[Bioc-devel] Python dependency

[Hervé Pagès]

Hi,

Yes Bioconductor packages can depend on Python modules. This should only 
happen behind the scene and be transparent to the end user (i.e. the end 
user is not expected to interact directly with the Python module).

You can use reticulate (from CRAN) directly or, even better, use 
basilisk (from Bioconductor):

   https://bioconductor.org/packages/basilisk

basilisk was only added to the devel version of Bioconductor recently. 
It aims at automating module installation on the end user machine and on 
the Bioconductor build machines (if you use reticulate directly, we 
would need to manually install the Python modules on the build machines).

Cheers,
H.

On 3/24/20 08:58, Daniele Muraro wrote:
> To whom it may concern,
> 
> I would like to upload onto Bioconductor a package which is currently developed in python.
> I was wondering if Bioconductor supports python dependencies or if I should re-program the package in R exclusively. Is calling python from R using the package "reticulate" acceptable for a package submission onto Bioconductor?
> Thank you for your attention.
> 
> All the best,
> 
> Daniele Muraro
> 
> 
> 
> 
> --
> Daniele Muraro
> 
> Computational Biologist - Staff Scientist
> 
> Wellcome Sanger Institute
> 
> Wellcome Genome Campus
> 
> Hinxton, Cambridgeshire
> 
> CB10 1SA, UK
> 
> Phone (direct) +44 (0)1223 494766
> 
> Phone (reception) +44 (0)1223 834244
> 
> e-mail: Daniele.Muraro using sanger.ac.uk
> 
> 
> Sanger profile:
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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