I stand corrected. Looking closer, there are conda packages
for both Python 2 and 3, e.g.

https://anaconda.org/conda-forge/biopython/files

However, in this case you're asking for an older Biopython
which has to date not been packaged in conda-forge or
bioconda, so I presume in Marius example it comes from
PyPI via pip?


Peter

On Mon, Mar 5, 2018 at 4:46 PM, Marius van den Beek
<m.vandenbeek@gmail.com> wrote:
> This should actually work properly if you install the dependencies via
> the Manage dependencies page in the admin menu or if you install the tool
> via the tool shed.
> This translates more or less to the following conda command:
> ```
> $ conda create -n mulled-v1xxxxxxxx python=2.7 biopython=1.65 -c iuc -c
> bioconda -c conda-forge -c defaults
> Fetching package metadata ...................
> Solving package specifications: .
>
> Package plan for installation in environment
> /Users/mvandenb/miniconda3/envs/test_resolution:
>
> The following NEW packages will be INSTALLED:
>
>     biopython:       1.65-np19py27_0
>     ca-certificates: 2018.1.18-0          conda-forge
>     certifi:         2018.1.18-py27_0     conda-forge
>     intel-openmp:    2018.0.0-h8158457_8
>     libgfortran:     3.0.1-h93005f0_2
>     mkl:             2018.0.1-hfbd8650_4
>     ncurses:         5.9-10               conda-forge
>     numpy:           1.9.3-py27hb3dd696_3
>     openssl:         1.0.2n-0             conda-forge
>     pip:             9.0.1-py27_1         conda-forge
>     python:          2.7.14-4             conda-forge
>     readline:        7.0-0                conda-forge
>     setuptools:      38.5.1-py27_0        conda-forge
>     sqlite:          3.20.1-2             conda-forge
>     tk:              8.6.7-0              conda-forge
>     wheel:           0.30.0-py27_2        conda-forge
>     zlib:            1.2.11-0             conda-forge
> ```
>
> So given a recent conda (latest version should work) and the correct channel
> order
> it should work.
>
> Best,
> Marius
>
> On 5 March 2018 at 17:39, Peter Cock <p.j.a.cock@googlemail.com> wrote:
>>
>> 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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>