Mercurial > repos > mvdbeek > docker_scriptrunner

comparison scriptrunner.py @ 7:17e93298c225 draft

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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 87a8f2ec706b231b2db20a9433efa34d967d35cf-dirty
author mvdbeek
date Fri, 08 Jul 2016 18:05:50 -0400
parents b28d3445992b
children 1b7f987270a6
comparison
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6:b28d3445992b 7:17e93298c225
392 """ 392 """
393 cmd = ["/usr/sbin/usermod", "-u", new_id, "galaxy"] 393 cmd = ["/usr/sbin/usermod", "-u", new_id, "galaxy"]
394 subprocess.call(cmd) 394 subprocess.call(cmd)
395 395
396 396
397 def update_permissions(): 397 def update_permissions(new_id,new_gid):
398 cmd = ["/bin/chown", "-R", "galaxy:galaxy", "/var/home/galaxy"] 398 cmd1 = ['/usr//bin/find', '/', '-user', '1450', '-exec', 'chown', '-h', new_id, '{}', '\\;']
399 subprocess.call(cmd) 399 cmd2 = ['/usr//bin/find', '/', '-group', '1450', '-exec', 'chgrp', '-h', new_gid, '{}', '\\;']
400 #cmd = ["/bin/chown", "-R", "galaxy:galaxy", "/var/home/galaxy"]
401 subprocess.call(cmd1)
402 subprocess.call(cmd2)
400 403
401 def main(): 404 def main():
402 u = """ 405 u = """
403 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as: 406 This is a Galaxy wrapper. It expects to be called by a special purpose tool.xml as:
404 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript" 407 <command interpreter="python">rgBaseScriptWrapper.py --script_path "$scriptPath" --tool_name "foo" --interpreter "Rscript"
437 return 440 return
438 change_user_id(opts.user_id) 441 change_user_id(opts.user_id)
439 change_group_id(opts.group_id) 442 change_group_id(opts.group_id)
440 os.setgid(int(opts.group_id)) 443 os.setgid(int(opts.group_id))
441 os.setuid(int(opts.user_id)) 444 os.setuid(int(opts.user_id))
442 update_permissions() 445 update_permissions(opts.user_id, opts.group_id)
443 r = ScriptRunner(opts) 446 r = ScriptRunner(opts)
444 retcode = r.run() 447 retcode = r.run()
445 os.unlink(r.sfile) 448 os.unlink(r.sfile)
446 if retcode: 449 if retcode:
447 sys.exit(retcode) # indicate failure to job runner 450 sys.exit(retcode) # indicate failure to job runner