Bldg Tel: (0161) 2751482
From: Peter Cock [p.j.a.c...@googlemail.com]
Sent: Monday, March 05, 2018 5:04 PM
To: Marius van den Beek
Cc: Peter Briggs; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies
fo
Oh yeah - thanks, I can see them in the default channel which does have
far older versions of Biopython packaged - currently 1.65 is on page 5:
https://anaconda.org/anaconda/biopython/files?sort=basename_order=desc=5
Peter
On Mon, Mar 5, 2018 at 5:00 PM, Marius van den Beek
It's coming from the defaults channel, I didn't check if this is actually
working,
it may very well not be compatible with the remaining packages form
conda-forge.
AFAIK you can't specify packages to install via the regular conda commands
(though you can use pip in a conda environemnt to do this
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
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-v1 python=2.7 biopython=1.65 -c iuc
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,
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"
