Hi All,

I am attempting to do a local install of Galaxy using the galaxy-dist source. 
While testing some of the the tools I have run into a problem with the laj 
Pairwise Alignment Viewer tool. I have also tested this on the test server 
http://test.g2.bx.psu.edu/ and I am getting a very similar error.

I have used blastz to create a test lav file.

On http://test.g2.bx.psu.edu/ the error is:

Traceback (most recent call last):
  File "/var/opt/galaxy/g2test/galaxy_test/lib/galaxy/jobs/runners/pbs.py", 
line 514, in finish_job
    pbs_job_state.job_wrapper.finish( stdout, stderr )
  File "/var/opt/galaxy/g2test/galaxy_test/lib/galaxy/jobs/__init__.py", line 
630, in finish
    tool=self.tool, stdout=stdout, stderr=stderr )
  File "/var/opt/galaxy/g2test/galaxy_test/lib/galaxy/tools/__init__.py", line 
1664, in call_hook
    return code( *args, **kwargs )
  File "./tools/visualization/LAJ_code.py", line 24, in exec_after_process
    elif name == "repeatfile" and data.state == data.states.OK and 
data.has_data():
AttributeError: ('E', 'r', 'r', 'o', 'r', ' ', 'i', 'n', ' ', "'", 'L', 'A', 
'J', "'", ' ', 'h', 'o', 'o', 'k', ' ', "'", 'e', 'x', 'e', 'c', '_', 'a', 'f', 
't', 'e', 'r', '_', 'p', 'r', 'o', 'c', 'e', 's', 's', "'", ',', ' ', 'o', 'r', 
'i', 'g', 'i', 'n', 'a', 'l', ' ', 'm', 'e', 's', 's', 'a', 'g', 'e', ':', ' ', 
"'", 'N', 'o', 'n', 'e', 'T', 'y', 'p', 'e', "'", ' ', 'o', 'b', 'j', 'e', 'c', 
't', ' ', 'h', 'a', 's', ' ', 'n', 'o', ' ', 'a', 't', 't', 'r', 'i', 'b', 'u', 
't', 'e', ' ', "'", 's', 't', 'a', 't', 'e', "'")

While on my local install it is :
Traceback (most recent call last):
  File "/storage/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 125, in 
run_job
    job_wrapper.finish( stdout, stderr )
  File "/storage/galaxy-dist/lib/galaxy/jobs/__init__.py", line 630, in finish
    tool=self.tool, stdout=stdout, stderr=stderr )
  File "/storage/galaxy-dist/lib/galaxy/tools/__init__.py", line 1632, in 
call_hook
    return code( *args, **kwargs )
  File "./tools/visualization/LAJ_code.py", line 24, in exec_after_process
    elif name == "repeatfile" and data.state == data.states.OK and 
data.has_data():
AttributeError: ('E', 'r', 'r', 'o', 'r', ' ', 'i', 'n', ' ', "'", 'L', 'A', 
'J', "'", ' ', 'h', 'o', 'o', 'k', ' ', "'", 'e', 'x', 'e', 'c', '_', 'a', 'f', 
't', 'e', 'r', '_', 'p', 'r', 'o', 'c', 'e', 's', 's', "'", ',', ' ', 'o', 'r', 
'i', 'g', 'i', 'n', 'a', 'l', ' ', 'm', 'e', 's', 's', 'a', 'g', 'e', ':', ' ', 
"'", 'N', 'o', 'n', 'e', 'T', 'y', 'p', 'e', "'", ' ', 'o', 'b', 'j', 'e', 'c', 
't', ' ', 'h', 'a', 's', ' ', 'n', 'o', ' ', 'a', 't', 't', 'r', 'i', 'b', 'u', 
't', 'e', ' ', "'", 's', 't', 'a', 't', 'e', "'")
Any help would be appreciated,

Thanks,
-- 

Jason Ellul 
Bioinformatician 
Cancer Research Division

Peter MacCallum Cancer Centre 
TEL: +61 3 9656 1512 
FAX: +61 3 9656 1411 
EMAIL: jason.el...@petermac.org  

Address: St Andrew's Place East Melbourne Victoria 3002 Australia 
Postal Address: Locked Bag No. 1 A'Beckett St., Victoria, 8006, Australia



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