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 <[email protected]> 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
> <[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
> >
> > ___________________________________________________________
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___________________________________________________________
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