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 [email protected]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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