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 <[email protected]> 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 [email protected] > Bioinformatics Core Facility University of Manchester > B.1083 Michael Smith Bldg Tel: (0161) 2751482 > > ___________________________________________________________ > 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: http://galaxyproject.org/search/
