Tricky, as I understand it the conda python packages are specific to
the conda version of Python - in this case Python 3 not 2.
It might actually be simpler to fix pal_finder/pal_filter.py to cope
with Python 3 - is the code online somewhere, I could probably cast an
eye over it.
Peter
On Mon, Mar 5, 2018 at 4:28 PM, Peter Briggs
<peter.briggs@manchester.ac.uk> wrote:
> Hello
>
> I'm in the process of updating our local Galaxy tools to use conda dependency resolution, and I've hit a snag with a tool that requires Python 2.7 along with the Python 2.7-compatible version of Biopython 1.65.
>
> I'd assumed that if I explicitly used the following in the "requirements" section of the tool XML:
>
> <requirement type="package" version="2.7">python</requirement>
> <requirement type="package" version="1.65">biopython</requirement>
>
> that the biopython install would respect the specified Python version, and that the command execution environment would be based on Python 2.7.
>
> But in practice it appears I'm getting Python3 as I'm seeing errors:
>
> File "XXXXXXXX/galaxy-tools/tools/pal_finder/pal_filter.py", line 129
> print "\n~~~~~~~~~~"
> ^
> SyntaxError: Missing parentheses in call to 'print'
>
> This is happening both when running the tool tests via the planemo tests, and also when I install the tool from a local toolshed instance.
>
> Can anyone advise how to coerce the Python dependencies to be 2.7-compatible?
>
> Thanks in advance for any help,
>
> Best wishes
>
> Peter
>
> --
> Peter Briggs peter.briggs@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
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