pkgname=fsl -pkgver=6.0.4 -pkgrel=2 +pkgver=6.0.5 +pkgrel=1 pkgdesc="A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data" arch=("x86_64") url="http://www.fmrib.ox.ac.uk/fsl/" license=(custom) -depends=(gd libxml2 libxml++2.6 gsl libpng nlopt newmat tcl tk zlib python glu boost-libs vtk sqlite python3 fslpy bc openblas) +depends=(gd libxml2 libxml++2.6 gsl libpng nlopt newmat tcl tk zlib python glu boost-libs vtk sqlite python3 'fslpy>=3.7.0' bc openblas) makedepends=(boost fftw gcc9) optdepends=(cuda) source=("https://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-sources.tar.gz" "https://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-feeds.tar.gz" "buildSettings.mk" - "imcp" - "imglob" - "immv" + "fsl_sub" "001-use_distribution_environment.patch" - "002-fix_meldata_usage_of_ifstream.patch" - "003-fix_fsl_exec_empty_errorCode.patch" - "004-fix_missing_LIB_PROB.patch" - "005-fix_cuda_thrust_include.patch" - "006-compile_ptx2_without_std-c++11.patch") + "002-fix_fsl_exec_empty_errorCode.patch" + "003-fix_missing_LIB_PROB.patch") -sha256sums=('58b88f38e080b05d70724d57342f58e1baf56e2bd3b98506a72b4446cad5033e' - '411daed14287d6ba536cb531450941ab1f570309cd561de4e2a4b0ec43a7e9f7' - 'c7f93adcf037a73182ae42ae6a59d3eb04a492888b6c2a6b528f9cd16539b2b2' - '8aac3a2ea61bb4c38eb363262ab7f89e55c49a5feb9912fd2ff71f2439f11fc9' - 'b3280bafc86d04dfa8835ef21f50469f2645bf09c36edcdd3f04349ce2c74225' - '8e343b0ff93477280fd9a980822ddc9980afa7201dea51c886376c189c234c99' +sha256sums=('df12b0b1161a26470ddf04e4c5d5d81580a04493890226207667ed8fd2b4b83f' + 'e68e1efeb45750f876f350442f56c4830d211e9fb16daa5ad134bb8e1ef1ae18' + '880c46d4ef8a8ee1401e1fdb71dadd0f79aad2154967a03232844845227394a3' + '2516982d151ab9e450a9ac6d5a6fc87099a7acc067514d80422c69950e618170' '906ac7de8068e5a5487b083844b50b6afd7562866088a4175fd88030182affdd' - '13d4cf35343e7a73bc2534c94b1b0d4db41c338d374e6982091e4cf7a421d420' '64b4ccefa63a3cf920b185dd52e94b918c24f2cedaebcec8efb767bd80a6418a' - 'adea0372f42026e72e385f1bec19ecc8cffa46de1f617271f14c9345c6b83c04' - '9471addfc2f880350eedadcb99cb8b350abf42be1c0652ccddf49e34e5e48734' - 'ab68cb802243ce715eff0d1136cfa29fa34a3e09934e5e20e02a092d69028df1') + 'adea0372f42026e72e385f1bec19ecc8cffa46de1f617271f14c9345c6b83c04') prepare() { cd "${srcdir}" @@ -48,15 +42,10 @@ prepare() { # Apply patches patch -Np1 -i "${srcdir}"/001-use_distribution_environment.patch - patch -Np1 -i "${srcdir}"/002-fix_meldata_usage_of_ifstream.patch # From https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;e8fa48c1.1501 patch -Np1 -i "${srcdir}"/003-fix_fsl_exec_empty_errorCode.patch # I'm not sure why -L${LIB_PROB} is missing in some Makefiles patch -Np1 -i "${srcdir}"/004-fix_missing_LIB_PROB.patch - # Adapted from Caspar van Leeuwen's patch: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;2b74023.2006 - patch -Np1 -i "${srcdir}"/005-fix_cuda_thrust_include.patch - # ptx2 does not compile when assuming C++11 standard - patch -Np1 -i "${srcdir}"/006-compile_ptx2_without_std-c++11.patch # Insert makepkg build flags into configuration sed -i '0,/${AccumulatedIncFlags}/{s^${AccumulatedIncFlags}^& '"${CFLAGS}"'^}' "${srcdir}/fsl/config/common/vars.mk" @@ -69,16 +58,22 @@ prepare() { build() { export FSLDIR="${srcdir}/fsl" cd "${FSLDIR}" - ./build - - # Install missing binaries, which are no longer shipped (depends on fslpy) - /usr/bin/install -m 755 "${srcdir}"/{imcp,imglob,immv} "${srcdir}/fsl/bin" + MAKEOPTIONS="-j $NJOBS" ./build extras CiftiLib-master utils znzlib NewNifti fslio giftiio miscmaths newimage libvis first_lib meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc + MAKEOPTIONS="" ./build fslsurface # fslsurface does not like parallel compiling + MAKEOPTIONS="-j $NJOBS" ./build libmeshutils newmesh DiscreteOpt FastPDlib MSMRegLib misc_c topup asl_mfree avwutils basil baycest bet2 bianca cluster fsl_deface eddy fabber_core fabber_models_asl fabber_models_cest fabber_models_dce fabber_models_dsc fabber_models_dualecho fabber_models_dwi fabber_models_pet fabber_models_qbold fabber_models_t1 fast4 fdt feat5 film filmbabe first flameo flirt fnirt fslvbm fugue gps lesions mcflirt melodic misc_scripts miscvis mist mm MSM oxford_asl possum ptx2 qboot randomise siena slicetimer susan swe tbss verbena xtract + # Install missing binaries, which are now Python scripts and shipped with fslpy + /usr/bin/install -m 755 /usr/bin/{imcp,imglob,immv} "${srcdir}"/fsl/bin + # Install missing fsl_sub script from 6.0.4 + /usr/bin/install -m 755 "${srcdir}"/fsl_sub "${srcdir}"/fsl/bin + # Create fake fslpython environment (all dependencies have been taken care of system-wide) + ln -s /usr/bin/python "${srcdir}"/fsl/bin/fslpython } check() { export FSLDIR="${srcdir}/fsl" export FEEDSDIR="${srcdir}/feeds" . "${FSLDIR}/etc/fslconf/fsl.sh" + export PATH="${FSLDIR}/bin":${PATH} cd "${FEEDSDIR}" time ./RUN all } |