[Bioc-devel] Question about external algorithms to Bioconductor package

Ryan Thompson rct at thompsonclan.org
Sun Nov 12 23:22:56 CET 2017


I don't know the Bioconductor policy for packages that rely on external
tools, but for the specific features you mention, there are Bioconductor
packages to accomplish most or all of them. You can use samtools via
Rsamtools, you can use the Rsubread package in place of bowtie for
alignment, and you can use the SRAdb package for For SRA access. (I believe
there are also several other alignment methods available in Bioconductor,
if Rsubread doesn't do what you need.) Using these packages should ensure
that biocLite() can fully satisfy all the requirements for your package
without the need for separate installation of other command-line tools.


Ryan Thompson

On Sun, Nov 12, 2017 at 2:12 PM Ioannis Vardaxis <ioannis.vardaxis at ntnu.no>

> Hi,
> I have developed a package and is current under review from
> Bioconductor. In the future I am considering of making some changes to
> the package, basically adding more functions etc.
> My package is currently a peak calling algorithm where the input it gets
> is either a BAM or SAM format. Because in general a user which runs such
> analysis needs to, for example, map the DNA sequences to the reference
> genome and obtaining the BAM/SAM file and then turn to my algorithm for
> the rest. I was wondering if I am allowed to add those processes to my
> package as preliminary stages such that it becomes easier for the user
> to have everything in one place.
> To do so I will need my package to make use of: SRAtoolkit, bowtie and
> SAMtools. Which  I could run in terminal (using system() in R). For
> running those stages need the user to have installed those algorithms
> off course.
> I was wondering if I am allowed to make use of those algorithms  in my
> bioconductor package, with the appropriate references off course.
> Best,
> --
> Ioannis Vardaxis
> Stipendiat IMF
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