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https://github.com/galaxyproject/galaxy.git
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Nicola Soranzo
d1bc98dfcb
Remove some debugging prints. Fix import order. Consolidate exception logging in ToolShed database migrations.
49 lines
1.2 KiB
Python
49 lines
1.2 KiB
Python
#!/usr/bin/env python
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"""
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Classes encapsulating decypher tool.
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James E Johnson - University of Minnesota
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"""
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from __future__ import print_function
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import os
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import subprocess
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import sys
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assert sys.version_info[:2] >= (2, 6)
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def stop_err(msg):
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sys.stderr.write("%s\n" % msg)
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sys.exit()
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def __main__():
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# Parse Command Line
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working_dir = sys.argv[1]
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inputs = ' '.join(sys.argv[2:])
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for _ in ('Roadmaps', 'Sequences'):
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os.symlink(os.path.join(working_dir, _), _)
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cmdline = 'velvetg . %s' % (inputs)
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print("Command to be executed: %s" % cmdline)
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try:
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proc = subprocess.Popen(args=cmdline, shell=True, stderr=subprocess.PIPE)
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returncode = proc.wait()
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# get stderr, allowing for case where it's very large
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stderr = ''
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buffsize = 1048576
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try:
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while True:
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stderr += proc.stderr.read(buffsize)
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if not stderr or len(stderr) % buffsize != 0:
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break
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except OverflowError:
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pass
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if returncode != 0:
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raise Exception(stderr)
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except Exception as e:
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stop_err('Error running velvetg ' + str(e))
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if __name__ == "__main__":
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__main__()
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