Hi,
(Python 2.5, OS X 10.4.10)
I have a program called pdb2pqr on my system. It is installed so that
"pdb2pqr" is in my path and looks like:
#\!/bin/zsh -f
/sw/share/pdb2pqr/pdb2pqr.py "$@"
When I call it via this script:
#!/usr/bin/env python
import subprocess
import tempfile
args = ('/sw/bin/pdb2pqr','--help')
output_file = tempfile.TemporaryFile(mode="w+")
print "Running",args
retcode =
subprocess.call(args,stdout=output_file.fileno(),s tderr=subprocess.STDOUT)
output_file.close()
I get this error:
localhost~/tmp$ ./x.py
Running ('/sw/bin/pdb2pqr', '--help')
Traceback (most recent call last):
File "./x.py", line 9, in <module>
retcode =
subprocess.call(args,stdout=output_file.fileno(),s tderr=subprocess.STDOUT)
File "/sw/lib/python2.5/subprocess.py", line 443, in call
return Popen(*popenargs, **kwargs).wait()
File "/sw/lib/python2.5/subprocess.py", line 593, in __init__
errread, errwrite)
File "/sw/lib/python2.5/subprocess.py", line 1051, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error
But when I change it to directly call the script that the zsh script
calls like this:
args = ('/sw/share/pdb2pqr/pdb2pqr.py','--help')
everything works:
localhost~/tmp$ ./x.py
Running ('/sw/share/pdb2pqr/pdb2pqr.py', '--help')
This is with 2.5 on OS X 10.4.10. I'm happy to provide whatever
additional information might be useful.
Thanks,
-michael 2 7540
Michael George Lerner <mg******@gmail.comwrites:
Hi,
(Python 2.5, OS X 10.4.10)
I have a program called pdb2pqr on my system. It is installed so that
"pdb2pqr" is in my path and looks like:
#\!/bin/zsh -f
Are you sure that this shebang is correct?
I've tested that on bash and have similar error:
# t1.sh
#\!/bin/sh
echo "t1"
>>from subprocess import call call(['./t1.sh'])
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib/python2.4/subprocess.py", line 413, in call
return Popen(*args, **kwargs).wait()
File "/usr/lib/python2.4/subprocess.py", line 543, in __init__
errread, errwrite)
File "/usr/lib/python2.4/subprocess.py", line 975, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error
But running that directly through the shell works:
>>call(['./t1.sh'], shell=True)
t1
0
However this script works fine also without `shell=True` option:
# t2.sh
#!/bin/sh
echo "t2"
>>call(['./t2.sh'])
t2
0
HTH,
Rob
On Nov 11, 3:25 pm, Rob Wolfe <r...@smsnet.plwrote:
Hi Rob,
Michael GeorgeLerner<mgler...@gmail.comwrites:
Hi,
(Python 2.5, OS X 10.4.10)
I have a program called pdb2pqr on my system. It is installed so that
"pdb2pqr" is in my path and looks like:
#\!/bin/zsh -f
Are you sure that this shebang is correct?
Well, it's correct in the sense that I have faithfully reproduced the
contents of the file. I didn't write it, though.
I don't know what the extra backslash is for. I suppose I'll contact
the authors and find out.
Any ideas how to make it work with the strange shebang syntax?
Thanks,
-michael
>
I've tested that on bash and have similar error:
# t1.sh
#\!/bin/sh
echo "t1"
>from subprocess import call call(['./t1.sh'])
Traceback (most recent call last):
File "<stdin>", line 1, in ?
File "/usr/lib/python2.4/subprocess.py", line 413, in call
return Popen(*args, **kwargs).wait()
File "/usr/lib/python2.4/subprocess.py", line 543, in __init__
errread, errwrite)
File "/usr/lib/python2.4/subprocess.py", line 975, in _execute_child
raise child_exception
OSError: [Errno 8] Exec format error
But running that directly through the shell works:
>call(['./t1.sh'], shell=True)
t1
0
However this script works fine also without `shell=True` option:
# t2.sh
#!/bin/sh
echo "t2"
>call(['./t2.sh'])
t2
0
HTH,
Rob
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