Calling python script from bash script while using GNU Parallel

Question

I am trying to run a python script in parallel (with GNU parallel 20110722). As it could be seen below, I am not able to run in any of the ways I tried. (^C marks the point where I interrupt the job with ctrl+C because there is no response from the system).

me@kubuntu:~/Programs/LeitMotifsParallel$ parallel python {1} :::: <(echo MainMult.18136.py)
^C
me@kubuntu:~/Programs/LeitMotifsParallel$ parallel python {1} ::: <(echo MainMult.18136.py)
File "/dev/fd/63", line 1
MainMult.18136.py
             ^
SyntaxError: invalid syntax
me@kubuntu:~/Programs/LeitMotifsParallel$ parallel MainMult.18136.py
parallel: Input is tty. Press CTRL-D to exit.
^C
me@kubuntu:~/Programs/LeitMotifsParallel$

However, the python script runs as expected when run directly from console.

me@kubuntu:~/Programs/LeitMotifsParallel$ MainMult.18136.py 
/home/me/Programs/LeitMotifsParallel/StAlg.py:6: DeprecationWarning: the sets module is deprecated
import sets #@UnusedImport
Start : 18:59:34 11Aug2011
['M']
['M']
(...)

I haven't been succesful in finding an answer for this situation, so I would really appreciate if you could help me solve this.

Ole Tange · Accepted Answer · 2013-07-12 22:00:34Z

2

If http://www.biostars.org/p/11132/#11139 does not answer your question, please elaborate what is missing.

edited Jul 12, 2013 at 22:00

answered Aug 13, 2011 at 20:51

Ole Tange

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1 Comment

NPalopoli Over a year ago

It actually does. Thanks a lot for your help.

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