bam_to_bigwig invalid syntax error

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bam_to_bigwig invalid syntax error

Marco Tangaro
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", 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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Re: bam_to_bigwig invalid syntax error

Nicola Soranzo-2
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", 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.


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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