[Bioc-devel] External dependencies and reproducibility in all platforms

Fabricio de Almeida |@br|c|o_@|me|d@@||v@ @end|ng |rom hotm@||@com
Mon Aug 23 16:10:30 CEST 2021

Dear Bioc developers,

I am writing a package that contains external dependencies, and I'd like to know what are the best practices to submit this kind of package to Bioconductor.

The external dependencies are standard RNA-seq analysis algorithms, such as SRAtoolkit, STAR and salmon. I have seen other Bioc packages with external dependencies, such as KnowSeq (https://bioconductor.org/packages/release/bioc/html/KnowSeq.html), ORFik (https://www.bioconductor.org/packages/release/bioc/html/ORFik.html), and openPrimeR (https://bioconductor.org/packages/release/bioc/html/openPrimeR.html), but it is not clear how they handle the dependencies in the Bioconductor build system.

I have a conda environment containing all the dependencies + R 4.1.0, which works fine. However, conda is not the best option, as some dependencies may not exist in all OS, particularly in Windows.

Perhaps a Docker container with the dependencies in an Ubuntu OS would ensure reproducibility in all platforms, but what should I do for the package to pass all checks in the Bioc build system?

Any help is appreciated.



Fabr�cio de Almeida Silva

Undergraduate degree in Biological Sciences (UENF)

MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil)

Laborat�rio de Qu�mica e Fun��o de Prote�nas e Pept�deos (LQFPP/CBB/UENF - RJ/Brazil)

Personal website: https://almeidasilvaf.github.io

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