Hi Marco, this tool has not been updated recently and it still uses tool_dependencies.xml for its dependencies. You can choose among 3 options (in order of my personal preference):
- add a new requirement for Python2 to the tool bam_to_bigwig.xml file: <requirement type="package" version="2.7.14">python</requirement> and reinstall the Conda dependencies under the Admin interface -> "Manage Tool Dependencies"
- port the bam_to_bigwig.py script to Python3 (usually it's not difficult with the help of 2to3)
- reinstall the tool and choose to install the repository and Tool Shed managed dependencies instead of the Conda ones.
Hope that helps! Nicola
On 26/10/17 15:53, Marco Tangaro wrote:
Dear experts, I've an issue with the bam_to_bigwig (brad-chapman) tool from the ToolShed. I've installed it using Conda to solve dependencies.
When I run it on a bam file I get this error:
Fatal error: Exit code 1 () File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py http://toolshed.g2.bx.psu.edu/repos/brad-chapman/bam_to_bigwig/9163e1db4c16/bam_to_bigwig/bam_to_bigwig.py", line 41 print "Have %i references" % len(sizes) ^ SyntaxError: invalid syntax
I had a look in the job working directory. In the tool_script.sh the conda environment set is "$CONDA_DEFAULT_ENV" = "/export/job_work_dir/000/6/conda-env" (just in my case). Sourcing the conda environment, the python version is
(/export/job_work_dir/000/6/conda-env) (.venv) [galaxy@vnode-0 6]$ python --version Python 3.6.2
Which is not compatible with the "print" code that we have in the bam_to_bigwig.py wrapper, at line 41.
Any idea? Am I missing something?
Best regards, Marco.
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