Date: Thu, 10 May 2007 10:40:33 -0500 (CDT) From: Jason Bacon <bacon@smithers.neuro.mcw.edu> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/112576: New port: science/fsl FMRIB Software Library Message-ID: <200705101540.l4AFeXup057223@smithers.neuro.mcw.edu> Resent-Message-ID: <200705101550.l4AFo57G010469@freefall.freebsd.org>
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>Number: 112576 >Category: ports >Synopsis: New port: science/fsl FMRIB Software Library >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Thu May 10 15:50:05 GMT 2007 >Closed-Date: >Last-Modified: >Originator: Jason Bacon >Release: FreeBSD 5.4-RELEASE i386 >Organization: Medical College of Wisconsin >Environment: System: FreeBSD smithers.neuro.mcw.edu 5.4-RELEASE FreeBSD 5.4-RELEASE #2: Wed Aug 24 14:54:53 CDT 2005 bacon@clone.neuro.mcw.edu:/usr/obj/usr/src/sys/clone i386 >Description: New port for FSL, the FMRIB Software Library from Oxford. FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data. http://www.fmrib.ox.ac.uk/fsl/ >How-To-Repeat: >Fix: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # science/fsl # science/fsl/files # science/fsl/files/arch-FreeBSD-gccx.x.x # science/fsl/files/arch-FreeBSD-gccx.x.x/systemvars.mk # science/fsl/files/arch-FreeBSD-gccx.x.x/externallibs.mk # science/fsl/files/patch-config-common-buildproj # science/fsl/files/fsl.1 # science/fsl/files/pkg-message.in # science/fsl/files/fix_fsl_gl # science/fsl/files/patch-etc-fslconf-fsl.sh # science/fsl/files/patch-etc-fslconf-fsl.csh # science/fsl/files/Patched # science/fsl/files/Patched/buildproj # science/fsl/files/Patched/fsl.csh # science/fsl/files/Patched/fsl.sh # science/fsl/pkg-descr # science/fsl/distinfo # science/fsl/Makefile # science/fsl/pkg-plist # echo c - science/fsl mkdir -p science/fsl > /dev/null 2>&1 echo c - science/fsl/files mkdir -p science/fsl/files > /dev/null 2>&1 echo c - science/fsl/files/arch-FreeBSD-gccx.x.x mkdir -p science/fsl/files/arch-FreeBSD-gccx.x.x > /dev/null 2>&1 echo x - science/fsl/files/arch-FreeBSD-gccx.x.x/systemvars.mk sed 's/^X//' >science/fsl/files/arch-FreeBSD-gccx.x.x/systemvars.mk << 'END-of-science/fsl/files/arch-FreeBSD-gccx.x.x/systemvars.mk' X# $Id: systemvars.mk,v 1.1 2004/07/09 13:06:21 duncan Exp $ X X# System dependent paths X XRM = /bin/rm XCHMOD = /bin/chmod XMKDIR = /bin/mkdir XCP = /bin/cp XINSTALL = /usr/bin/install -p XTCLSH = /usr/local/bin/tclsh8.4 XRANLIB = /usr/bin/ranlib X XFSLML = ${FSLDIR}/bin/fslml X X# for SHELL, do not change the type of shell - only use Bourne or BASH XSHELL = /bin/sh X X# Compiler dependent variables X XCC ?= gcc XCXX ?= g++ XCSTATICFLAGS ?= -static XCXXSTATICFLAGS ?= -static XCXXFLAGS += -Wno-deprecated X X#ARCHFLAGS ?= "" X XDEPENDFLAGS ?= -MM X X#OPTFLAGS ?= -O ${ARCHFLAGS} XOPTFLAGS ?= -O XMACHDBGFLAGS ?= -g XANSI_FLAGS ?= -Wall -ansi -pedantic -Wno-long-long X END-of-science/fsl/files/arch-FreeBSD-gccx.x.x/systemvars.mk echo x - science/fsl/files/arch-FreeBSD-gccx.x.x/externallibs.mk sed 's/^X//' >science/fsl/files/arch-FreeBSD-gccx.x.x/externallibs.mk << 'END-of-science/fsl/files/arch-FreeBSD-gccx.x.x/externallibs.mk' X# $Id: externallibs.mk,v 1.2 2004/07/13 17:05:32 duncan Exp $ X X# External Library and Include Paths X XFSLEXTLIB=${FSLDIR}/extras/lib XFSLEXTINC=${FSLDIR}/extras/include X X# CEPHES library XLIB_CEPHES = ${FSLEXTLIB} XINC_CEPHES = ${FSLEXTINC}/cephes X X# FFTW library XLIB_FFTW = ${FSLEXTLIB} XINC_FFTW = ${FSLEXTINC}/fftw X X# GD library XLIB_GD = ${FSLEXTLIB} XINC_GD = ${FSLEXTINC}/libgd X X# GDC library XLIB_GDC = ${FSLEXTLIB} XINC_GDC = ${FSLEXTINC}/libgdc X X# GSL library XLIB_GSL = ${FSLEXTLIB} XINC_GSL = ${FSLEXTINC}/gsl X X# PNG library XLIB_PNG = ${FSLEXTLIB} XINC_PNG = ${FSLEXTINC}/libpng X X# PROB library XLIB_PROB = ${FSLEXTLIB} XINC_PROB = ${FSLEXTINC}/libprob X X# CPROB library XLIB_CPROB = ${FSLEXTLIB} XINC_CPROB = ${FSLEXTINC}/libcprob X X# NEWMAT library XLIB_NEWMAT = ${FSLEXTLIB} XINC_NEWMAT = ${FSLEXTINC}/newmat X X# NEWRAN library XLIB_NEWRAN = ${FSLEXTLIB} XINC_NEWRAN = ${FSLEXTINC}/newran X X# ZLIB library XLIB_ZLIB = ${FSLEXTLIB} XINC_ZLIB = ${FSLEXTINC}/zlib X X# BOOST library XBOOSTDIR = ${LOCALBASE} XLIB_BOOST = ${BOOSTDIR}/lib XINC_BOOST = ${BOOSTDIR}/include X X# QT library XQTDIR = ${X11BASE} XLIB_QT = ${QTDIR}/lib XINC_QT = ${QTDIR}/include X X# QWT library XQWTDIR = ${LOCALBASE} XLIB_QWT = ${QWTDIR}/lib XINC_QWT = ${QWTDIR}/include/qwt X X# FFTW3 library XLIB_FFTW3 = ${FSLEXTLIB} XINC_FFTW3 = ${FSLEXTINC}/fftw3 END-of-science/fsl/files/arch-FreeBSD-gccx.x.x/externallibs.mk echo x - science/fsl/files/patch-config-common-buildproj sed 's/^X//' >science/fsl/files/patch-config-common-buildproj << 'END-of-science/fsl/files/patch-config-common-buildproj' X--- config/common/buildproj.orig Wed Apr 5 09:06:16 2006 X+++ config/common/buildproj Thu Apr 26 13:31:46 2007 X@@ -14,7 +14,11 @@ X FSLDIR=`pwd` X FSLDEVDIR=${FSLDIR} X FSLCONFDIR=${FSLDIR}/config X-FSLMACHTYPE=`gcc -dumpmachine`-gcc`gcc -dumpversion` X+if [ `uname` = FreeBSD ]; then X+ FSLMACHTYPE=`uname -m`-`uname`-gcc`gcc -dumpversion` X+else X+ FSLMACHTYPE=`gcc -dumpmachine`-gcc`gcc -dumpversion` X+fi X export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE X if [ X$FSLPPC32 = X ] ; then X if [ X`echo $FSLMACHTYPE | grep "powerpc"`X != "XX" ]; then X@@ -36,9 +40,11 @@ X ( cd ${FSLCONFDIR} ; ln -s generic ${FSLMACHTYPE} ; buildmessages="WARNING: Did not find specific configuration for ${FSLMACHTYPE} - trying generic version instead"; echo "$buildmessages" ; ) X fi X X- # Make freeware if it exists X- if [ -d ${FSLDIR}/src/freeware ] ; then X- ( cd ${FSLDIR}/src/freeware ; make FSLDIR=${FSLDIR} FSLCONFDIR=${FSLCONFDIR} ) X+ if [ `uname` != FreeBSD ]; then X+ # Make freeware if it exists X+ if [ -d ${FSLDIR}/src/freeware ] ; then X+ ( cd ${FSLDIR}/src/freeware ; make FSLDIR=${FSLDIR} FSLCONFDIR=${FSLCONFDIR} ) X+ fi X fi X X # Make the extras if they are installed in the same fsl tree END-of-science/fsl/files/patch-config-common-buildproj echo x - science/fsl/files/fsl.1 sed 's/^X//' >science/fsl/files/fsl.1 << 'END-of-science/fsl/files/fsl.1' X.TH FSL 1 X.SH NAME \" Section header X.PP X XFSL - FMRIB Software Library X X.SH SYNOPSIS X.PP X.nf X.na Xfsl X.ad X.fi X X\" Optional sections X.SH "DESCRIPTION" X X.B FSL Xis a comprehensive library of image analysis and statistical tools for XFMRI, MRI and DTI brain imaging data. FSL is written mainly by members of Xthe Analysis Group, FMRIB, Oxford, UK. X X.B FSL Xis far too complex to document in a man page. For documentation, please Xvisit http://www.fmrib.ox.ac.uk/fsl/. X X.SH ENVIRONMENT X X.B FSL Xrequires many environment variables to be properly configured. XThis is generally done by setting FSLDIR, and then running X X.nf X.na X source $FSLDIR/etc/fslconf/fsl.csh X Xor X X . $FSLDIR/etc/fslconf/fsl.sh X.ad X.fi X X.SH "SEE ALSO" Xafni(1), caret(1), freesurfer(1), dtiquery(1), nifticlib(3) X X.SH AUTHOR X.nf X.na XFMRIB Analysis Group Xhttp://www.fmrib.ox.ac.uk/analysis X END-of-science/fsl/files/fsl.1 echo x - science/fsl/files/pkg-message.in sed 's/^X//' >science/fsl/files/pkg-message.in << 'END-of-science/fsl/files/pkg-message.in' X============================================================================= X XBefore running FSL, you must set the environment variable FSLDIR to X%%DATADIR%%, and source %%DATADIR%%/etc/fslconf/fsl.csh Xor %%DATADIR%%/etc/fslconf/fsl.sh. X X============================================================================= X XIMPORTANT: The DR binaries are closed-source Linux binaries, and require Xthe following GL libraries in /compat/linux/usr/X11R6/lib: X XlibGL.so.1 XlibGLcore.so.1 Xlibnvidia-tls.so.1 X XThe nvidia-driver port installs the Linux GL libraries in X/compat/linux/usr/lib, and removes those in /compat/linux/usr/X11R6/lib. XIf you are using the nvidia-driver port, you may need to link the above Xlibraries into /compat/linux/usr/X11R6/lib. To do this, simply run X%%PREFIX%%/bin/fix_fsl_gl. X X============================================================================= END-of-science/fsl/files/pkg-message.in echo x - science/fsl/files/fix_fsl_gl sed 's/^X//' >science/fsl/files/fix_fsl_gl << 'END-of-science/fsl/files/fix_fsl_gl' X#!/bin/csh X Xset nvidia_base = /compat/linux/usr/lib Xset fsl_base = /compat/linux/usr/X11R6/lib X Xforeach lib (libGL.so.1 libGLcore.so.1 libnvidia-tls.so.1) X if ( -e ${nvidia_base}/${lib} && ! -e ${fsl_base}/${lib} ) then X echo "Linking ${lib} to ${fsl_base}..." X ln -s ${nvidia_base}/${lib} ${fsl_base} X endif Xend X END-of-science/fsl/files/fix_fsl_gl echo x - science/fsl/files/patch-etc-fslconf-fsl.sh sed 's/^X//' >science/fsl/files/patch-etc-fslconf-fsl.sh << 'END-of-science/fsl/files/patch-etc-fslconf-fsl.sh' X--- etc/fslconf/fsl.sh.orig Thu Mar 2 11:08:31 2006 X+++ etc/fslconf/fsl.sh Thu Apr 26 13:34:40 2007 X@@ -26,13 +26,13 @@ X # The following variables specify paths for programs and can be changed X # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) X X-FSLTCLSH=$FSLDIR/bin/tclsh X-FSLWISH=$FSLDIR/bin/wish X-FSLGNUPLOT=$FSLDIR/bin/gnuplot X-FSLDISPLAY=$FSLDIR/bin/display X-FSLCONVERT=$FSLDIR/bin/convert X+FSLTCLSH=tclsh8.4 X+FSLWISH=wish8.4 X+FSLGNUPLOT=gnuplot X+FSLDISPLAY=display X+FSLCONVERT=convert X X-FSLBROWSER=$FSLDIR/tcl/fslwebbrowser X+FSLBROWSER=firefox X X export FSLTCLSH FSLWISH FSLGNUPLOT FSLDISPLAY FSLCONVERT FSLBROWSER X X@@ -51,7 +51,7 @@ X FSLCONFDIR=$FSLDIR/config X FSLMACHTYPE= X if [ "`which gcc | grep no`" = "" ] ; then X- FSLMACHTYPE=`gcc -dumpmachine`-gcc`gcc -dumpversion`; X+ FSLMACHTYPE=$MACHTYPE-$OSTYPE-gcc`gcc -dumpversion`; X if [ `uname` = Darwin ] ; then X if [ "`system_profiler -detailLevel -2 | grep -i 'Machine Name' | grep G5`" != "" ] ; then X FSLMACHTYPE=${FSLMACHTYPE}-G5 END-of-science/fsl/files/patch-etc-fslconf-fsl.sh echo x - science/fsl/files/patch-etc-fslconf-fsl.csh sed 's/^X//' >science/fsl/files/patch-etc-fslconf-fsl.csh << 'END-of-science/fsl/files/patch-etc-fslconf-fsl.csh' X--- etc/fslconf/fsl.csh.orig Thu Mar 2 11:08:30 2006 X+++ etc/fslconf/fsl.csh Thu Apr 26 13:34:40 2007 X@@ -25,13 +25,13 @@ X # The following variables specify paths for programs and can be changed X # or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) X X-setenv FSLTCLSH $FSLDIR/bin/tclsh X-setenv FSLWISH $FSLDIR/bin/wish X-setenv FSLGNUPLOT $FSLDIR/bin/gnuplot X-setenv FSLDISPLAY $FSLDIR/bin/display X-setenv FSLCONVERT $FSLDIR/bin/convert X+setenv FSLTCLSH tclsh8.4 X+setenv FSLWISH wish8.4 X+setenv FSLGNUPLOT gnuplot X+setenv FSLDISPLAY display X+setenv FSLCONVERT convert X X-setenv FSLBROWSER $FSLDIR/tcl/fslwebbrowser X+setenv FSLBROWSER firefox X X X # The following variables are used for running code in parallel across X@@ -45,11 +45,11 @@ X X setenv FSLCONFDIR $FSLDIR/config X if ( "`which gcc | grep no`" == "" ) then X- setenv FSLMACHTYPE `gcc -dumpmachine`-gcc`gcc -dumpversion` X+ setenv FSLMACHTYPE $MACHTYPE-$OSTYPE-gcc`gcc -dumpversion` X if ( `uname` == "Darwin" ) then X- if ( "`system_profiler -detailLevel -2 | grep -i 'Machine Name' | grep G5`" != "" ) then X- setenv FSLMACHTYPE ${FSLMACHTYPE}-G5 X- endif X+ if ( "`system_profiler -detailLevel -2 | grep -i 'Machine Name' | grep G5`" != "" ) then X+ setenv FSLMACHTYPE ${FSLMACHTYPE}-G5 X+ endif X endif X endif X END-of-science/fsl/files/patch-etc-fslconf-fsl.csh echo c - science/fsl/files/Patched mkdir -p science/fsl/files/Patched > /dev/null 2>&1 echo x - science/fsl/files/Patched/buildproj sed 's/^X//' >science/fsl/files/Patched/buildproj << 'END-of-science/fsl/files/Patched/buildproj' X#!/bin/sh X Xif [ $# -lt 1 ] ; then X echo "Usage: $0 <list of projects>" X exit 2 ; Xfi X Xstrict=false; export strict; Xif [ X$1 = X-strict ] ; then X strict=true; export strict; Xfi XPROJECTS="$@" ; export PROJECTS ; X XFSLDIR=`pwd` XFSLDEVDIR=${FSLDIR} XFSLCONFDIR=${FSLDIR}/config Xif [ `uname` == FreeBSD ]; then X FSLMACHTYPE=`uname -m`-`uname`-gcc`gcc -dumpversion` Xelse X FSLMACHTYPE=`gcc -dumpmachine`-gcc`gcc -dumpversion` Xfi Xexport FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE Xif [ X$FSLPPC32 = X ] ; then X if [ X`echo $FSLMACHTYPE | grep "powerpc"`X != "XX" ]; then X PROCESSOR=`system_profiler -detailLevel -2 | grep "CPU Type" | sed 's/^[ \t]*//' | sed 's/CPU Type: PowerPC \(G[3-6]\).*/\1/'` X export PROCESSOR X if [ X$PROCESSOR = "XG5" ]; then X FSLMACHTYPE=${FSLMACHTYPE}-G5 X fi X echo "PowerPC $FSLMACHTYPE" X fi Xfi X Xbuildmessages="" ; export buildmessages ; X Xif [ $strict = false ] ; then X X # If this machine doesn't exist in standard config, link to the generic form X if [ ! -d ${FSLCONFDIR}/${FSLMACHTYPE} ] ; then X ( cd ${FSLCONFDIR} ; ln -s generic ${FSLMACHTYPE} ; buildmessages="WARNING: Did not find specific configuration for ${FSLMACHTYPE} - trying generic version instead"; echo "$buildmessages" ; ) X fi X X if [ `uname` != FreeBSD ]; then X # Make freeware if it exists X if [ -d ${FSLDIR}/src/freeware ] ; then X ( cd ${FSLDIR}/src/freeware ; make FSLDIR=${FSLDIR} FSLCONFDIR=${FSLCONFDIR} ) X fi X fi X X # Make the extras if they are installed in the same fsl tree X if [ -d ${FSLDIR}/extras ] ; then X ( cd ${FSLDIR}/extras ; ./build ) ; X MAKEOPTIONS="${MAKEOPTIONS} FSLEXTLIB=${FSLDIR}/extras/lib FSLEXTINC=${FSLDIR}/extras/include" ; X fi X Xfi X X X# Determine which make command to use XMAKE=none Xif [ X"`make --version 2>&1 | grep -i gnu`"X != XX ] ; then X MAKE=make; Xelse if [ X"`gmake --version 2>&1 | grep -i gnu`"X != XX ] ; then X MAKE=gmake; Xfi; fi Xif [ ${MAKE} = none ] ; then X echo "Could not find the gnu make utility in path" ; X exit 1 ; Xfi X X Xerrorprojs="" ; export errorprojs ; Xerrorinstall="" ; export errorinstall ; X Xfor projname in $PROJECTS; do X X if [ -d $FSLDIR/src/$projname ] ; then X X echo " " ; X echo " " ; X echo "Making project src/$projname" ; X echo " " ; X cd $FSLDIR/src/$projname ; X # ${MAKE} distclean ; X if [ -x fslconfig ] ; then X ./fslconfig ; X fi X if ${MAKE} -k ${MAKEOPTIONS} ; then X if ${MAKE} install ; then X installok=true; X else X installok=false; X errorinstall="$errorinstall $projname" ; export errorinstall ; X fi X echo " " X echo " ------------------------- " X echo "Successfully made $projname"; X if [ $installok = false ] ; then X echo " " X echo "ERROR::Could not install $projname successfully" ; X fi X else X echo " " X echo " ========================= " X echo "ERROR::Could not make $projname successfully" ; X echo " " X echo " " X errorprojs="$errorprojs $projname" ; export errorprojs ; X fi X X fi Xdone X Xcd $FSLDIR X Xecho " "; Xecho " "; Xecho " "; Xif [ "X${errorprojs}X" != XX ] ; then X echo "!!ERROR in BUILD!!" ; X echo " Could not make the following projects successfully:" ; X echo " $errorprojs" ; Xelse X echo "BUILD successfully made all projects" ; Xfi Xecho " "; Xif [ "X${errorinstall}X" != XX ] ; then X echo "!!ERROR in INSTALL!!" ; X echo " Could not fully install the following projects successfully:" ; X echo " $errorinstall" ; Xelse X echo " "; Xfi Xecho " "; Xecho "${buildmessages}" X END-of-science/fsl/files/Patched/buildproj echo x - science/fsl/files/Patched/fsl.csh sed 's/^X//' >science/fsl/files/Patched/fsl.csh << 'END-of-science/fsl/files/Patched/fsl.csh' X# FSL configuration file X# - to be sourced by the user, typically in .bashrc or equivalent X# - note that the user should set X X# Written by Mark Jenkinson X# FMRIB Analysis Group, University of Oxford X X# SHCOPYRIGHT X X X#### Set up standard FSL user environment variables #### X X# The following variable selects the default output image type X# Legal values are: ANALYZE NIFTI NIFTI_PAIR ANALYZE_GZ NIFTI_GZ NIFTI_PAIR_GZ X# This would typically be overwritten in ${HOME}/.fslconf/fsl.csh if the user wished X# to write files with a different format Xsetenv FSLOUTPUTTYPE NIFTI_GZ X X# Comment out the definition of FSLMULTIFILEQUIT to enable X# FSL programs to soldier on after detecting multiple image X# files with the same basename ( e.g. epi.hdr and epi.nii ) Xsetenv FSLMULTIFILEQUIT TRUE X X X# The following variables specify paths for programs and can be changed X# or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) X Xsetenv FSLTCLSH tclsh8.4 Xsetenv FSLWISH wish8.4 Xsetenv FSLGNUPLOT gnuplot Xsetenv FSLDISPLAY display Xsetenv FSLCONVERT convert X Xsetenv FSLBROWSER firefox X X X# The following variables are used for running code in parallel across X# several machines ( i.e. for FDT ) X Xsetenv FSLLOCKDIR Xsetenv FSLMACHINELIST Xsetenv FSLREMOTECALL X X# Set up development variables (not for the faint-hearted) X Xsetenv FSLCONFDIR $FSLDIR/config Xif ( "`which gcc | grep no`" == "" ) then X setenv FSLMACHTYPE $MACHTYPE-$OSTYPE-gcc`gcc -dumpversion` X if ( `uname` == "Darwin" ) then X if ( "`system_profiler -detailLevel -2 | grep -i 'Machine Name' | grep G5`" != "" ) then X setenv FSLMACHTYPE ${FSLMACHTYPE}-G5 X endif X endif Xendif X X X################################################### X### Add other global environment variables here ### X### or change the definitions above ### X################################################### X X X# USER VARIABLES HERE X X X################################################### X#### DO NOT ADD ANYTHING BELOW THIS LINE #### X################################################### X Xif ( -f /usr/local/etc/fslconf/fsl.csh ) then X source /usr/local/etc/fslconf/fsl.csh Xendif X X Xif ( -f /etc/fslconf/fsl.csh ) then X source /etc/fslconf/fsl.csh Xendif X X Xif ( -f "${HOME}/.fslconf/fsl.csh" ) then X source "${HOME}/.fslconf/fsl.csh" Xendif END-of-science/fsl/files/Patched/fsl.csh echo x - science/fsl/files/Patched/fsl.sh sed 's/^X//' >science/fsl/files/Patched/fsl.sh << 'END-of-science/fsl/files/Patched/fsl.sh' X# FSL configuration file X# - to be sourced by the user, typically in .bashrc or equivalent X# - note that the user should set X X# Written by Mark Jenkinson X# FMRIB Analysis Group, University of Oxford X X# SHCOPYRIGHT X X X#### Set up standard FSL user environment variables #### X X# The following variable selects the default output image type X# Legal values are: ANALYZE NIFTI NIFTI_PAIR ANALYZE_GZ NIFTI_GZ NIFTI_PAIR_GZ X# This would typically be overwritten in ${HOME}/.fslconf/fsl.sh if the user wished X# to write files with a different format XFSLOUTPUTTYPE=NIFTI_GZ Xexport FSLOUTPUTTYPE X X# Comment out the definition of FSLMULTIFILEQUIT to enable X# FSL programs to soldier on after detecting multiple image X# files with the same basename ( e.g. epi.hdr and epi.nii ) XFSLMULTIFILEQUIT=TRUE ; export FSLMULTIFILEQUIT X X X# The following variables specify paths for programs and can be changed X# or replaced by different programs ( e.g. FSLDISPLAY=open for MacOSX) X XFSLTCLSH=tclsh8.4 XFSLWISH=wish8.4 XFSLGNUPLOT=gnuplot XFSLDISPLAY=display XFSLCONVERT=convert X XFSLBROWSER=firefox X Xexport FSLTCLSH FSLWISH FSLGNUPLOT FSLDISPLAY FSLCONVERT FSLBROWSER X X X# The following variables are used for running code in parallel across X# several machines ( i.e. for FDT ) X XFSLLOCKDIR= XFSLMACHINELIST= XFSLREMOTECALL= X Xexport FSLLOCKDIR FSLMACHINELIST FSLREMOTECALL X X# Set up development variables (not for the faint-hearted) X XFSLCONFDIR=$FSLDIR/config XFSLMACHTYPE= Xif [ "`which gcc | grep no`" = "" ] ; then X FSLMACHTYPE=$MACHTYPE-$OSTYPE-gcc`gcc -dumpversion`; X if [ `uname` = Darwin ] ; then X if [ "`system_profiler -detailLevel -2 | grep -i 'Machine Name' | grep G5`" != "" ] ; then X FSLMACHTYPE=${FSLMACHTYPE}-G5 X fi X fi Xfi Xexport FSLCONFDIR FSLMACHTYPE X X X################################################### X### Add other global environment variables here ### X### or change the definitions above ### X################################################### X X X# USER VARIABLES HERE X X X################################################### X#### DO NOT ADD ANYTHING BELOW THIS LINE #### X################################################### X Xif [ -f /usr/local/etc/fslconf/fsl.sh ] ; then X . /usr/local/etc/fslconf/fsl.sh ; Xfi X X Xif [ -f /etc/fslconf/fsl.sh ] ; then X . /etc/fslconf/fsl.sh ; Xfi X X Xif [ -f "${HOME}/.fslconf/fsl.sh" ] ; then X . "${HOME}/.fslconf/fsl.sh" ; Xfi END-of-science/fsl/files/Patched/fsl.sh echo x - science/fsl/pkg-descr sed 's/^X//' >science/fsl/pkg-descr << 'END-of-science/fsl/pkg-descr' XFSL is a comprehensive library of image analysis and statistical tools for XFMRI, MRI and DTI brain imaging data. FSL is written mainly by members of Xthe Analysis Group, FMRIB, Oxford, UK. X XWWW: http://www.fmrib.ox.ac.uk/fsl/ X XPort maintainer: Jason W. Bacon X bacon@smithers.neuro.mcw.edu END-of-science/fsl/pkg-descr echo x - science/fsl/distinfo sed 's/^X//' >science/fsl/distinfo << 'END-of-science/fsl/distinfo' XMD5 (fsl-3.3.8-sources.tar.gz) = b992af96dc013bb20b062818ba3892c3 XSHA256 (fsl-3.3.8-sources.tar.gz) = 01a572bb4532ea8436c5312aeae933b880bda5a638ca43fec6c9c628a098b7c1 XSIZE (fsl-3.3.8-sources.tar.gz) = 67778816 END-of-science/fsl/distinfo echo x - science/fsl/Makefile sed 's/^X//' >science/fsl/Makefile << 'END-of-science/fsl/Makefile' X############################################################################ X# New ports collection Makefile for: fsl X# Date created: 20 Apr 2006 X# Whom: Jason W. Bacon <bacon@smithers.neuro.mcw.edu> X# X# $FreeBSD$ X# X X############################################################################ X# www.neuro.mcw.edu has the latest source distribution from which this port X# is built. It will be updated as time permits and necessiaty requires. X# X XPORTNAME= fsl XPORTVERSION= 3.3.8 XCATEGORIES= science biology XMASTER_SITES= XDISTNAME= ${PORTNAME}-${PORTVERSION}-sources X XMAINTAINER= bacon@smithers.neuro.mcw.edu XCOMMENT= FMRIB Software Library X X# Linux depends are for DR binaries. Be sure to test these after any X# updates to the port, since they depend on several Linux libraries X# that could get moved. The nvidia driver installs GL and GLcore in X# /compat/linux/usr/lib, and disables the ones in /compat/linux/${X11BASE}/lib. XLIB_DEPENDS= png.5:${PORTSDIR}/graphics/png \ X gd.4:${PORTSDIR}/graphics/gd XRUN_DEPENDS= gnuplot:${PORTSDIR}/math/gnuplot \ X convert:${PORTSDIR}/graphics/ImageMagick \ X tixwish:${PORTSDIR}/x11-toolkits/tix XBUILD_DEPENDS= tclsh8.4:${PORTSDIR}/lang/tcl84 \ X ginstall:${PORTSDIR}/sysutils/coreutils X XOPTIONS= FSLVIEW "Build fslview (Requires tcl,cmake,qt,qwt,boost,vtk)" on X X.include <bsd.port.pre.mk> X X# Need Linux GL libs. Which port? X X.if defined(WITH_FSLVIEW) XLIB_DEPENDS+= qwt.4:${PORTSDIR}/x11-toolkits/qwt \ X boost_regex.3:${PORTSDIR}/devel/boost \ X vtkCommon.5:${PORTSDIR}/math/vtk5 XBUILD_DEPENDS+= qt>=3.3.6:${PORTSDIR}/x11-toolkits/qt33 \ X cmake>=2.2.3:${PORTSDIR}/devel/cmake X.endif X XCONFLICTS= fsl-3.3.3* X XRESTRICTED= Must register to download at http://www.fmrib.ox.ac.uk/fsldownloads/ X XSUB_FILES= pkg-message XPKGMESSAGE= ${WRKDIR}/pkg-message X X.if defined(WITH_FSLVIEW) XPLIST_FILES+= bin/fslview X.endif X X.if !exists(${DISTDIR}/${DISTNAME}${EXTRACT_SUFX}) XIGNORE= you must manually fetch ${DISTNAME}${EXTRACT_SUFX} from http://www.fmrib.ox.ac.uk/fsldownloads/, place it in ${DISTDIR}, and then run make again X.endif X XWRKSRC= ${WRKDIR}/fsl X XMAN1= fsl.1 X Xpost-extract: X ${REINPLACE_CMD} "s|PROJECTS=\"freeware utils|PROJECTS=\"utils|g" \ X ${WRKSRC}/build X ${REINPLACE_CMD} 's|`gcc -dumpmachine`|`uname -m`-`uname`|g' \ X ${WRKSRC}/extras/build X ${CP} -Rf ${FILESDIR}/arch-FreeBSD-gccx.x.x \ X ${WRKSRC}/config/`uname -m`-`uname`-gcc`gcc -dumpversion` X Xdo-build: X (cd ${WRKSRC} && ./build) X.if defined(WITH_FSLVIEW) X ${MKDIR} ${WRKDIR}/fslview-release X (cd ${WRKDIR}/fslview-release && \ X cmake ../fsl/src/fslview \ X -DCMAKE_INSTALL_PREFIX=${LOCALBASE} \ X -DVTK_DIR=${LOCALBASE}/lib/vtk-5.0 \ X -DBOOST_DIR=${LOCALBASE}/include \ X -DQWT_DIR=${LOCALBASE} \ X -DDESIRED_QT_VERSION=3 \ X -DFSL_DIR=../fsl \ X -DCMAKE_CXX_FLAGS="-I${LOCALBASE}/include -I${LOCALBASE}/include/vtk-5.0 -I${LOCALBASE}/include/qwt" \ X -DCMAKE_VERBOSE_MAKEFILE="OFF" \ X -DCMAKE_EXE_LINKER_FLAGS="-L../../../fsl/extras/lib -L../../../fsl/lib" \ X && make) X.endif X X# Do not use .if !defined(NOPORTDOCS). FSL will not run without some of X# the image files stored in the docs dir. These files must be found under X# $FSLDIR ($DATADIR), so we create links to the docs there. Xdo-install: X ${MKDIR} ${DATADIR} ${DOCSDIR} X ${CP} -R ${WRKSRC}/etc ${DATADIR} X ${CP} -R ${WRKSRC}/lib ${DATADIR} X ${CP} -R ${WRKSRC}/tcl ${DATADIR} X ${CP} -p ${WRKSRC}/src/freeware/Linux/bin/DR/*.par ${DATADIR}/etc X ${CP} -R ${WRKSRC}/doc ${DOCSDIR} X ${CP} -R ${WRKSRC}/refdoc ${DOCSDIR} X ${CP} -p ${WRKSRC}/src/freeware/Linux/bin/DR/irtk_licence.doc \ X ${DOCSDIR} X ${CHMOD} -R 555 ${DATADIR} ${DOCSDIR} X ${FIND} ${DATADIR} ${DOCSDIR} -type f -exec ${CHMOD} 444 '{}' \; X X ${STRIP_CMD} `file -F ' ' ${WRKSRC}/bin/* | \ X fgrep ELF | ${AWK} ' { print $$1 }'` X ${CHMOD} 555 ${WRKSRC}/bin/* X ${CP} -p ${WRKSRC}/bin/* ${PREFIX}/bin X X ${CHMOD} 555 ${WRKSRC}/src/freeware/Linux/bin/DR/* X ${CP} -p `file -F ' ' ${WRKSRC}/src/freeware/Linux/bin/DR/* | \ X fgrep ELF | ${AWK} ' { print $$1 }'` ${PREFIX}/bin X X ${LN} -s ${DOCSDIR}/* ${DATADIR} X ${LN} -s ${PREFIX}/bin ${DATADIR} X ${INSTALL_SCRIPT} ${FILESDIR}/fix_fsl_gl ${PREFIX}/bin X.if defined(WITH_FSLVIEW) X ${INSTALL_PROGRAM} 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X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/bet2 X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/bet X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/avwutils X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/afni X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc X%%PORTDOCS%%@dirrm %%DOCSDIR%% X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/znzlib X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/tbss X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/susan X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/slicetimer X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/siena X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/randomise X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/niftiio X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/mm X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/miscvis X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/miscmaths X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/misc_c X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/meshclass X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/melodic2 X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/mcflirt X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/libvis X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/libss X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/fugue X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/fslpres X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/fslio X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/flirt X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/flame X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/filmbabe X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/film X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/feat5 X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/fdt X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/fast X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/cluster X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/bint X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/bet2 X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/bet X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/avwutils X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/refdoc/afni X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/znzlib X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/utils X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/niftiio X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/newimage X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/miscmaths X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/misc_tcl X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/misc_c X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/libvis X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/libss X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/libhfunc X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/fslio X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/flame X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/film X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/cluster X%%PORTDOCS%%@exec mkdir -p %D/%%DOCSDIR%%/doc/bint END-of-science/fsl/pkg-plist exit >Release-Note: >Audit-Trail: >Unformatted:
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