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Date: Thu, 10 May 2007 10:40:33 -0500 (CDT)
From: Jason Bacon <bacon@smithers.neuro.mcw.edu>
Reply-To: Jason Bacon <bacon@smithers.neuro.mcw.edu>
To: FreeBSD-gnats-submit@freebsd.org
Cc:
Subject: New port: science/fsl FMRIB Software Library
X-Send-Pr-Version: 3.113
X-GNATS-Notify:

>Number:         112576
>Category:       ports
>Synopsis:       New port: science/fsl FMRIB Software Library
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Thu May 10 15:50:05 GMT 2007
>Closed-Date:    Fri Jun 15 19:57:11 GMT 2007
>Last-Modified:  Fri Jun 15 19:57:11 GMT 2007
>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} ${WRKDIR}/fslview-release/bin/fslview ${PREFIX}/bin
X.endif
X	${INSTALL_MAN} ${FILESDIR}/fsl.1 ${PREFIX}/man/man1
X
Xpost-install:
X	${PREFIX}/bin/fix_fsl_gl
X	@${CAT} ${PKGMESSAGE}
X
X.include <bsd.port.post.mk>
END-of-science/fsl/Makefile
echo x - science/fsl/pkg-plist
sed 's/^X//' >science/fsl/pkg-plist << 'END-of-science/fsl/pkg-plist'
Xbin/ApplyXFM
Xbin/Bet
Xbin/ConcatXFM
Xbin/Fast
Xbin/Fdt
Xbin/Feat
Xbin/Featquery
Xbin/Featwatcher
Xbin/Flirt
Xbin/Glm
Xbin/InvertXFM
Xbin/Make_flobs
Xbin/Melodic
Xbin/Nudge
Xbin/Renderhighres
Xbin/Renderstats
Xbin/Runtcl
Xbin/Susan
Xbin/afni2avw
Xbin/applywarp
Xbin/applyxfm4D
Xbin/areg
Xbin/avscale
Xbin/avw2afni
Xbin/avw2ascii
Xbin/avw2ascii++
Xbin/avw2ascii_16SI
Xbin/avw2ascii_32R
Xbin/avw2ascii_32SI
Xbin/avw2ascii_64R
Xbin/avw2ascii_8UI
Xbin/avwanimate
Xbin/avwcc
Xbin/avwcc++
Xbin/avwcc_16SI
Xbin/avwcc_32R
Xbin/avwcc_32SI
Xbin/avwcc_64R
Xbin/avwcc_8UI
Xbin/avwcheck
Xbin/avwchfiletype
Xbin/avwchpixdim
Xbin/avwcomplex
Xbin/avwconv
Xbin/avwcpgeom
Xbin/avwcpgeom++
Xbin/avwcreatehd
Xbin/avwcreatehd++
Xbin/avwedithd
Xbin/avwfft
Xbin/avwfill
Xbin/avwhd
Xbin/avwhd++
Xbin/avwinfo
Xbin/avwinterleave
Xbin/avwinterleave++
Xbin/avwinterleave_16SI
Xbin/avwinterleave_32R
Xbin/avwinterleave_32SI
Xbin/avwinterleave_64R
Xbin/avwinterleave_8UI
Xbin/avwmaths
Xbin/avwmaths++
Xbin/avwmaths_16SI
Xbin/avwmaths_32R
Xbin/avwmaths_32SI
Xbin/avwmaths_64R
Xbin/avwmaths_8UI
Xbin/avwmeants
Xbin/avwmerge
Xbin/avwmerge++
Xbin/avwnvols
Xbin/avwnvols++
Xbin/avworient
Xbin/avwpspec
Xbin/avwroi
Xbin/avwroi++
Xbin/avwroi_16SI
Xbin/avwroi_32R
Xbin/avwroi_32SI
Xbin/avwroi_64R
Xbin/avwroi_8UI
Xbin/avwsize
Xbin/avwslice
Xbin/avwsplit
Xbin/avwsplit++
Xbin/avwstats
Xbin/avwstats++
Xbin/avwswapdim
Xbin/avwval
Xbin/bedpost
Xbin/bedpost_cleanup
Xbin/bedpost_datacheck
Xbin/bedpost_kill_all
Xbin/bedpost_kill_pid
Xbin/bedpost_proc
Xbin/bet
Xbin/bet2
Xbin/bet_16SI
Xbin/bet_32R
Xbin/bet_32SI
Xbin/bet_8UI
Xbin/betall
Xbin/betfunc
Xbin/betpremask
Xbin/betsmallz
Xbin/betsurf
Xbin/ccops
Xbin/cluster
Xbin/cluster2html
Xbin/connectedcomp
Xbin/contrast_mgr
Xbin/convert_xfm
Xbin/convertwarp
Xbin/create_lut
Xbin/cylsamp
Xbin/design_ttest2
Xbin/diff_pvm
Xbin/distancemap
Xbin/dof2gipl
Xbin/drawmesh
Xbin/dtifit
Xbin/easythresh
Xbin/eddy_correct
Xbin/eqn2gif
Xbin/estnoise
Xbin/extractfidparams
Xbin/extracttxt
Xbin/fast
Xbin/fast_exe
Xbin/fdr
Xbin/feat
Xbin/feat2afni
Xbin/feat_model
Xbin/featquery
Xbin/featregapply
Xbin/film_gls
Xbin/filmbabe
Xbin/filmbabescript
Xbin/find_the_biggest
Xbin/fix_fsl_gl
Xbin/flame
Xbin/flirt
Xbin/freqtest
Xbin/fsl
Xbin/fsl_gui
Xbin/fslerrorreport
Xbin/fslpres
Xbin/ftoz
Xbin/fugue
Xbin/gifmerge
Xbin/groupttest
Xbin/halfcosbasis
Xbin/hist2prob
Xbin/imcp
Xbin/img2imgcoord
Xbin/img2stdcoord
Xbin/imglob
Xbin/imln
Xbin/immv
Xbin/imrm
Xbin/imtest
Xbin/ip
Xbin/ip_16SI
Xbin/ip_16UI
Xbin/ip_32R
Xbin/ip_32SI
Xbin/ip_32UI
Xbin/ip_8SI
Xbin/ip_8UI
Xbin/jacobian
Xbin/make_dyadic_vectors
Xbin/makehtmeqns
Xbin/makerot
Xbin/mccutup
Xbin/mcflirt
Xbin/mean
Xbin/medianfilter
Xbin/melodic
Xbin/mfast
Xbin/mfast_exe
Xbin/midtrans
Xbin/mm
Xbin/morph_kernel
Xbin/nreg
Xbin/overlay
Xbin/pairreg
Xbin/perfusion_subtract
Xbin/pngappend
Xbin/pointflirt
Xbin/prelude
Xbin/prewhiten
Xbin/probtrack
Xbin/proj_thresh
Xbin/ptoz
Xbin/randomise
Xbin/remove_ext
Xbin/renderhighres
Xbin/rmsdiff
Xbin/runavw
Xbin/selfintersection
Xbin/siena
Xbin/siena_cal
Xbin/siena_diff
Xbin/siena_flirt
Xbin/siena_flow2std
Xbin/sienax
Xbin/sigloss
Xbin/sliceanimate
Xbin/slicer
Xbin/slices
Xbin/slicesdir
Xbin/slicetimer
Xbin/smoothest
Xbin/sphere
Xbin/standard_space_roi
Xbin/std2imgcoord
Xbin/surface_norm
Xbin/susan_smooth
Xbin/susan_smooth_16SI
Xbin/tbss_1_preproc
Xbin/tbss_2_reg
Xbin/tbss_3_postreg
Xbin/tbss_4_prestats
Xbin/tbss_non_FA
Xbin/tbss_reg
Xbin/tbss_skeleton
Xbin/tmpnam
Xbin/transformation
Xbin/transformation2
Xbin/tsplot
Xbin/ttologp
Xbin/ttoz
Xbin/updatefeatreg
Xbin/vmapper
Xbin/wpng
Xbin/zeropad
Xbin/ztop
X%%PORTDOCS%%%%DOCSDIR%%/doc/afni/afnilogo.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/afni/index.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/avwutils/index.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/bet/index.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/bet2/bet2_eg.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/bet2/bet2_eg_small.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/bet2/bet2_eg_vsmall.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/bet2/index.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fast/index.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_bedpost.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_bedpost_parallel.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_before.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_biggest.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_bottom.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_display.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_documentation.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_dtifit.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_eddy.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/eddy.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/eddy.tif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/eddy2.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_fa.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_fa_big.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_l1.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_lines.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_lines_subs.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_rgb.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_rgb_subs.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_seeds2targets_quant_eg.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_seeds2targets_thal.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_simple_tract3.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_spherical_polars.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fdt_twomasks_tracts.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fsl-bg.jpg
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fsl-logo.jpg
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/fslview_dti.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/gui_intro.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_images/gui_intro.tif
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_intro.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_modelling.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_pipeline.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_probtrack.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_reg.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_thresh.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/fdt_top.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/fdt/index.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/DO
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/ORIGtop.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/basics.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/before.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/bottom.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/cr1.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/detail.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/dm.html
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/dm1.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/dm2.gif
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg1.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg1_con.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg1_dm.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg1_evs.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg2.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg2_con.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg2_dm.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg2_evs.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg3.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg3_con.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg3_dm.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg3_evs.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg3b.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg3b_con.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg3b_dm.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg3b_evs.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg4a.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg4a_con.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg4a_dm.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg4a_evs.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg4b.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg4b_con.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg4b_dm.png
X%%PORTDOCS%%%%DOCSDIR%%/doc/feat5/eg4b_evs.png
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X%%DATADIR%%/tcl/nudge.tcl
X%%DATADIR%%/tcl/renderhighres.tcl
X%%DATADIR%%/tcl/renderstats.tcl
X%%DATADIR%%/tcl/susan.tcl
X%%DATADIR%%/tcl/susan_proc.tcl
X%%DATADIR%%/tcl/tclIndex
X%%DATADIR%%/tcl/triangled.xbm
X%%DATADIR%%/tcl/triangler.xbm
X%%DATADIR%%/tcl/webhelp.tcl
X@dirrm %%DATADIR%%/tcl
X@dirrm %%DATADIR%%/lib
X@dirrm %%DATADIR%%/etc/standard
X@dirrm %%DATADIR%%/etc/matlab
X@dirrm %%DATADIR%%/etc/luts
X@dirrm %%DATADIR%%/etc/fslpres
X@dirrm %%DATADIR%%/etc/fslconf
X@dirrm %%DATADIR%%/etc/flirtsch
X@dirrm %%DATADIR%%/etc/default_flobs.flobs
X@dirrm %%DATADIR%%/etc
X@dirrm %%DATADIR%%
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/znzlib
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/utils
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/tbss
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/susan
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/slicetimer
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/siena
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/randomise
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/niftiio
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/newimage
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/mm
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/miscvis
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/miscmaths
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/misc_tcl
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/misc_c
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/meshclass
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/melodic2
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/mcflirt
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/libvis
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/libss
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/libhfunc
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/fugue
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/fslpres
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/fslio
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/flirt
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/flame
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/filmbabe
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/film
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/feat5
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/fdt
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/fast
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/cluster
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/bint
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/bet2
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/bet
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/avwutils
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc/afni
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/refdoc
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/znzlib
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/utils
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/tbss
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/susan
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/slicetimer
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/siena
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/randomise
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/niftiio
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/newimage
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/mm
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/miscvis
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/miscmaths
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/misc_tcl
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/misc_c
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/meshclass
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/melodic2
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/mcflirt
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/libvis
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/libss
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/libhfunc
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/images
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/fugue
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/fslview
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/fslpres
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/fslio
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/fsl
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/flirt
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/flame
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/filmbabe
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/film
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/feat5
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/fdt/fdt_images
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/fdt
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/fast
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/cluster
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/bint
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:
Responsible-Changed-From-To: freebsd-ports-bugs->miwi 
Responsible-Changed-By: miwi 
Responsible-Changed-When: Thu May 10 16:20:48 UTC 2007 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=112576 
State-Changed-From-To: open->feedback 
State-Changed-By: miwi 
State-Changed-When: Mon Jun 4 15:03:58 UTC 2007 
State-Changed-Why:  
Hello, 

Your patchset is too big, i think you should add a patchset as tarball. 
As example take a look in audio/gramofile/. 

Ps: When you need a distfile mirror for it. I can add this to my 
distfile mirror. 
Also, creating subdirectories in ${FILESDIR} is highly discouraged. 

Thanks Martin 


http://www.freebsd.org/cgi/query-pr.cgi?pr=112576 
Responsible-Changed-From-To: miwi->freebsd-ports-bugs 
Responsible-Changed-By: miwi 
Responsible-Changed-When: Thu Jun 14 08:25:57 UTC 2007 
Responsible-Changed-Why:  
Back to pool. I stop my works for FreeBSD. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=112576 

From: Jason Bacon <bacon@smithers.neuro.mcw.edu>
To: bug-followup@FreeBSD.org,  bacon@smithers.neuro.mcw.edu
Cc:  
Subject: Re: ports/112576: New port: science/fsl FMRIB Software Library
Date: Fri, 15 Jun 2007 13:05:05 -0500

 We should probably close this PR for now.  FSL depends on VTK5, which 
 we've postponed committing.  Another group was working on VTK5 in 
 parallel with my efforts, and we need to review both ports and decide 
 which parts of each will go into the final product.  In the meantime, 
 the FSL port and my VTK5 port will continue be available on my WEB site: 
 http://www.neuro.mcw.edu/~bacon/Ports/.  After VTK5 is committed, I'll 
 submit another FSL port.
 
 Regards,
 
     Jason
 
State-Changed-From-To: feedback->closed 
State-Changed-By: linimon 
State-Changed-When: Fri Jun 15 19:56:31 UTC 2007 
State-Changed-Why:  
Submitter notes that this is going to need some rework due to dependencies, 
and that he will resubmit it at a later time. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=112576 
>Unformatted:
