fsl: updated package, added v6.0.4 (#20201)

- added several patches
- added some missing dependencies
- remove unneeded dependencies
- add CUDA support
- disable queue support, which was limited, and broken anyway
- move package text that was specific to the package to a comment, so it
  does not show up the environment module
- set conflicts for cuda and compilers

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

8 files changed, 411 insertions, 32 deletions

diff --git a/var/spack/repos/builtin/packages/fsl/build_log.patch b/var/spack/repos/builtin/packages/fsl/build_log.patch
new file mode 100644
index 0000000000..c0553b4c35
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fsl/build_log.patch
@@ -0,0 +1,11 @@
+--- a/build	2020-06-29 10:30:36.000000000 -0500
++++ b/build	2020-11-02 12:34:25.408157699 -0600
+@@ -158,7 +158,7 @@
+ fi #full build
+ 
+ echo "Building projects - see build.log file for progress..."
+-./config/common/buildproj $PROJECTS > ./build.log 2>&1
++./config/common/buildproj $PROJECTS
+ finalStatus=$?
+ if [ $finalStatus -eq 0 ]; then
+     echo "Build completed successfully.";
diff --git a/var/spack/repos/builtin/packages/fsl/eddy_Makefile.patch b/var/spack/repos/builtin/packages/fsl/eddy_Makefile.patch
new file mode 100644
index 0000000000..22057bf8fd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fsl/eddy_Makefile.patch
@@ -0,0 +1,11 @@
+--- a/src/eddy/Makefile	2020-07-22 09:11:14.000000000 -0500
++++ b/src/eddy/Makefile	2020-11-10 23:31:09.898903635 -0600
+@@ -46,7 +46,7 @@
+ 
+ 	CUDACXXFLAGS=-DCOMPILE_GPU
+ 	CUDAOBJS=CBFKernelDefinitions.o CBFSparseDiagonalMatrix.o CBFSplineField.o LSResampler_cuda.o DiffusionGP_cuda.o PostEddyCF_cuda.o EddyGpuUtils.o EddyInternalGpuUtils.o CudaVolume.o EddyMatrixKernels.o EddyKernels.o GpuPredictorChunk.o StackResampler.o DerivativeCalculator.o
+-	CUDALDFLAGS= -Xlinker -rpath $(LIB_CUDA) -L$(LIB_CUDA) -lcublas -lcudart
++	CUDALDFLAGS= -Xlinker -rpath -Xlinker $(LIB_CUDA) -L$(LIB_CUDA) -lcublas -lcudart
+ 	ifeq ($(fastbuild),1)
+ 		GENCODE_FLAGS    := -gencode arch=compute_30,code=sm_30
+ 	endif
diff --git a/var/spack/repos/builtin/packages/fsl/fsl_sub_v5.patch b/var/spack/repos/builtin/packages/fsl/fsl_sub_v5.patch
new file mode 100644
index 0000000000..561800962a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fsl/fsl_sub_v5.patch
@@ -0,0 +1,66 @@
+--- a/src/sgeutils/fsl_sub	2017-04-24 05:19:14.000000000 -0500
++++ b/src/sgeutils/fsl_sub	2020-11-15 17:42:28.100657607 -0600
+@@ -80,7 +80,7 @@
+ # "NONE". Note that a user can unset SGE_ROOT if they don't want the
+ # cluster to be used.
+ ###########################################################################
+-METHOD=SGE
++METHOD=NONE
+ unset module
+ if [ "x$SGE_ROOT" = "x" ] ; then
+ 	METHOD=NONE
+@@ -141,7 +141,9 @@
+ 
+ usage ()
+ {
+-  cat <<EOF
++  case $METHOD in
++    SGE)
++      cat <<EOF
+ 
+ $command V1.1 - wrapper for job control system such as SGE
+ 
+@@ -186,7 +188,23 @@
+ bigmem.q:   This queue is like the verylong.q but has no memory limits.
+ 
+ EOF
++      ;;
++    NONE)
++      cat <<EOF
+ 
++$command V1.1 - wrapper for job control system such as SGE
++
++Usage: $command [options] <command>
++
++$command gzip *.img *.hdr
++
++  -t <filename>         Specify a task file of commands to execute in parallel
++  -l <logdirname>       Where to output logfiles
++  -v                    Verbose mode.
++
++EOF
++      ;;
++  esac
+   exit 1
+ }
+ 
+@@ -195,8 +213,17 @@
+   usage
+ fi
+ 
+-set -- `getopt T:q:a:p:M:j:t:z:N:R:Fvm:l:s: $*`
+-result=$?
++case $METHOD in
++  SGE)
++    set -- `getopt T:q:a:p:M:j:t:z:N:R:Fvm:l:s: $*`
++    result=$?
++    ;;
++  NONE)
++    set -- `getopt t:vl: $*`
++    result=$?
++    ;;
++esac
++
+ if [ $result != 0 ] ; then
+   echo "What? Your arguments make no sense!"
+ fi
diff --git a/var/spack/repos/builtin/packages/fsl/fsl_sub_v6.patch b/var/spack/repos/builtin/packages/fsl/fsl_sub_v6.patch
new file mode 100644
index 0000000000..e209ba9282
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fsl/fsl_sub_v6.patch
@@ -0,0 +1,86 @@
+--- a/src/sgeutils/fsl_sub	2020-07-25 09:36:17.000000000 -0500
++++ b/src/sgeutils/fsl_sub	2020-11-15 17:04:41.484972803 -0600
+@@ -81,7 +81,7 @@
+ # "NONE". Note that a user can unset SGE_ROOT if they don't want the
+ # cluster to be used.
+ ###########################################################################
+-METHOD=SGE
++METHOD=NONE
+ unset module
+ if [[ "x$SGE_ROOT" = "x" ]] ; then
+   METHOD=NONE
+@@ -145,7 +145,10 @@
+ 
+ usage ()
+ {
+-  cat <<EOF
++  case "$METHOD" in
++    SGE)
++  
++      cat <<EOF
+ 
+ $command V1.1 - wrapper for job control system such as SGE
+ 
+@@ -190,7 +193,24 @@
+ bigmem.q:   This queue is like the verylong.q but has no memory limits.
+ 
+ EOF
++      ;;
++    NONE)
++  
++      cat <<EOF
+ 
++$command V1.1 - wrapper for job control system such as SGE
++
++Usage: $command [options] <command>
++
++$command gzip *.img *.hdr
++
++  -t <filename>         Specify a task file of commands to execute in parallel
++  -l <logdirname>       Where to output logfiles
++  -v                    Verbose mode.
++
++EOF
++      ;;
++    esac
+   exit 1
+ }
+ 
+@@ -199,14 +219,29 @@
+   usage
+ fi
+ 
+-#if the newer whitespace-safe getopt format is available, use it
+-if [[ $(getopt -T >/dev/null 2>&1; echo $?) == 4 ]]; then
+-  eval set -- $(getopt -s bash T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
+-  result=$?
+-else
+-  set -- $(getopt T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
+-  result=$?
+-fi
++case "$METHOD" in
++  SGE)
++    #if the newer whitespace-safe getopt format is available, use it
++    if [[ $(getopt -T >/dev/null 2>&1; echo $?) == 4 ]]; then
++      eval set -- $(getopt -s bash T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
++      result=$?
++    else
++      set -- $(getopt T:q:a:p:M:j:t:z:N:R:Fvm:l:s: "$@")
++      result=$?
++    fi
++    ;;
++  NONE)
++    #if the newer whitespace-safe getopt format is available, use it
++    if [[ $(getopt -T >/dev/null 2>&1; echo $?) == 4 ]]; then
++      eval set -- $(getopt -s bash t:vl: "$@")
++      result=$?
++    else
++      set -- $(getopt t:vl: "$@")
++      result=$?
++    fi
++    ;;
++esac
++
+ if [[ "$result" != 0 ]] ; then
+   echo "What? Your arguments make no sense!"
+ fi
diff --git a/var/spack/repos/builtin/packages/fsl/fslpython_install_v5.patch b/var/spack/repos/builtin/packages/fsl/fslpython_install_v5.patch
new file mode 100644
index 0000000000..7e22534251
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fsl/fslpython_install_v5.patch
@@ -0,0 +1,18 @@
+--- a/etc/fslconf/fslpython_install.sh	2017-04-07 10:29:52.000000000 -0500
++++ b/etc/fslconf/fslpython_install.sh	2020-11-12 13:34:06.665816528 -0600
+@@ -129,7 +129,7 @@
+     exit 2
+ fi
+ 
+-curl_opts='--fail' # Returns 22 on error
++curl_opts='--fail -L' # Returns 22 on error
+ if [ ${quiet} -eq 1 ]; then
+     curl_opts="${curl_opts} -s"
+ fi
+@@ -184,4 +184,4 @@
+ # binary into $FSLDIR/bin/
+ ln -sf "${fslpython_env_dir}/bin/python" "${fsl_dir}/bin/fslpython"
+ rm "${miniconda_install_log}"
+-drop_sudo rmdir "${miniconda_tmp}"
+\ No newline at end of file
++drop_sudo rmdir "${miniconda_tmp}"
diff --git a/var/spack/repos/builtin/packages/fsl/fslpython_install_v6.patch b/var/spack/repos/builtin/packages/fsl/fslpython_install_v6.patch
new file mode 100644
index 0000000000..93eac4cb73
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fsl/fslpython_install_v6.patch
@@ -0,0 +1,39 @@
+--- a/etc/fslconf/fslpython_install.sh	2020-07-25 09:20:04.000000000 -0500
++++ b/etc/fslconf/fslpython_install.sh	2020-11-09 20:12:59.458736979 -0600
+@@ -204,19 +204,19 @@
+ #  - https://github.com/conda/conda/issues/8804
+ 
+ # Try to make downloads more resilient
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs    240
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_max_retries          10
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_backoff_factor       5
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set safety_checks               warn
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs    240
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_max_retries          10
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_backoff_factor       5
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set safety_checks               warn
+ 
+ # Channel priority:
+ #  - conda-forge (highest priority)
+ #  - defaults (gets automatically added on the first call)
+ #  - fsl (lowest priority)
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set    channel_priority strict
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --add    channels         conda-forge
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --append channels         https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set    channel_priority strict
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --add    channels         conda-forge
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --append channels         https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel
+ 
+ 
+ ##############################
+@@ -229,7 +229,7 @@
+ if [ ${quiet} -ne 1 ]; then
+     echo "Stage 2"
+ fi
+-FSLDIR=$fsl_dir "${miniconda_bin_dir}/conda" env create -v \
++FSLDIR=$fsl_dir "${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda-env" create -v \
+     -f "${script_dir}/fslpython_environment.yml" \
+     2>> "${miniconda_install_log}" | \
+     ${script_dir}/progress.sh 133 ${quiet} 1>> "${miniconda_install_log}"
diff --git a/var/spack/repos/builtin/packages/fsl/iconv.patch b/var/spack/repos/builtin/packages/fsl/iconv.patch
new file mode 100644
index 0000000000..d62b0f8a7b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fsl/iconv.patch
@@ -0,0 +1,28 @@
+diff -ru a/src/flameo/Makefile b/src/flameo/Makefile
+--- a/src/flameo/Makefile	2018-10-02 08:46:58.000000000 -0500
++++ b/src/flameo/Makefile	2020-11-07 20:19:56.732547025 -0600
+@@ -6,9 +6,7 @@
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
+ 
+ UNAME := $(shell uname)
+-ifeq (${UNAME},Darwin)
+-        LIBS = -liconv
+-endif
++LIBS = -liconv
+ 
+ LIBS += -lutils -lnewimage -lmiscmaths -lm -lnewmat -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lprob -lz 
+ 
+diff -ru a/src/melodic/Makefile b/src/melodic/Makefile
+--- a/src/melodic/Makefile	2020-03-30 08:51:19.000000000 -0500
++++ b/src/melodic/Makefile	2020-11-07 20:21:45.625518576 -0600
+@@ -11,9 +11,7 @@
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
+ 
+ UNAME := $(shell uname)
+-ifeq (${UNAME},Darwin)
+-        LIBS = -liconv
+-endif
++LIBS = -liconv
+ 
+ LIBS += -lutils -lnewimage -lmiscplot -lmiscpic -lmiscmaths -lNewNifti -lcifti -lxml++-2.6 -lxml2 -lboost_filesystem -lboost_system -lznz -lnewmat -lprob -lm  -lgdc -lgd -lpng -lz
+ 
diff --git a/var/spack/repos/builtin/packages/fsl/package.py b/var/spack/repos/builtin/packages/fsl/package.py
index 35f4978698..5511096e53 100644
--- a/var/spack/repos/builtin/packages/fsl/package.py
+++ b/var/spack/repos/builtin/packages/fsl/package.py
@@ -8,42 +8,157 @@ from spack.util.environment import EnvironmentModifications
 import os
 
 
-class Fsl(Package):
+class Fsl(Package, CudaPackage):
     """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI
-       brain imaging data.
+       brain imaging data."""
 
-       Note: A manual download is required for FSL.
-       Spack will search your current directory for the download file.
-       Alternatively, add this file to a mirror so that Spack can find it.
-       For instructions on how to set up a mirror, see
-       http://spack.readthedocs.io/en/latest/mirrors.html"""
+    # NOTE: A manual download is required for FSL.  Spack will search your
+    # current directory for the download file.  Alternatively, add this file to
+    # a mirror so that Spack can find it.  For instructions on how to set up a
+    # mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
 
     homepage = "https://fsl.fmrib.ox.ac.uk"
     url      = "file://{0}/fsl-5.0.10-sources.tar.gz".format(os.getcwd())
     manual_download = True
 
-    version('5.0.10', '64823172a08aad679833240ba64c8e30')
+    version('6.0.4', sha256='58b88f38e080b05d70724d57342f58e1baf56e2bd3b98506a72b4446cad5033e')
+    version('5.0.10', sha256='ca183e489320de0e502a7ba63230a7f55098917a519e8c738b005d526e700842')
 
     depends_on('python', type=('build', 'run'))
     depends_on('expat')
     depends_on('libx11')
     depends_on('glu')
-    depends_on('zlib')
-    depends_on('libpng')
-    depends_on('boost')
-    depends_on('sqlite')
-
-    conflicts('%gcc@6:', when='@5.0.10')
+    depends_on('libiconv')
+    depends_on('openblas', when='@6:')
+    depends_on('vtk@:8')
+
+    conflicts('%gcc@:4.7,5.5:')
+    conflicts('^cuda@9.2:')
+    conflicts('cuda_arch=none', when='+cuda',
+              msg='must select a CUDA architecture')
+    conflicts('platform=darwin',
+              msg='currently only packaged for linux')
+
+    patch('build_log.patch')
+    patch('eddy_Makefile.patch', when='@6:')
+    patch('iconv.patch')
+    patch('fslpython_install_v5.patch', when='@:5')
+    patch('fslpython_install_v6.patch', when='@6:')
+
+    # These patches disable FSL's attempts to try to submit a subset of FSL
+    # computations to an SGE queue system. That auto-submit mechanism only
+    # works for SGE and requires someone to edit the fsl_sub script to
+    # accommodate their system. These patches disable the auto submission
+    # scheme and allow the fsl_sub script to behave the same on all systems,
+    # and without further modification, whether the computation is submitted to
+    # a "local" system, like a workstation, or as a batch job to a cluster
+    # queueing system, regardless of queue system type.
+    patch('fsl_sub_v5.patch', when='@:5')
+    patch('fsl_sub_v6.patch', when='@6:')
 
     def patch(self):
         # Uncomment lines in source file to allow building from source
         with working_dir(join_path(self.stage.source_path, 'etc', 'fslconf')):
             sourced = FileFilter('fsl.sh')
             sourced.filter('#FSLCONFDIR', 'FSLCONFDIR')
-            sourced.filter('#FSLMACHTYPE', 'FSLMACHTYPE')
-        # Fix error in build script
-        buildscript = FileFilter('build')
-        buildscript.filter('mist-clean', 'mist')
+
+            if self.spec.satisfies('@6:'):
+                sourced.filter('#FSLMACHTYPE', 'FSLMACHTYPE')
+            else:
+                sourced.filter(r'#(FSLMACHTYPE).*', r'\1=linux_64-gcc4.8')
+
+        if self.spec.satisfies('@:5'):
+            with working_dir(join_path(self.stage.source_path, 'config',
+                                       'common')):
+                buildproj = FileFilter('buildproj')
+                buildproj.filter(r'(^FSLMACHTYPE).*', r'\1=linux_64-gcc4.8')
+
+        # Capture the settings file
+        if self.spec.satisfies('@6:'):
+            settings_file = join_path(self.stage.source_path, 'config',
+                                      'buildSettings.mk')
+            vtk_file = settings_file
+        else:
+            settings_file = join_path(self.stage.source_path, 'config',
+                                      'linux_64-gcc4.8', 'systemvars.mk')
+            externals_file = join_path(self.stage.source_path, 'config',
+                                       'linux_64-gcc4.8', 'externallibs.mk')
+            vtk_file = externals_file
+
+        build_settings = FileFilter(settings_file)
+        vtk_settings = FileFilter(vtk_file)
+
+        build_settings.filter(r'^CUDAVER', '#CUDAVER')
+        build_settings.filter(r'(^CC)\s*=.*', r'\1 = {0}'.format(spack_cc))
+        build_settings.filter(r'(^CXX)\s*=.*', r'\1 = {0}'.format(spack_cxx))
+        build_settings.filter(r'(^CXX11)\s*=.*', r'\1 = {0}'.format(spack_cxx))
+
+        vtk_suffix = self.spec['vtk'].version.up_to(2)
+        vtk_lib_dir = self.spec['vtk'].prefix.lib64
+        vtk_include_dir = join_path(self.spec['vtk'].prefix.include,
+                                    'vtk-{0}'.format(vtk_suffix))
+
+        vtk_settings.filter(r'(^VTKDIR_INC)\s*=.*',
+                            r'\1 = {0}'.format(vtk_include_dir))
+        vtk_settings.filter(r'(^VTKDIR_LIB)\s*=.*',
+                            r'\1 = {0}'.format(vtk_lib_dir))
+        vtk_settings.filter(r'(^VTKSUFFIX)\s*=.*',
+                            r'\1 = -{0}'.format(vtk_suffix))
+
+        if '+cuda' in self.spec:
+            cuda_arch = self.spec.variants['cuda_arch'].value
+            cuda_gencode = ' '.join(self.cuda_flags(cuda_arch))
+            cuda_installation = self.spec['cuda'].prefix
+
+            build_settings.filter(r'(^CUDA_INSTALLATION)\s*=.*',
+                                  r'\1 = {0}'.format(cuda_installation))
+            build_settings.filter(r'(^LIB_CUDA)\s*=.*',
+                                  r'\1 = {0}'.format(
+                                      join_path(
+                                          cuda_installation,
+                                          'lib64')))
+            build_settings.filter(r'(^INC_CUDA)\s*=.*',
+                                  r'\1 = {0}'.format(
+                                      join_path(
+                                          cuda_installation,
+                                          'include')))
+            build_settings.filter(r'(^NVCC11)\s*=.*',
+                                  r'\1 = {0}'.format(
+                                      join_path(
+                                          cuda_installation, 'bin',
+                                          'nvcc')))
+            build_settings.filter(r'(^NVCC)\s*=.*',
+                                  r'\1 = {0}'.format(
+                                      join_path(
+                                          cuda_installation, 'bin',
+                                          'nvcc')))
+            build_settings.filter(r'(^GENCODE_FLAGS)\s*=.*',
+                                  r'\1 = {0}'.format(cuda_gencode))
+
+            if self.spec.satisfies('@6:'):
+                build_settings.filter(r'(^EDDYBUILDPARAMETERS)\s*=.*',
+                                      r'\1 = "cuda=1" "cpu=1"')
+                build_settings.filter(r'(^fdt_MASTERBUILD)\s*=.*',
+                                      r'\1 = COMPILE_GPU=1')
+                build_settings.filter(r'(^ptx2_MASTERBUILD)\s*=.*',
+                                      r'\1 = COMPILE_GPU=1')
+            else:
+                with open(settings_file, 'a') as f:
+                    f.write('COMPILE_GPU=1\n')
+        else:
+            build_settings.filter(r'^CUDA_INSTALLATION', '#CUDA_INSTALLATION')
+            build_settings.filter(r'^GENCODE_FLAGS', '#GENCODE_FLAGS')
+            build_settings.filter(r'^LIB_CUDA', '#LIB_CUDA')
+            build_settings.filter(r'^INC_CUDA', '#INC_CUDA')
+            build_settings.filter(r'^NVCC', '#NVCC')
+
+            if self.spec.satisfies('@6:'):
+                build_settings.filter(r'(^EDDYBUILDPARAMETERS)\s*=.*',
+                                      r'\1 = "cpu=1"')
+                build_settings.filter(r'(^fdt_MASTERBUILD)\s*=.*',
+                                      r'\1 = COMPILE_GPU=0')
+                build_settings.filter(r'(^ptx2_MASTERBUILD)\s*=.*',
+                                      r'\1 = COMPILE_GPU=0')
 
     def install(self, spec, prefix):
         build = Executable('./build')
@@ -51,6 +166,20 @@ class Fsl(Package):
 
         install_tree('.', prefix)
 
+    @run_after('install')
+    def postinstall(self):
+        # The PYTHON  related environment variables need to be unset here so
+        # the post install script does not get confused.
+        vars_to_unset = ['PYTHONPATH', 'PYTHONHOME']
+
+        with spack.util.environment.preserve_environment(*vars_to_unset):
+            for v in vars_to_unset:
+                del os.environ[v]
+
+            script = Executable(join_path(prefix, 'etc', 'fslconf',
+                                          'post_install.sh'))
+            script('-f', prefix)
+
     def setup_build_environment(self, env):
         if not self.stage.source_path:
             self.stage.fetch()
@@ -66,18 +195,9 @@ class Fsl(Package):
             env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))
 
     def setup_run_environment(self, env):
-        # Here, run-time environment variables are being set manually.
-        # Normally these would be added to the modulefile at build-time
-        # by sourcing fsl.sh, but incorrect paths were being set, pointing to
-        # the staging directory rather than the install directory.
+        # Set the environment variables after copying tree
         env.set('FSLDIR', self.prefix)
-        env.set('FSLOUTPUTTYPE', 'NIFTI_GZ')
-        env.set('FSLMULTIFILEQUIT', 'TRUE')
-        env.set('FSLTCLSH', self.prefix.bin.fsltclsh)
-        env.set('FSLWISH', self.prefix.bin.fslwish)
-        env.set('FSLLOCKDIR', '')
-        env.set('FSLMACHINELIST', '')
-        env.set('FSLREMOTECALL', '')
-        env.set('FSLGECUDAQ', 'cuda.q')
-
-        env.prepend_path('PATH', self.prefix)
+        fslsetup = join_path(self.prefix, 'etc', 'fslconf', 'fsl.sh')
+
+        if os.path.isfile(fslsetup):
+            env.extend(EnvironmentModifications.from_sourcing_file(fslsetup))