I am using R and reticulate library to run some python code in a mainly R project. My goal is to somehow wrap a snakemake workflow in an R script so that the Snakefile uses the same environment as the rest of R code. If it was a regular script instead of a Snakefile, it would be possible to do so with reticulate, however I have not yet succeeded in converting a Snakefile to a python script. I am aware of the option to snakemake '--print-compilation' which compiles the Snakefile to a python script, but I have not been able to run it successfully even with a minimal example.
Has anyone had any luck with running snakemake purely from python environment?
In the unlikely case I understood your problem, a solution could be to pass between one snakemake rule and another an R session saved as an image. In this way different rules would share the same environment. For example:
rule all:
input:
'stuff.txt',
'plot.pdf',
rule one:
input:
rdata= config['rdata'], # This may come from outside snakemake
output:
rdata= 'step2.Rdata',
run:
R(r"""
load('{input.rdata}')
x <- 1:10
# More stuff in R...
save.image('{output.rdata}')
""")
rule two:
input:
rdata= 'step2.Rdata',
output:
stuff= 'stuff.txt',
plot= 'plot.pdf',
shell:
R(r"""
load('{input.rdata}')
# ...
write.table('{output.stuff}')
""")
Execute as snakemake ... --config rdata=my_input.Rdata. For the R() function see scripting-with-r. Note that, as far as I can tell, snakemake is designed to be run as a command line program rather than as a library inside another script.
(If you post a brief example of your problem you may get better answers)