Dear Galaxy Community,
I recently update my cluster-oriented local instance of Galaxy from version 17.01 to 17.05. Since then, I have faced an issue with some of my tools (such as bismark methylation extractor, which I got from the toolshed). Galaxy is unable to finish any of the jobs with this tool and display the following error message
Traceback (most recent call last): File "/mnt/extStorage/galaxy-app/lib/galaxy/jobs/runners/__init__.py", line 630, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/mnt/extStorage/galaxy-app/lib/galaxy/jobs/__init__.py", line 1301, in finish dataset.set_peek() File "/mnt/extStorage/galaxy-app/lib/galaxy/model/__init__.py", line 2031, in set_peek return self.datatype.set_peek( self, is_multi_byte=is_multi_byte ) File "/mnt/extStorage/galaxy-app/lib/galaxy/datatypes/data.py", line 782, in set_peek dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars, line_wrap=line_wrap ) File "/mnt/extStorage/galaxy-app/lib/galaxy/datatypes/data.py", line 1007, in get_file_peek temp = compression_utils.get_fileobj( file_name, "U" ) File "/mnt/extStorage/galaxy-app/lib/galaxy/util/compression_utils.py", line 32, in get_fileobj return zipfile.os_zipfile(filename, cmode) AttributeError: 'module' object has no attribute 'os_zipfile'
The tool was working without any issues prior to upgrading galaxy, and now all jobs fail this way. The tool generate three reports (in the form of a text file) and a gzipped file containing several more (large) text files). Would anyone has a clue about what's going on?