diff seal-galaxy-cc1b1911/seal/generate_sam_header.py @ 0:244073d9abc1 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seal-galaxy-cc1b1911/seal/generate_sam_header.py	Wed Oct 15 09:41:10 2014 -0400
@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+
+# Copyright (C) 2011-2014 CRS4.
+#
+# This file is part of Seal.
+#
+# Seal 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, either version 3 of the License, or (at your option)
+# any later version.
+#
+# Seal 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 Seal.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+# A really really thin wrapper.  We only seem to need it because Galaxy won't
+# search for the command in the PATH
+
+import os
+import subprocess
+import sys
+
+if __name__ == '__main__':
+  output_path = sys.argv[-1]
+  try:
+    # seal merge_alignments won't overwrite an existing file, so we first remove
+    # the file Galaxy creates for us.
+    os.remove(output_path)
+  except IOError:
+    pass
+  hadoopized_output_path = 'file://' + os.path.abspath(output_path)
+  cmd = [ 'seal', 'merge_alignments' ] + sys.argv[1:-1]
+  cmd.append(hadoopized_output_path)
+  print "running command:", str(cmd)
+  subprocess.check_call(cmd)