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ropensci / phylotaR

An automated pipeline for retrieving orthologous DNA sequences from GenBank in R
https://docs.ropensci.org/phylotaR
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Resolve BLAST dependency #4

Closed hettling closed 6 years ago

hettling commented 7 years ago

The code relies on blastn for the clustering. I'm not sure if this is acceptable for a CRAN (or bioconductor or similar) submission.

This should be checked and if it is impossible to depend on an external tool, blastn should be included in the package.

As far as I know, all blast R packages do remote blasting, which is however not an option for this package.

rvosa commented 7 years ago

Maybe check with @rOpenSci to see how they deal with this?

DomBennett commented 6 years ago

CRAN, bioconductor and ropensci all seem to allow it.

This R package does image processing through external programs and is on CRAN and is part of ropensci. Looks like you just need to list external deps under 'SystemRequirements' in DESCRIPTION.