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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