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", 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
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?