Dear devs

I was wondering if anyone had any suggestions as to the cause of a peculiar error I'm seeing when running the latest versions of the devteam "join" and "fastq_paired_end_joiner".


The tools appear to be picking up Python modules from the Galaxy library, rather than from the installed dependencies. The PYTHONPATH appears to be correct (i.e. tool dependency appears before Galaxy library path) but sys.path shows the dependency's Python egg appearing after the Galaxy library path.

E.g. for the paired-end joiner:

PYTHONPATH=/mnt/rvmi/centaurus/galaxy/devel/tool_dependencies/galaxy_sequence_utils/1.0.1/iuc/package_galaxy_sequence_utils_1_0_1/c1ab450748ba/lib/python:/mnt/rvmi/centaurus/galaxy/devel/galaxy-dist/lib

sys.path = ['', '/mnt/rvmi/centaurus/galaxy/devel/tool_dependencies/galaxy_sequence_utils/1.0.1/iuc/package_galaxy_sequence_utils_1_0_1/c1ab450748ba/lib/python', '/mnt/rvmi/centaurus/galaxy/devel/galaxy-dist/lib', '/mnt/rvmi/centaurus/galaxy/devel/tool_dependencies/galaxy_sequence_utils/1.0.1/iuc/package_galaxy_sequence_utils_1_0_1/c1ab450748ba/lib/python/galaxy_sequence_utils-1.0.1-py2.7.egg', '/home/centaurus-galaxy/fastq_paired_end_joiner_problem/venv/lib/python27.zip', '/home/centaurus-galaxy/fastq_paired_end_joiner_problem/venv/lib/python2.7', '/home/centaurus-galaxy/fastq_paired_end_joiner_problem/venv/lib/python2.7/plat-linux2', '/home/centaurus-galaxy/fastq_paired_end_joiner_problem/venv/lib/python2.7/lib-tk', '/home/centaurus-galaxy/fastq_paired_end_joiner_problem/venv/lib/python2.7/lib-old', '/home/centaurus-galaxy/fastq_paired_end_joiner_problem/venv/lib/python2.7/lib-dynload', '/mnt/rvmi/centaurus/galaxy/python/2.7.10/lib/python2.7', '/mnt/rvmi/centaurus/galaxy/python/2.7.10/lib/python2.7/plat-linux2', '/mnt/rvmi/centaurus/galaxy/python/2.7.10/lib/python2.7/lib-tk', '/home/centaurus-galaxy/fastq_paired_end_joiner_problem/venv/lib/python2.7/site-packages']

Error:

Traceback (most recent call last):
File "/mnt/rvmi/centaurus/galaxy/devel/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/6a7f5da7c76d/fastq_paired_end_joiner/fastq_paired_end_joiner.py", line 158, in <module>
    main()
File "/mnt/rvmi/centaurus/galaxy/devel/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/6a7f5da7c76d/fastq_paired_end_joiner/fastq_paired_end_joiner.py", line 136, in main
    joiner = fq.fastqJoiner( input1_type, paste=paste )
TypeError: __init__() got an unexpected keyword argument 'paste'

I know it's a long shot but can anyone suggest where to start looking at where this is going wrong?

Thanks,

Peter

Ps I'm using Galaxy v16.07 and the problem occurs on our production platform but not in a local Galaxy install on my desktop.

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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