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
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fredhutch.org
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Fax: (206) 667-1319
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