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. Best, ========================= 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 [[alternative HTML version deleted]]
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