Merge pull request #278 from boegel/picard_GATK

add ported easyblocks for picard and GenomeAnalysisTK

easybuild/easyblocks/g/genomeanalysistk.py

@@ -0,0 +1,90 @@
+##
+# Copyright 2009-2013 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/>.
+##
+"""
+Support for building and installing GenomeAnalysisTK, implemented as an easyblock.
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+"""
+
+import os
+import shutil
+
+from easybuild.framework.easyblock import EasyBlock
+
+
+class EB_GenomeAnalysisTK(EasyBlock):
+    """Support for building and installing GenomeAnalysisTK."""
+
+    def configure_step(self):
+        """No configure step for GenomeAnalysisTK"""
+        pass
+
+    def build_step(self):
+        """No build step for GenomeAnalysisTK"""
+        pass
+
+    def install_step(self):
+        """Install GenomeAnalysisTK by copying required files/directories"""
+        srcdir = self.cfg['start_dir']
+        for jar in ["AnalyzeCovariates.jar", "GenomeAnalysisTK.jar"]:
+            src = os.path.join(srcdir, jar)
+            dst = os.path.join(self.installdir, jar)
+            try:
+                if os.path.exists(src):
+                    shutil.copy2(src, dst)
+                    self.log.info("Successfully copied %s to %s" % (src, dst))
+            except OSError, err:
+                self.log.error("Failed to copy %s to %s: %s" % (src, dst, err))
+
+        for subdir in ['resources']:
+            try:
+                src_dir = os.path.join(self.cfg['start_dir'], subdir)
+                dst_dir = os.path.join(self.installdir, subdir)
+                if os.path.exists(src_dir):
+                    shutil.copytree(src_dir, dst_dir)
+                else:
+                    self.log.warning("No directory %s, so not copying it." % src_dir)
+                self.log.info("Successfully copied %s to %s" % (src_dir, dst_dir))
+            except OSError, err:
+                self.log.error("Failed to copy %s to %s: %s" % (src_dir, dst_dir, err))
+
+    def sanity_check_step(self):
+        """Custom sanity check for GenomeAnalysisTK"""
+        custom_paths = {
+            'files': ["GenomeAnalysisTK.jar"],
+            'dirs': ["resources"],
+        }
+        super(EB_GenomeAnalysisTK, self).sanity_check_step(custom_paths=custom_paths)
+
+    def make_module_extra(self):
+        """Add module entries specific to GenomeAnalysisTK"""
+        txt = super(EB_GenomeAnalysisTK, self).make_module_extra()
+        txt += self.moduleGenerator.prepend_paths('PATH', '')
+        return txt
+

easybuild/easyblocks/p/picard.py

@@ -0,0 +1,83 @@
+##
+# Copyright 2009-2013 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/>.
+##
+"""
+Support for building and installing picard, implemented as an easyblock.
+
+@author: Stijn De Weirdt (Ghent University)
+@author: Dries Verdegem (Ghent University)
+@author: Kenneth Hoste (Ghent University)
+@author: Pieter De Baets (Ghent University)
+@author: Jens Timmerman (Ghent University)
+"""
+
+import os
+import re
+import shutil
+
+from easybuild.framework.easyblock import EasyBlock
+
+
+class EB_picard(EasyBlock):
+    """Support for building and installing picard."""
+
+    def configure_step(self):
+        """No configure step for picard"""
+        pass
+
+    def build_step(self):
+        """No build step for picard"""
+        pass
+
+    def install_step(self):
+        """Install picard by copying required files"""
+        # recent version may contain more than just the picard-tools subdirectory
+        picard_tools_dir = 'picard-tools-%s' % self.version
+        if not re.search("%s/?$" % picard_tools_dir, self.cfg['start_dir']):
+            self.cfg['start_dir'] = os.path.join(self.cfg['start_dir'], picard_tools_dir)
+            if not os.path.exists(self.cfg['start_dir']):
+                self.log.error("Path %s to copy files from doesn't exist." % self.cfg['start_dir'])
+
+        for jar in os.listdir(self.cfg['start_dir']):
+            src = os.path.join(self.cfg['start_dir'], jar)
+            dst = os.path.join(self.installdir, jar)
+            try:
+                shutil.copy2(src, dst)
+                self.log.info("Successfully copied %s to %s" % (src, dst))
+            except OSError, err:
+                self.log.error("Failed to copy %s to %s (%s)" % (src, dst, err))
+
+    def sanity_check_step(self):
+        """Custom sanity check for picard"""
+        custom_paths = {
+            'files': ["%s-%s.jar" % (x, self.version) for x in ['picard', 'sam']],
+            'dirs': [],
+        }
+        super(EB_picard, self).sanity_check_step(custom_paths=custom_paths)
+
+    def make_module_extra(self):
+        """Add module entries specific to picard"""
+        txt = super(EB_picard, self).make_module_extra()
+        txt += self.moduleGenerator.prepend_paths('PATH', '')
+        return txt