From 17139b575d52f786967eaf75ddbbb089df7b25f3 Mon Sep 17 00:00:00 2001
From: Audrey Thoma <las_thoma15@iastate.edu>
Date: Thu, 5 Oct 2017 13:57:57 -0500
Subject: fsl: new package (#5605)

---
 var/spack/repos/builtin/packages/fsl/package.py | 102 ++++++++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/fsl/package.py

diff --git a/var/spack/repos/builtin/packages/fsl/package.py b/var/spack/repos/builtin/packages/fsl/package.py
new file mode 100644
index 0000000000..a5fd81cbd6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fsl/package.py
@@ -0,0 +1,102 @@
+##############################################################################
+# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+from spack.environment import EnvironmentModifications
+import os
+import distutils.dir_util
+
+
+class Fsl(Package):
+    """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI
+       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"""
+
+    homepage = "https://fsl.fmrib.ox.ac.uk"
+    url      = "file://{0}/fsl-5.0.10-sources.tar.gz".format(os.getcwd())
+
+    version('5.0.10', '64823172a08aad679833240ba64c8e30')
+
+    depends_on('python', type=('build', 'run'))
+    depends_on('expat')
+    depends_on('libx11')
+    depends_on('mesa-glu')
+    depends_on('zlib')
+    depends_on('libpng')
+    depends_on('boost')
+    depends_on('sqlite')
+
+    conflicts('%gcc@6:', when='@5.0.10')
+
+    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')
+
+    def install(self, spec, prefix):
+        build = Executable('./build')
+        build()
+
+        distutils.dir_util.copy_tree(".", prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        if not self.stage.source_path:
+            self.stage.fetch()
+            self.stage.expand_archive()
+
+        spack_env.set('FSLDIR', self.stage.source_path)
+
+        # 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.
+        run_env.set('FSLDIR', self.prefix)
+        run_env.set('FSLOUTPUTTYPE', 'NIFTI_GZ')
+        run_env.set('FSLMULTIFILEQUIT', 'TRUE')
+        run_env.set('FSLTCLSH', self.prefix.bin.fsltclsh)
+        run_env.set('FSLWISH', self.prefix.bin.fslwish)
+        run_env.set('FSLLOCKDIR', '')
+        run_env.set('FSLMACHINELIST', '')
+        run_env.set('FSLREMOTECALL', '')
+        run_env.set('FSLGECUDAQ', 'cuda.q')
+
+        run_env.prepend_path('PATH', self.prefix)
+
+        # Below is for sourcing purposes during building
+        fslsetup = join_path(self.stage.source_path, 'etc', 'fslconf',
+                             'fsl.sh')
+
+        if os.path.isfile(fslsetup):
+            spack_env.extend(EnvironmentModifications.from_sourcing_file(
+                             fslsetup))
-- 
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