buccaneer_pipeline failure (ccp4 6.2.0) (SOLUTION)

From: Frank von Delft <frank.vondelft@sgc.ox.ac.uk>

Date: 19 October 2011 06:47



We discovered the problem:  the file $CBIN/buccaneer_pipeline needs to be told to expand its lookup path, so we inserted in the 2nd line:

   sys.path.append("/usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python/")

We had this fix in our previous installation as well, but can't remember where we got it from;  I have no idea why only we seem to need it (is nobody else running buccaneer?  Then they're fools:  it's massively useful...)

Cheers
phx


On 18/10/2011 10:52, Tim Gruene wrote:

And you do have read access to
/usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python/CCP4pipeline.py
(on our installation, the mode is actually 755, but I suppose 644 should
be sufficient).
You can set PYTHONVERBOSE to 1 or higher in the shell you start ccp4i
from to see what python is doing ('man python').

Tim

On 10/18/2011 11:34 AM, Frank von Delft wrote:

Mine reads:
/usr/local/ccp4/6.2.0/ccp4-6.2.0/share/python:/usr/local/ccpnmr/ccpnmr1.0/python


That should work, right?  Where else can I look, for the failing
import?  This is a lettuce-fresh install, pulled straight off web and
installed with all defaults.

Cheers
phx.


On 18/10/2011 08:38, Tim Gruene wrote:
Hi Frank,

it may not be the python binary itself but the PYTHONPATH which is
incorrectly set. After initialising ccp4, mine reads
    tg@slartibartfast:~$ echo $PYTHONPATH
    /xtal/Suites/CCP4/ccp4-6.2.0/share/python:
which is modified around line 231 in $CBIN/include/ccp4.setup

My python binary is /usr/bin/python, and I have used buccaneer without
errors.

Tim



On 10/17/2011 09:30 PM, Frank von Delft wrote:

Hi, we got around to switching to ccp4 version 6.2.0, but now buccaneer
fails from the GUI.  Below is what shows up if you view the com file
before execution; and below that the logfile.

Seems to me it's using the wrong python executable;  the first one on my
path is certainly nothing to do with ccp4, so now wonder it can't
import.

Shouldn't python be invoked explicitly with its full path?  Where can I
set this?  (Mind you, setting it in the Run&View didn't work.)
Cheers
phx




*Run&View Com File: *
python -u /usr/local/ccp4/6.2.0/ccp4-6.2.0/bin/buccaneer_pipeline -stdin


*Logfile*
#CCP4I VERSION CCP4Interface 2.1.0
#CCP4I SCRIPT LOG buccaneer_pipeline
#CCP4I DATE 17 Oct 2011  18:45:20
#CCP4I USER loretta
#CCP4I PROJECT PROJECT
#CCP4I JOB_ID 13
#CCP4I SCRATCH /tmp/loretta
#CCP4I HOSTNAME hestia.sgc.ox.ac.uk
#CCP4I PID 13684

***************************************************************************

* Information from CCP4Interface script
***************************************************************************

The program run with command: python -u
/usr/local/ccp4/6.2.0/ccp4-6.2.0/bin/buccaneer_pipeline -stdin
has failed with error message
Traceback (most recent call last):
   File "/usr/local/ccp4/6.2.0/ccp4-6.2.0/bin/buccaneer_pipeline", line
3, in<module>
     from CCP4pipeline import Control
ImportError: No module named CCP4pipeline
***************************************************************************

-- - --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

- -- - --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen