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jessieren / VirFinder

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
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Command line usage? #26

Closed jolespin closed 3 years ago

jolespin commented 3 years ago

I'd like to add VirFinder into some command line pipelines. Is it possible to run this from the command line instead of in R?

jessieren commented 3 years ago

Yes, you can write a script and run it from command line using Rscript. See here https://support.rstudio.com/hc/en-us/articles/218012917-How-to-run-R-scripts-from-the-command-line

jolespin commented 3 years ago

Do you have any command line executables that wrap the pipeline together with the parameters defaulted and predefined?

Something like:

run_virfinder -i input.fasta -o output.fasta

jolespin commented 3 years ago

Finding one right here!
https://github.com/jessieren/VirFinder/blob/master/bin/VirFinder_wrapper.R. Awesome