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
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