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:
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!
On 26/10/17 15:53, Marco Tangaro wrote:
I've an issue with the bam_to_bigwig (brad-chapman) tool from the
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 ()
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 "$CONDA_DEFAULT_ENV" =
(just in my case). Sourcing the conda environment, the python version is
(/export/job_work_dir/000/6/conda-env) (.venv) [galaxy@vnode-0 6]$
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?
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