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.briggs(a)manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482