Question: Force galaxy to use the python 2 version of a dependency of a new tool
gravatar for Thon deBoer
6 months ago by
Thon deBoer20
Thon deBoer20 wrote:

I am creating a new tool for galaxy based on the NEAT-genReads tool from Zachary Stephens and I am trying to define the dependencies.

The tool requires the matplotlib.pyplot library since it calls out this import statement:

import matplotlib.pyplot as mpl

I defined the dependency for the tool like this in the tool XML file:

<requirement type="package">matplotlib</requirement>

But when I look at the log files I see it installing Python version 3.6 instead of using the python 2 version that is need...

So, when the tool runs, it complains that it cannot find the correct module

Fatal error: Exit code 1 ()
Traceback (most recent call last):
  File "/opt/galaxy/tools/neat-genreads/utilities/", line 10, in <module>
    import matplotlib.pyplot as mpl
ImportError: No module named matplotlib.pyplot

How do I force galaxy to install the python 2 version of matplotlib?

ADD COMMENTlink modified 6 months ago by Jennifer Hillman Jackson25k • written 6 months ago by Thon deBoer20
gravatar for Jennifer Hillman Jackson
6 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Using Conda, instead of dependency packages, is the best practice for tool development now and any Galaxy server might need to have more than one version of a dependency installed.


Thanks! Jen, Galaxy team

ADD COMMENTlink written 6 months ago by Jennifer Hillman Jackson25k

UH?! By using the requirement tag i AM using conda, no? Conda is just one of the dependency resolvers I understand...

I am actually using PLANEMO (on the VM) and that is where I see that CONDA is installing the python 3.6 version of all the dependencies

ADD REPLYlink written 6 months ago by Thon deBoer20

Just checked, and indeed matplotlib is installed using CONDA...

genMutModel     /home/ubuntu/miniconda3/envs/mulled-v1-808d181c256ea1be661871e558eb70bf5d9047a0855ff85f21331747f4819086     numpy   1.9.1   Conda   True    
        /home/ubuntu/miniconda3/envs/mulled-v1-808d181c256ea1be661871e558eb70bf5d9047a0855ff85f21331747f4819086     matplotlib  None    Conda   True
ADD REPLYlink written 6 months ago by Thon deBoer20
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