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.vandenb...@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.c...@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.bri...@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.bri...@manchester.ac.uk >> > 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/ > > ___________________________________________________________ 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/
