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,