CODEWITHSUNDEEP
pythonsnakemake
berkelem
berkelem

Reputation: 2115

Specifying Python version within Snakemake using script parameter

I have some code that I am incorporating into a Snakemake pipeline. I also want to be able to run the code independently of Snakemake, so I want to write flexible code. I have a config file that can be read by Snakemake and an alternative config file that will be parsed if the code is run outside Snakemake.

I had the following structure in a rule in my Snakemake file:

rule some_rule:
    input:
        input_file
    output:
        output_file
    script:
        runfile.py

and then in runfile.py I tested to see if the script was being run within Snakemake as follows:

if 'snakemake' in globals():
    # Get config params from Snakemake
else:
    # Load config params from alternative config file

This was fine, except that I am working within a virtual environment and the Python version I want to use is different from the one Snakemake uses by default. So I had to restructure the rule as follows:

rule some_rule:
    input:
        input_file
    output:
        output_file
    shell:
        /path/to/python runfile.py

but now because I am using shell instead of script I don't have access to the global parameter 'snakemake' in my python file.

So my question is either

(i) Can I specify a Python version and still use script?

or

(ii) Can I use shell but still access the 'snakemake' object within the script that will allow me to test whether or not the script is being run in a Snakemake pipeline?

Upvotes: 3

Views: 1818

Answers (1)

merv
merv

Reputation: 76700

You could use Conda - it would both provide fine-grained control over execution contexts and improve the pipeline reproducibility. See Documentation.

First, you'll need an environment definition YAML file. For example,

envs/py37.yml

channels:
  - defaults
dependencies:
  - python=3.7

Add in any other requirements you need in that file. Then your rule would be

Snakefile 

rule some_rule:
    input:
        input_file
    output:
        output_file
    conda:
        envs/py37.yml
    script:
        runfile.py

Lastly, you now need to use the additional flag --use-conda when launching this job, e.g.,

shell

snakemake --use-conda output_file

Upvotes: 1

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