diff options
| author | Tobias Bachmann | 2018-11-26 17:47:59 +0100 |
|---|---|---|
| committer | Tobias Bachmann | 2018-11-26 17:47:59 +0100 |
| commit | 5b6a58592b3b3f47d83fe4199a0413861a980209 (patch) | |
| tree | 276b6e3ccf039b1834f914d7d72417ce330302bd | |
| parent | 9a505b4833ab107ae2a5829e81648b773e3be10f (diff) | |
| download | aur-5b6a58592b3b3f47d83fe4199a0413861a980209.tar.gz | |
Initial commit for FSL 6.0
| -rw-r--r-- | .SRCINFO | 34 | ||||
| -rw-r--r-- | 001-use_distribution_environment.patch | 232 | ||||
| -rw-r--r-- | 002-fix_meldata_usage_of_ifstream.patch | 11 | ||||
| -rw-r--r-- | 003-fix_fsl_exec_empty_errorCode.patch | 12 | ||||
| -rwxr-xr-x | PKGBUILD | 118 | ||||
| -rwxr-xr-x | imcp | 124 | ||||
| -rwxr-xr-x | imglob | 124 | ||||
| -rwxr-xr-x | immv | 123 |
8 files changed, 331 insertions, 447 deletions
@@ -1,9 +1,8 @@ pkgbase = fsl pkgdesc = A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data - pkgver = 5.0.11 + pkgver = 6.0.0 pkgrel = 1 url = http://www.fmrib.ox.ac.uk/fsl/ - arch = i686 arch = x86_64 license = custom makedepends = boost @@ -21,25 +20,28 @@ pkgbase = fsl depends = python depends = glu depends = boost-libs - depends = vtk6 + depends = vtk depends = sqlite + depends = python3 + depends = fslpy + depends = bc optdepends = cuda - source = http://www.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-sources.tar.gz - source = http://www.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.11-feeds.tar.gz - source = systemvars.mk - source = externallibs.mk - source = fsl_exec.patch + source = http://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.0-sources.tar.gz + source = http://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.0-feeds.tar.gz source = imcp source = imglob source = immv - sha1sums = 4e80fce7b9626c351766966ba3be5d428e1c27cc - sha1sums = 7f9d1289887f6ff684599ce3d7a260f3d81011f2 - sha1sums = 679c65c90e79b7f748ad1c2d4b5abeebebf05dfd - sha1sums = db514c2eaa48ae924cb1c26d8b0b25d47a812876 - sha1sums = 2df550b126a6ec6022a164a18dddffe4e59962f9 - sha1sums = e2d4cc873a23eedcea093715b49ace41fc6f6e1c - sha1sums = f6d6d0177561b0f036a7e1fae4443332becd134b - sha1sums = efb997fbaaffb5129eca2ea9388b45421e6e6de4 + source = 001-use_distribution_environment.patch + source = 002-fix_meldata_usage_of_ifstream.patch + source = 003-fix_fsl_exec_empty_errorCode.patch + sha256sums = 94853ddd1c16d03050a0ef58b8801fd094a7b3636cc3cf35b36c576091143276 + sha256sums = 0d41376add12a6dbf67da19c1875f18bb6fa05e24e8a43d97eff160c70881ad2 + sha256sums = c61f185fbe7e297c4518e96377aa5ff4852f90eda0dbb9ae8edc5e24735e14ad + sha256sums = 7a1039cdc38b4d728f14efce3b0fda0cadc7bfcd3432556c3f3113985bf2720a + sha256sums = b6f61a6d5672b6684f19150f6e21ded1bd04ec6415dcf07a32291e4002bfa5d8 + sha256sums = d1dada74e7625ce3a9031af851ff1f3aed9a3f5600dc49a5db13f829cb8c41cb + sha256sums = 13d4cf35343e7a73bc2534c94b1b0d4db41c338d374e6982091e4cf7a421d420 + sha256sums = 64b4ccefa63a3cf920b185dd52e94b918c24f2cedaebcec8efb767bd80a6418a pkgname = fsl diff --git a/001-use_distribution_environment.patch b/001-use_distribution_environment.patch new file mode 100644 index 000000000000..ef84b6e115d8 --- /dev/null +++ b/001-use_distribution_environment.patch @@ -0,0 +1,232 @@ +--- a/fsl/etc/fslconf/fsl.sh 2014-05-19 16:54:10.000000000 +0200 ++++ b/fsl/etc/fslconf/fsl.sh 2018-11-25 11:26:42.623047078 +0100 +@@ -26,8 +26,8 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-FSLTCLSH=$FSLDIR/bin/fsltclsh +-FSLWISH=$FSLDIR/bin/fslwish ++FSLTCLSH=/usr/bin/tclsh ++FSLWISH=/usr/bin/wish + + export FSLTCLSH FSLWISH + +--- a/fsl/etc/fslconf/fsl.csh 2014-05-19 16:54:10.000000000 +0200 ++++ b/fsl/etc/fslconf/fsl.csh 2018-11-25 11:26:42.623047078 +0100 +@@ -25,8 +25,8 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-setenv FSLTCLSH $FSLDIR/bin/fsltclsh +-setenv FSLWISH $FSLDIR/bin/fslwish ++setenv FSLTCLSH /usr/bin/tclsh ++setenv FSLWISH /usr/bin/wish + + # The following variables are used for running code in parallel across + # several machines ( i.e. for FDT ) +--- a/fsl/etc/fslconf/fsl-devel.sh 2014-05-19 16:54:10.000000000 +0200 ++++ b/fsl/etc/fslconf/fsl-devel.sh 2018-11-25 11:26:42.623047078 +0100 +@@ -26,8 +26,8 @@ + # The following variables specify paths for programs and can be changed + # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) + +-FSLTCLSH=$FSLDIR/bin/fsltclsh +-FSLWISH=$FSLDIR/bin/fslwish ++FSLTCLSH=/usr/bin/tclsh ++FSLWISH=/usr/bin/wish + + export FSLTCLSH FSLWISH + +--- a/fsl/extras/build 2016-11-15 15:30:21.000000000 +0100 ++++ b/fsl/extras/build 2018-11-25 14:10:48.382885194 +0100 +@@ -96,21 +96,20 @@ + BUILDICONV=1 + fi + fi +-PROJECTS="tcl tk" ++PROJECTS="" + if [ ${BUILDZLIB} -eq 1 ]; then +- PROJECTS="${PROJECTS} zlib" ++ PROJECTS="${PROJECTS}" + fi +-PROJECTS="${PROJECTS} libpng" ++PROJECTS="${PROJECTS}" + if [ ${BUILDICONV} -eq 1 ]; then +- PROJECTS="${PROJECTS} libiconv" ++ PROJECTS="${PROJECTS}" + fi +-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" +-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxml++-2.34.0 libsqlite libnlopt ../include/armawrap/dummy_newmat" ++PROJECTS="${PROJECTS} libgdc libprob libcprob cprob newran ../include/armawrap/dummy_newmat" + for projname in $PROJECTS; do + if [ -d $FSLESRCDIR/$projname ] ; then + buildIt $FSLESRCDIR $projname 1 + elif [ "$projname" = "boost" -a -d ${FSLEXTINC}/boost/boost ]; then +- buildIt $FSLEXTINC boost 0 ++ buildIt $FSLEXTINC 0 + fi + done + +--- a/fsl/src/mist-clean/Makefile 2018-10-17 13:00:28.000000000 +0200 ++++ b/fsl/src/mist-clean/Makefile 2018-11-25 11:26:42.643047048 +0100 +@@ -2,15 +2,15 @@ + + NLOPT_INC = ${FSLEXTINC} + NLOPT_LIB = ${FSLEXTLIB} +-SQLITE_INC = ${FSLEXTINC}/libsqlite +-SQLITE_LIB = ${FSLEXTLIB} ++SQLITE_INC = /usr/include/libsqlite ++SQLITE_LIB = /usr/lib + + PROJNAME = mist + + XFILES = mist/mist + SCRIPTS = bin/mist_1_train bin/mist_2_fit bin/mist_FA_reg bin/mist_display bin/mist_mesh_utils + +-USRCXXFLAGS = -std=c++11 ++USRCXXFLAGS = -std=c++11 -DBOOST_LOG_DYN_LINK + USRINCFLAGS = -I${FSLDIR}/include/newimage -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_GDC} -I${INC_GD} -I${SQLITE_INC} -I${NLOPT_INC} -I${VTKDIR_INC} -Icommon + USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_ZLIB} -L${LIB_BOOST} -L${LIB_GDC} -L${LIB_GD} -L${NLOPT_LIB} -L${VTKDIR_LIB} + +@@ -19,14 +19,14 @@ + LIBRT = -lrt + endif + +-LDLIBS = -lvtkIOLegacy${VTKSUFFIX} -lvtkIOCore${VTKSUFFIX} -lvtkFiltersModeling${VTKSUFFIX} -lvtkFiltersCore${VTKSUFFIX} \ ++LDLIBS = -lsqlite3 -lvtkIOLegacy${VTKSUFFIX} -lvtkIOCore${VTKSUFFIX} -lvtkFiltersModeling${VTKSUFFIX} -lvtkFiltersCore${VTKSUFFIX} \ + -lvtkCommonExecutionModel${VTKSUFFIX} -lvtkCommonDataModel${VTKSUFFIX} -lvtkCommonMisc${VTKSUFFIX} \ + -lvtkCommonSystem${VTKSUFFIX} -lvtkCommonTransforms${VTKSUFFIX} -lvtkCommonMath${VTKSUFFIX} \ + -lvtkCommonCore${VTKSUFFIX} -lvtksys${VTKSUFFIX} \ + -lboost_log -lboost_log_setup -lboost_thread -lboost_filesystem -lboost_date_time -lboost_chrono \ + -lboost_system -lboost_serialization -lboost_regex -lwarpfns -lbasisfield -lnewimage -lmiscmaths \ + -lnewmat -lgdc -lgd -lpng -lNewNifti -lutils -lznz -lm -lz -lnlopt -lpthread -ldl \ +- ${SQLITE_LIB}/libsqlite3.a ${LIBRT} ++ ${LIBRT} + + HDRS = common/gibbsshapemodel.h common/mrfshapemodel.h common/mvnshapemodel.h common/plotting.h common/profilefilters.h common/profilemixtures.h common/profilemodel.h common/profilepriors.h common/serialisation.h common/shape.h common/shapemodel.h common/stats.h common/transformation.h mist/builddate.h + +--- a/fsl/config/_FSLMACHTYPE/externallibs.mk 2018-10-10 13:12:48.000000000 +0200 ++++ b/fsl/config/_FSLMACHTYPE/externallibs.mk 2018-11-25 11:26:48.363038307 +0100 +@@ -7,26 +7,27 @@ + FSLEXTBIN=${FSLDIR}/extras/bin + + # GD library +-LIB_GD = ${FSLEXTLIB} +-INC_GD = ${FSLEXTINC} ++LIB_GD = /usr/lib ++INC_GD = /usr/include + + # GDC library + LIB_GDC = ${FSLEXTLIB} + INC_GDC = ${FSLEXTINC}/libgdc + + # LIBXML2 library +-INC_XML2 = ${FSLEXTINC}/libxml2 ++INC_XML2 = /usr/include/libxml2 + + # LIBXML++ library +-INC_XML++ = ${FSLEXTINC}/libxml++-2.6 +-INC_XML++CONF = ${FSLEXTLIB}/libxml++-2.6/include ++INC_XML++ = /usr/include/libxml++-2.6 ++INC_XML++CONF = /usr/lib/libxml++-2.6/include ++ + # GSL library +-LIB_GSL = ${FSLEXTLIB} +-INC_GSL = ${FSLEXTINC}/gsl ++LIB_GSL = /usr/lib ++INC_GSL = /usr/include/gsl + + # PNG library +-LIB_PNG = ${FSLEXTLIB} +-INC_PNG = ${FSLEXTINC} ++LIB_PNG = /usr/lib ++INC_PNG = /usr/include/libpng1.6 + + # PROB library + LIB_PROB = ${FSLEXTLIB} +@@ -38,7 +39,9 @@ + + # NEWMAT library + #LIB_NEWMAT = ${FSLEXTLIB} -llapack -lblas or just -lopenblas +-LIB_NEWMAT = ${FSLEXTLIB} -lopenblas ++#LIB_NEWMAT = /usr/lib/newmat ++#INC_NEWMAT = /usr/include/newmat ++LIB_NEWMAT = ${FSLEXTLIB} -llapack -lblas + INC_NEWMAT = ${FSLEXTINC}/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD + + # NEWRAN library +@@ -46,29 +49,29 @@ + INC_NEWRAN = ${FSLEXTINC}/newran + + # ZLIB library +-LIB_ZLIB = /lib64 ++LIB_ZLIB = /usr/lib + INC_ZLIB = /usr/include + + # BOOST library +-BOOSTDIR = ${FSLEXTINC}/boost +-LIB_BOOST = ${BOOSTDIR} +-INC_BOOST = ${BOOSTDIR} ++#BOOSTDIR = ${FSLEXTINC}/boost ++LIB_BOOST = /usr/lib ++INC_BOOST = /usr/include/boost + + # QT library +-QTDIR = /usr/lib/qt3 +-LIB_QT = ${QTDIR}/lib +-INC_QT = ${QTDIR}/include ++#QTDIR = /usr/lib/qt5 ++LIB_QT = /usr/lib ++INC_QT = ${QTDIR}/include/qt + + # QWT library +-QWTDIR = /usr/local/qwt +-LIB_QWT = ${QWTDIR}/lib +-INC_QWT = ${QWTDIR}/include ++#QWTDIR = /usr/local/qwt ++LIB_QWT = /usr/lib ++INC_QWT = /usr/include/qwt + + # FFTW3 library +-LIB_FFTW3 = ${FSLEXTLIB} +-INC_FFTW3 = ${FSLEXTINC}/fftw3 ++LIB_FFTW3 = /usr/lib ++INC_FFTW3 = /usr/include + + # VTK library +-VTKDIR_INC = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/include/vtk-7.0 +-VTKDIR_LIB = /home/fs0/cowboy/var/caper_linux_64-gcc4.4/VTK7/lib +-VTKSUFFIX = -7.0 +\ No newline at end of file ++VTKDIR_INC = /usr/include/vtk ++VTKDIR_LIB = /usr/lib ++VTKSUFFIX = +--- a/fsl/config/_FSLMACHTYPE/systemvars.mk 2017-09-04 14:09:26.000000000 +0200 ++++ b/fsl/config/_FSLMACHTYPE/systemvars.mk 2018-11-25 11:26:48.363038307 +0100 +@@ -8,7 +8,7 @@ + CP = /bin/cp + MV = /bin/mv + INSTALL = install -p +-TCLSH = ${FSLDIR}/bin/fsltclsh ++TCLSH = /usr/bin/tclsh + RANLIB = echo + + FSLML = ${FSLDIR}/bin/fslml +@@ -30,14 +30,14 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS = -march=native -g -O3 -fexpensive-optimizations ${ARCHFLAGS} + MACHDBGFLAGS = -g +-GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long ++GNU_ANSI_FLAGS = -Wall -ansi -pedantic -std=c++11 -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn + ANSI_FLAGS = ${GNU_ANSI_FLAGS} + + # CUDA development environment +-CUDA_INSTALLATION = /opt/cuda-7.5 ++CUDA_INSTALLATION = /opt/cuda + GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION}) + LIB_CUDA = ${CUDA_INSTALLATION}/lib64 + INC_CUDA = ${CUDA_INSTALLATION}/include diff --git a/002-fix_meldata_usage_of_ifstream.patch b/002-fix_meldata_usage_of_ifstream.patch new file mode 100644 index 000000000000..e35e74b7e2b0 --- /dev/null +++ b/002-fix_meldata_usage_of_ifstream.patch @@ -0,0 +1,11 @@ +--- a/fsl/src/melodic/meldata.cc 2018-10-23 18:49:51.000000000 +0200 ++++ b/fsl/src/melodic/meldata.cc 2018-11-25 11:26:42.639047054 +0100 +@@ -1015,7 +1015,7 @@ + Resels = 1.0; + + in.open(logger.appendDir("smoothest").c_str(), ios::in); +- if(in>0){ ++ if(!!in){ + for(int ctr=1; ctr<7; ctr++) + in >> str; + in.close(); diff --git a/003-fix_fsl_exec_empty_errorCode.patch b/003-fix_fsl_exec_empty_errorCode.patch new file mode 100644 index 000000000000..5e8cb0269cd2 --- /dev/null +++ b/003-fix_fsl_exec_empty_errorCode.patch @@ -0,0 +1,12 @@ +--- a/fsl/src/misc_tcl/fsl_exec.tcl 2018-10-23 18:49:44.000000000 +0200 ++++ b/fsl/src/misc_tcl/fsl_exec.tcl 2018-11-25 18:52:30.636934316 +0100 +@@ -175,6 +175,9 @@ + set logout "" + } + ++ # make sure errorCode is set ++ if { ! [ info exists ::errorCode ] } { set ::errorCode "NONE" } ++ + # run and log the actual command + if { $do_logout } { + fsl:echo $logout "\n$thecommand" @@ -1,117 +1,68 @@ +# Maintainer: Tobias Bachmann <tobachmann@gmx.de> # Contributor: fishburn <frankthefishburn@gmail.com> -# Note: As of 5.0.11 certain key scripts (imcp, imglob, immv) are no longer shipped by upstream -# Their recommendation is to install fslpython, but this requires running an opaque installer and -# doubles the package size with no additional obvious benefit than these 3 tiny scripts. So I -# have decided to just bundle the scripts from 5.0.10 with the package from now on. - pkgname=fsl -pkgver=5.0.11 +pkgver=6.0.0 pkgrel=1 pkgdesc="A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data" -arch=("i686" "x86_64") +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 vtk6 sqlite) +depends=(gd libxml2 libxml++2.6 gsl libpng nlopt newmat tcl tk zlib python glu boost-libs vtk sqlite python3 fslpy bc) makedepends=(boost fftw) optdepends=(cuda) -sha1sums=('4e80fce7b9626c351766966ba3be5d428e1c27cc' - '7f9d1289887f6ff684599ce3d7a260f3d81011f2' - '679c65c90e79b7f748ad1c2d4b5abeebebf05dfd' - 'db514c2eaa48ae924cb1c26d8b0b25d47a812876' - '2df550b126a6ec6022a164a18dddffe4e59962f9' - 'e2d4cc873a23eedcea093715b49ace41fc6f6e1c' - 'f6d6d0177561b0f036a7e1fae4443332becd134b' - 'efb997fbaaffb5129eca2ea9388b45421e6e6de4') - source=("http://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-sources.tar.gz" "http://www.fmrib.ox.ac.uk/fsldownloads/fsl-${pkgver}-feeds.tar.gz" - "systemvars.mk" - "externallibs.mk" - "fsl_exec.patch" "imcp" "imglob" - "immv") + "immv" + "001-use_distribution_environment.patch" + "002-fix_meldata_usage_of_ifstream.patch" + "003-fix_fsl_exec_empty_errorCode.patch") + +sha256sums=('94853ddd1c16d03050a0ef58b8801fd094a7b3636cc3cf35b36c576091143276' + '0d41376add12a6dbf67da19c1875f18bb6fa05e24e8a43d97eff160c70881ad2' + 'c61f185fbe7e297c4518e96377aa5ff4852f90eda0dbb9ae8edc5e24735e14ad' + '7a1039cdc38b4d728f14efce3b0fda0cadc7bfcd3432556c3f3113985bf2720a' + 'b6f61a6d5672b6684f19150f6e21ded1bd04ec6415dcf07a32291e4002bfa5d8' + 'd1dada74e7625ce3a9031af851ff1f3aed9a3f5600dc49a5db13f829cb8c41cb' + '13d4cf35343e7a73bc2534c94b1b0d4db41c338d374e6982091e4cf7a421d420' + '64b4ccefa63a3cf920b185dd52e94b918c24f2cedaebcec8efb767bd80a6418a') prepare() { - cd "${srcdir}" - export FSLDIR="${srcdir}/fsl" . "${FSLDIR}/etc/fslconf/fsl.sh" - export FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` - - # Create new configuration - mkdir -p "${FSLDIR}/config/${FSLMACHTYPE}" - cp "${srcdir}/systemvars.mk" "${FSLDIR}/config/${FSLMACHTYPE}/" - cp "${srcdir}/externallibs.mk" "${FSLDIR}/config/${FSLMACHTYPE}/" - - # Copy makepkg build flags into configuration + export FSLMACHTYPE=$(${FSLDIR}/etc/fslconf/fslmachtype.sh) + mkdir "${FSLDIR}/config/${FSLMACHTYPE}" + # Use config linux_64-gcc4.8 as template + cp "${FSLDIR}"/config/linux_64-gcc4.8/{externallibs.mk,systemvars.mk} "${FSLDIR}/config/${FSLMACHTYPE}" + sed -i "s/_FSLMACHTYPE/${FSLMACHTYPE}/g" "${srcdir}/001-use_distribution_environment.patch" + + # Apply patches + patch -Np1 -i "${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" + + # Insert makepkg build flags into configuration sed -i '0,/${AccumulatedIncFlags}/{s^${AccumulatedIncFlags}^& '"${CFLAGS}"'^}' "${srcdir}/fsl/config/common/vars.mk" sed -i '0,/${AccumulatedIncFlags}/{s^${AccumulatedIncFlags}^& '"${CPPFLAGS}"'^}' "${srcdir}/fsl/config/common/vars.mk" sed -i '1,/${AccumulatedIncFlags}/!{s^${AccumulatedIncFlags}^& '"${CXXFLAGS}"'^}' "${srcdir}/fsl/config/common/vars.mk" sed -i '1,/${AccumulatedIncFlags}/!{s^${AccumulatedIncFlags}^& '"${CPPFLAGS}"'^}' "${srcdir}/fsl/config/common/vars.mk" sed -i 's^LDFLAGS = .*$^& '"${LDFLAGS}"'^g' "${srcdir}/fsl/config/common/vars.mk" - - # Fix 32-bit - if test "$CARCH" == i686; then - sed -i "s^-m64^^g" "${FSLDIR}/config/${FSLMACHTYPE}/systemvars.mk" - fi - - # Use system TCL/Tk - sed -i 's^$FSLDIR/bin/fsltclsh^/usr/bin/tclsh^g' "${FSLDIR}/etc/fslconf/fsl.sh" - sed -i 's^$FSLDIR/bin/fsltclsh^/usr/bin/tclsh^g' "${FSLDIR}/etc/fslconf/fsl-devel.sh" - sed -i 's^$FSLDIR/bin/fsltclsh^/usr/bin/tclsh^g' "${FSLDIR}/etc/fslconf/fsl.csh" - sed -i 's^$FSLDIR/bin/fslwish^/usr/bin/wish^g' "${FSLDIR}/etc/fslconf/fsl.sh" - sed -i 's^$FSLDIR/bin/fslwish^/usr/bin/wish^g' "${FSLDIR}/etc/fslconf/fsl-devel.sh" - sed -i 's^$FSLDIR/bin/fslwish^/usr/bin/wish^g' "${FSLDIR}/etc/fslconf/fsl.csh" - - # Disable building of system libraries - sed -i 's/ libgd / /g' "${FSLDIR}/extras/build" - sed -i 's/ libxml2-2.9.2 / /g' "${FSLDIR}/extras/build" - sed -i 's/ libxml++-2.34.0 / /g' "${FSLDIR}/extras/build" - sed -i 's/ newmat / /g' "${FSLDIR}/extras/build" - sed -i 's/ boost / /g' "${FSLDIR}/extras/build" - sed -i 's/ libnlopt / /g' "${FSLDIR}/extras/build" - sed -i 's/ libpng"/"/g' "${FSLDIR}/extras/build" - sed -i 's/ libiconv"/"/g' "${FSLDIR}/extras/build" - sed -i 's/ zlib"/"/g' "${FSLDIR}/extras/build" - sed -i 's/ fftw"/"/g' "${FSLDIR}/extras/build" - sed -i 's/"tcl tk"/""/g' "${FSLDIR}/extras/build" - - # Link mist-clean against system sqlite - sed -i 's^${SQLITE_LIB}/libsqlite3.a^-lsqlite3^g' "${srcdir}/fsl/src/mist-clean/Makefile" - - # Fix Melodic use of ifstream - sed -i 's^if(in>0)^if(!!in)^g' "${FSLDIR}/src/melodic/meldata.cc" - - # Add missing library directories - sed -i 's^-L${LIB_ZLIB}$^& -L${LIB_PROB}^g' "${FSLDIR}/src/asl_mfree/Makefile" - sed -i 's^-L${LIB_NEWMAT} $^&-L${LIB_PROB}^g' "${FSLDIR}/src/first/Makefile" - sed -i 's^-L${LIB_NEWMAT} $^&-L${LIB_PROB}^g' "${FSLDIR}/src/topup/Makefile" - - # Fix problem w/ dynamically-linked boost - sed -i 's^USRCXXFLAGS = -std=c++11$^& -DBOOST_LOG_DYN_LINK^g' "${FSLDIR}/src/mist-clean/Makefile" - - # Fix fsl_exec.tcl session issue (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;e8fa48c1.1501) - patch -p0 < fsl_exec.patch - - # Fix missing library path in Eddy makefile - sed -i 's^USRLDFLAGS=-L${LIB_NEWMAT}^USRLDFLAGS=-L${LIB_PROB} -L${LIB_NEWMAT}^g' "${FSLDIR}/src/eddy/Makefile" - } build() { - export FSLDIR="${srcdir}/fsl" cd "${FSLDIR}" ./build - cp -v "${srcdir}"/{imcp,imglob,immv} "${srcdir}/fsl/bin" + # Install missing binaries, which are no longer shipped (depends on fslpy) + /usr/bin/install -m 755 "${srcdir}"/{imcp,imglob,immv} "${srcdir}/fsl/bin" } check() { - export FSLDIR="${srcdir}/fsl" export FEEDSDIR="${srcdir}/feeds" . "${FSLDIR}/etc/fslconf/fsl.sh" @@ -120,7 +71,6 @@ check() { } package() { - rm -rf "${srcdir}/fsl/src" rm -rf "${srcdir}/fsl/extras/src" rm -rf "${srcdir}/fsl/extras/include" @@ -145,6 +95,7 @@ package() { mkdir -p "${pkgdir}/usr/share/licenses/fsl" grep -v \< "${srcdir}/fsl/doc/fsl/licence.html" | cat -s > "${pkgdir}/usr/share/licenses/fsl/LICENSE" + # Fix permissions find "${pkgdir}" -type f -exec chmod 644 {} \; find "${pkgdir}" -type d -exec chmod 755 {} \; find "${pkgdir}/opt/fsl/bin" -exec chmod 755 {} \; @@ -154,7 +105,8 @@ package() { mkdir -p "${pkgdir}/opt/fsl/feeds/results" chmod -R 777 "${pkgdir}/opt/fsl/feeds/results" chmod 755 "${pkgdir}/opt/fsl/feeds/RUN" - + + # Clean up find "${pkgdir}" -empty -delete find "${pkgdir}" -type f -exec sed -i 's^/usr/local/fsl^/opt/fsl^g' "{}" \; } @@ -1,118 +1,10 @@ -#!/bin/sh - -# imcp - copy image files -# -# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group -# -# Copyright (C) 1999-2004 University of Oxford -# -# Part of FSL - FMRIB's Software Library -# http://www.fmrib.ox.ac.uk/fsl -# fsl@fmrib.ox.ac.uk -# -# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -# Imaging of the Brain), Department of Clinical Neurology, Oxford -# University, Oxford, UK -# -# -# LICENCE -# -# FMRIB Software Library, Release 5.0 (c) 2012, The University of -# Oxford (the "Software") -# -# The Software remains the property of the University of Oxford ("the -# University"). -# -# The Software is distributed "AS IS" under this Licence solely for -# non-commercial use in the hope that it will be useful, but in order -# that the University as a charitable foundation protects its assets for -# the benefit of its educational and research purposes, the University -# makes clear that no condition is made or to be implied, nor is any -# warranty given or to be implied, as to the accuracy of the Software, -# or that it will be suitable for any particular purpose or for use -# under any specific conditions. Furthermore, the University disclaims -# all responsibility for the use which is made of the Software. It -# further disclaims any liability for the outcomes arising from using -# the Software. -# -# The Licensee agrees to indemnify the University and hold the -# University harmless from and against any and all claims, damages and -# liabilities asserted by third parties (including claims for -# negligence) which arise directly or indirectly from the use of the -# Software or the sale of any products based on the Software. -# -# No part of the Software may be reproduced, modified, transmitted or -# transferred in any form or by any means, electronic or mechanical, -# without the express permission of the University. The permission of -# the University is not required if the said reproduction, modification, -# transmission or transference is done without financial return, the -# conditions of this Licence are imposed upon the receiver of the -# product, and all original and amended source code is included in any -# transmitted product. You may be held legally responsible for any -# copyright infringement that is caused or encouraged by your failure to -# abide by these terms and conditions. -# -# You are not permitted under this Licence to use this Software -# commercially. Use for which any financial return is received shall be -# defined as commercial use, and includes (1) integration of all or part -# of the source code or the Software into a product for sale or license -# by or on behalf of Licensee to third parties or (2) use of the -# Software or any derivative of it for research with the final aim of -# developing software products for sale or license to a third party or -# (3) use of the Software or any derivative of it for research with the -# final aim of developing non-software products for sale or license to a -# third party, or (4) use of the Software to provide any service to an -# external organisation for which payment is received. If you are -# interested in using the Software commercially, please contact Oxford -# University Innovation ("OUI"), the technology transfer company of the -# University, to negotiate a licence. Contact details are: -# Innovation@innovation.ox.ac.uk quoting reference DE/9564. -export LC_ALL=C - -if [ $# -lt 2 ] ; then - echo "Usage: $0 <file1> <file2>" - echo "Usage: $0 <file1> <file2> ... <fileN> <directory>" - echo " Copies images from file1 to file2 (including all extensions)" - echo " NB: filenames can be basenames or include an extension" - exit 1; -fi - -if [ $# -eq 2 -a ! -d $2 ] ; then - f1=`${FSLDIR}/bin/remove_ext $1`; - f2=`${FSLDIR}/bin/remove_ext $2`; - # do the copies - if [ -f ${f1}.hdr ] ; then /bin/cp ${f1}.hdr ${f2}.hdr ; fi - if [ -f ${f1}.hdr.gz ] ; then /bin/cp ${f1}.hdr.gz ${f2}.hdr.gz ; fi - if [ -f ${f1}.img ] ; then /bin/cp ${f1}.img ${f2}.img ; fi - if [ -f ${f1}.img.gz ] ; then /bin/cp ${f1}.img.gz ${f2}.img.gz ; fi - if [ -f ${f1}.nii ] ; then /bin/cp ${f1}.nii ${f2}.nii ; fi - if [ -f ${f1}.nii.gz ] ; then /bin/cp ${f1}.nii.gz ${f2}.nii.gz ; fi - if [ -f ${f1}.mnc ] ; then /bin/cp ${f1}.mnc ${f2}.mnc ; fi - if [ -f ${f1}.mnc.gz ] ; then /bin/cp ${f1}.mnc.gz ${f2}.mnc.gz ; fi -fi - -if [ $# -gt 2 -o -d $2 ] ; then - for nm in $@ ; do - dir=$nm; - done - if [ ! -d $dir ] ; then - echo "When using multiple arguments, last name must be a directory" - exit 1; - fi - # remove directory from list of files - flist="echo $@ | sed s/$dir \*\$//"; - for fn in $flist ; do - f1=`${FSLDIR}/bin/remove_ext $fn`; - # do the copies - if [ -f ${f1}.hdr ] ; then /bin/cp ${f1}.hdr ${dir} ; fi - if [ -f ${f1}.hdr.gz ] ; then /bin/cp ${f1}.hdr.gz ${dir} ; fi - if [ -f ${f1}.img ] ; then /bin/cp ${f1}.img ${dir} ; fi - if [ -f ${f1}.img.gz ] ; then /bin/cp ${f1}.img.gz ${dir} ; fi - if [ -f ${f1}.nii ] ; then /bin/cp ${f1}.nii ${dir} ; fi - if [ -f ${f1}.nii.gz ] ; then /bin/cp ${f1}.nii.gz ${dir} ; fi - if [ -f ${f1}.mnc ] ; then /bin/cp ${f1}.mnc ${dir} ; fi - if [ -f ${f1}.mnc.gz ] ; then /bin/cp ${f1}.mnc.gz ${dir} ; fi - done -fi +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +import re +import sys +from fsl.scripts.imcp import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) @@ -1,120 +1,10 @@ -#!/usr/bin/env python -# imglob - expand list of image filenames -# Stephen Smith, Mark Jenkinson and Matthew Webster FMRIB Image Analysis Group -# Copyright (C) 2009 University of Oxford -# Part of FSL - FMRIB's Software Library -# http://www.fmrib.ox.ac.uk/fsl -# fsl@fmrib.ox.ac.uk -# -# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -# Imaging of the Brain), Department of Clinical Neurology, Oxford -# University, Oxford, UK -# -# -# LICENCE -# -# FMRIB Software Library, Release 5.0 (c) 2012, The University of -# Oxford (the "Software") -# -# The Software remains the property of the University of Oxford ("the -# University"). -# -# The Software is distributed "AS IS" under this Licence solely for -# non-commercial use in the hope that it will be useful, but in order -# that the University as a charitable foundation protects its assets for -# the benefit of its educational and research purposes, the University -# makes clear that no condition is made or to be implied, nor is any -# warranty given or to be implied, as to the accuracy of the Software, -# or that it will be suitable for any particular purpose or for use -# under any specific conditions. Furthermore, the University disclaims -# all responsibility for the use which is made of the Software. It -# further disclaims any liability for the outcomes arising from using -# the Software. -# -# The Licensee agrees to indemnify the University and hold the -# University harmless from and against any and all claims, damages and -# liabilities asserted by third parties (including claims for -# negligence) which arise directly or indirectly from the use of the -# Software or the sale of any products based on the Software. -# -# No part of the Software may be reproduced, modified, transmitted or -# transferred in any form or by any means, electronic or mechanical, -# without the express permission of the University. The permission of -# the University is not required if the said reproduction, modification, -# transmission or transference is done without financial return, the -# conditions of this Licence are imposed upon the receiver of the -# product, and all original and amended source code is included in any -# transmitted product. You may be held legally responsible for any -# copyright infringement that is caused or encouraged by your failure to -# abide by these terms and conditions. -# -# You are not permitted under this Licence to use this Software -# commercially. Use for which any financial return is received shall be -# defined as commercial use, and includes (1) integration of all or part -# of the source code or the Software into a product for sale or license -# by or on behalf of Licensee to third parties or (2) use of the -# Software or any derivative of it for research with the final aim of -# developing software products for sale or license to a third party or -# (3) use of the Software or any derivative of it for research with the -# final aim of developing non-software products for sale or license to a -# third party, or (4) use of the Software to provide any service to an -# external organisation for which payment is received. If you are -# interested in using the Software commercially, please contact Oxford -# University Innovation ("OUI"), the technology transfer company of the -# University, to negotiate a licence. Contact details are: -# Innovation@innovation.ox.ac.uk quoting reference DE/9564. - -from __future__ import print_function +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +import re import sys -import os -import glob - -def usage(): - print("Usage: $0 [-extension/extensions] <list of names>") - print(" -extension for one image with full extension") - print(" -extensions for image list with full extensions") - sys.exit(1) - -def isImage(input,allExtensions): #Returns whether an input filename has an image extension ( and the basename and extension pair ) - for extension in allExtensions: - if input[-len(extension):] == extension: - return True, input[:-len(extension)], extension - return False, input, '' - -def removeImageExtension(input,allExtensions): - return isImage(input,allExtensions)[1] - -if len(sys.argv) <= 1: - usage() - -deleteExtensions=True -primaryExtensions=['.nii.gz', '.nii', '.hdr.gz', '.hdr'] -secondaryExtensions=['.img.gz', '.img'] -allExtensions=primaryExtensions+secondaryExtensions -validExtensions=primaryExtensions -startingArg=1 -if sys.argv[1] == "-extensions": - validExtensions=allExtensions - deleteExtensions=False - startingArg=2 -if sys.argv[1] == "-extension": - deleteExtensions=False - startingArg=2 - -filelist=[] -for arg in range(startingArg, len(sys.argv)): -# if isImage(sys.argv[arg],allExtensions)[0]: #These enable a "pedantic" style mode currently not used -# filelist.extend(glob.glob(sys.argv[arg])) -# else: -# for currentExtension in validExtensions: -# filelist.extend(glob.glob(sys.argv[arg]+currentExtension)) - for currentExtension in validExtensions: - filelist.extend(glob.glob(removeImageExtension(sys.argv[arg],allExtensions)+currentExtension)) +from fsl.scripts.imglob import main -if deleteExtensions: - filelist = [ removeImageExtension(file,allExtensions) for file in filelist ] -filelist=list(set(filelist)) -filelist.sort() -if len(filelist) > 0: - print(' '.join(filelist)) +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) @@ -1,117 +1,10 @@ -#!/bin/sh - -# immv - rename/move image files -# -# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group -# -# Copyright (C) 1999-2004 University of Oxford -# -# Part of FSL - FMRIB's Software Library -# http://www.fmrib.ox.ac.uk/fsl -# fsl@fmrib.ox.ac.uk -# -# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance -# Imaging of the Brain), Department of Clinical Neurology, Oxford -# University, Oxford, UK -# -# -# LICENCE -# -# FMRIB Software Library, Release 5.0 (c) 2012, The University of -# Oxford (the "Software") -# -# The Software remains the property of the University of Oxford ("the -# University"). -# -# The Software is distributed "AS IS" under this Licence solely for -# non-commercial use in the hope that it will be useful, but in order -# that the University as a charitable foundation protects its assets for -# the benefit of its educational and research purposes, the University -# makes clear that no condition is made or to be implied, nor is any -# warranty given or to be implied, as to the accuracy of the Software, -# or that it will be suitable for any particular purpose or for use -# under any specific conditions. Furthermore, the University disclaims -# all responsibility for the use which is made of the Software. It -# further disclaims any liability for the outcomes arising from using -# the Software. -# -# The Licensee agrees to indemnify the University and hold the -# University harmless from and against any and all claims, damages and -# liabilities asserted by third parties (including claims for -# negligence) which arise directly or indirectly from the use of the -# Software or the sale of any products based on the Software. -# -# No part of the Software may be reproduced, modified, transmitted or -# transferred in any form or by any means, electronic or mechanical, -# without the express permission of the University. The permission of -# the University is not required if the said reproduction, modification, -# transmission or transference is done without financial return, the -# conditions of this Licence are imposed upon the receiver of the -# product, and all original and amended source code is included in any -# transmitted product. You may be held legally responsible for any -# copyright infringement that is caused or encouraged by your failure to -# abide by these terms and conditions. -# -# You are not permitted under this Licence to use this Software -# commercially. Use for which any financial return is received shall be -# defined as commercial use, and includes (1) integration of all or part -# of the source code or the Software into a product for sale or license -# by or on behalf of Licensee to third parties or (2) use of the -# Software or any derivative of it for research with the final aim of -# developing software products for sale or license to a third party or -# (3) use of the Software or any derivative of it for research with the -# final aim of developing non-software products for sale or license to a -# third party, or (4) use of the Software to provide any service to an -# external organisation for which payment is received. If you are -# interested in using the Software commercially, please contact Oxford -# University Innovation ("OUI"), the technology transfer company of the -# University, to negotiate a licence. Contact details are: -# Innovation@innovation.ox.ac.uk quoting reference DE/9564. -export LC_ALL=C - -if [ $# -lt 1 ] ; then - echo "Usage: $0 <file1> <file2>" - echo " Moves images from file1 to file2 (including all extensions)" - echo " NB: filenames can be basenames or include an extension" - exit 1; -fi - -if [ $# -eq 2 -a ! -d $2 ] ; then - f1=`${FSLDIR}/bin/remove_ext $1`; - f2=`${FSLDIR}/bin/remove_ext $2`; - # do the moves - if [ -f ${f1}.hdr ] ; then /bin/mv ${f1}.hdr ${f2}.hdr ; fi - if [ -f ${f1}.hdr.gz ] ; then /bin/mv ${f1}.hdr.gz ${f2}.hdr.gz ; fi - if [ -f ${f1}.img ] ; then /bin/mv ${f1}.img ${f2}.img ; fi - if [ -f ${f1}.img.gz ] ; then /bin/mv ${f1}.img.gz ${f2}.img.gz ; fi - if [ -f ${f1}.nii ] ; then /bin/mv ${f1}.nii ${f2}.nii ; fi - if [ -f ${f1}.nii.gz ] ; then /bin/mv ${f1}.nii.gz ${f2}.nii.gz ; fi - if [ -f ${f1}.mnc ] ; then /bin/mv ${f1}.mnc ${f2}.mnc ; fi - if [ -f ${f1}.mnc.gz ] ; then /bin/mv ${f1}.mnc.gz ${f2}.mnc.gz ; fi -fi - -if [ $# -gt 2 -o -d $2 ] ; then - for nm in $@ ; do - dir=$nm; - done - if [ ! -d $dir ] ; then - echo "When using multiple arguments, last name must be a directory" - exit 1; - fi - # remove directory from list of files - flist="echo $@ | sed s/$dir \*\$//"; - for fn in $flist ; do - f1=`${FSLDIR}/bin/remove_ext $fn`; - # do the copies - if [ -f ${f1}.hdr ] ; then /bin/mv ${f1}.hdr ${dir} ; fi - if [ -f ${f1}.hdr.gz ] ; then /bin/mv ${f1}.hdr.gz ${dir} ; fi - if [ -f ${f1}.img ] ; then /bin/mv ${f1}.img ${dir} ; fi - if [ -f ${f1}.img.gz ] ; then /bin/mv ${f1}.img.gz ${dir} ; fi - if [ -f ${f1}.nii ] ; then /bin/mv ${f1}.nii ${dir} ; fi - if [ -f ${f1}.nii.gz ] ; then /bin/mv ${f1}.nii.gz ${dir} ; fi - if [ -f ${f1}.mnc ] ; then /bin/mv ${f1}.mnc ${dir} ; fi - if [ -f ${f1}.mnc.gz ] ; then /bin/mv ${f1}.mnc.gz ${dir} ; fi - done -fi +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +import re +import sys +from fsl.scripts.immv import main +if __name__ == '__main__': + sys.argv[0] = re.sub(r'(-script\.pyw?|\.exe)?$', '', sys.argv[0]) + sys.exit(main()) |