Mercurial > repos > crs4 > seal_galaxy
view seal-galaxy-cc1b1911/seal/generate_sam_header.py @ 0:244073d9abc1 draft default tip
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author | crs4 |
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date | Wed, 15 Oct 2014 09:41:10 -0400 |
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#!/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)