Mercurial > repos > mvdbeek > docker_scriptrunner

comparison scriptrunner.py @ 10:ed7cf3f35799 draft

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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit d8d8e8e063698813c9eb646e0df7d93118fd0520
author mvdbeek
date Sat, 09 Jul 2016 07:12:40 -0400
parents 77dca93454b7
children 5a3652633289
comparison
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9:77dca93454b7 10:ed7cf3f35799
335 if self.opts.output_dir: 335 if self.opts.output_dir:
336 ste = open(self.elog,'w') 336 ste = open(self.elog,'w')
337 sto = open(self.tlog,'w') 337 sto = open(self.tlog,'w')
338 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl)) 338 sto.write('## Toolfactory generated command line = %s\n' % ' '.join(self.cl))
339 sto.flush() 339 sto.flush()
340 print("commandline is %s" % (self.cl))
341 print("environment is %s" % (os.environ))
342 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir) 340 p = subprocess.Popen(self.cl,shell=False,stdout=sto,stderr=ste,stdin=subprocess.PIPE,cwd=self.opts.output_dir)
343 else: 341 else:
344 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE) 342 p = subprocess.Popen(self.cl,shell=False,stdin=subprocess.PIPE)
345 p.stdin.write(self.script) 343 p.stdin.write(self.script)
346 p.stdin.close() 344 p.stdin.close()
380 To avoid issues with wrong user ids, we change the user id of the 'galaxy' user in the container 378 To avoid issues with wrong user ids, we change the user id of the 'galaxy' user in the container
381 to the user id with which the script has been called initially. 379 to the user id with which the script has been called initially.
382 """ 380 """
383 cmd1 = ["/usr/sbin/usermod", "-d", "/var/home/galaxy", "galaxy"] 381 cmd1 = ["/usr/sbin/usermod", "-d", "/var/home/galaxy", "galaxy"]
384 cmd2 = ["/usr/sbin/usermod", "-u", new_uid, "galaxy"] 382 cmd2 = ["/usr/sbin/usermod", "-u", new_uid, "galaxy"]
385 cmd3 = ["/usr/sbin/groupmod", "-g", "1450", new_gid] 383 cmd3 = ["/usr/sbin/groupmod", "-g", new_gid, "galaxy"]
386 cmd4 = ["/usr/sbin/usermod", "-d", "/home/galaxy", "galaxy"] 384 cmd4 = ["/usr/sbin/usermod", "-d", "/home/galaxy", "galaxy"]
387 [subprocess.call(cmd) for cmd in [cmd1, cmd2, cmd3, cmd4]] 385 [subprocess.call(cmd) for cmd in [cmd1, cmd2, cmd3, cmd4]]
388 386
389 387
390 def main(): 388 def main():