add easyblock for MRtrix

easybuild/easyblocks/m/mrtrix.py

@@ -0,0 +1,89 @@
+##
+# Copyright 2009-2015 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Hercules foundation (http://www.herculesstichting.be/in_English)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# http://github.com/hpcugent/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild 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
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for building and installing MRtrix, implemented as an easyblock
+"""
+import os
+from distutils.version import LooseVersion
+
+import easybuild.tools.environment as env
+from easybuild.framework.easyblock import EasyBlock
+from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.run import run_cmd
+
+
+class EB_MRtrix(EasyBlock):
+    """Support for building/installing MRtrix."""
+
+    def __init__(self, *args, **kwargs):
+        """Initialize easyblock, enable build-in-installdir based on version."""
+        super(EB_MRtrix, self).__init__(*args, **kwargs)
+
+        if LooseVersion(self.version) >= LooseVersion('0.3'):
+            self.build_in_installdir = True
+            self.log.debug("Enabled build-in-installdir for version %s", self.version)
+
+    def extract_step(self):
+        """Extract MRtrix sources."""
+        # strip off 'mrtrix*' part to avoid having everything in a 'mrtrix*' subdirectory
+        if LooseVersion(self.version) >= LooseVersion('0.3'):
+            self.cfg.update('unpack_options', '--strip-components=1')
+
+        super(EB_MRtrix, self).extract_step()
+
+    def configure_step(self):
+        """No configuration step for MRtrix."""
+        if LooseVersion(self.version) >= LooseVersion('0.3'):
+            env.setvar('LD', "%s LDFLAGS OBJECTS -o EXECUTABLE" % os.getenv('CXX'))
+            env.setvar('LDLIB', "%s -shared LDLIB_FLAGS OBJECTS -o LIB" % os.getenv('CXX'))
+            env.setvar('QMAKE_CXX', os.getenv('CXX'))
+            cmd = "python configure -verbose"
+            run_cmd(cmd, log_all=True, simple=True, log_ok=True)
+
+    def build_step(self):
+        """Custom build procedure for MRtrix."""
+        extra_inc_path = os.path.join(get_software_root('GCC'), 'include', 'c++', get_software_version('GCC'))
+        env.setvar('CPATH', ':'.join([extra_inc_path, os.getenv('CPATH', '')]))
+
+        cmd = "python build -verbose"
+        run_cmd(cmd, log_all=True, simple=True, log_ok=True)
+
+    def install_step(self):
+        """Custom install procedure for MRtrix."""
+        if LooseVersion(self.version) < LooseVersion('0.3'):
+            cmd = "python build -verbose install=%s linkto=" % self.installdir
+            run_cmd(cmd, log_all=True, simple=True, log_ok=True)
+
+    def sanity_check_step(self):
+        """Custom sanity check for MRtrix."""
+        if LooseVersion(self.version) >= LooseVersion('0.3'):
+            libso = 'libmrtrix.so'
+        else:
+            libso = 'libmrtrix-%s.so' % '_'.join(self.version.split('.'))
+        custom_paths = {
+            'files': [os.path.join('lib', libso)],
+            'dirs': ['bin'],
+        }
+        super(EB_MRtrix, self).sanity_check_step(custom_paths=custom_paths)