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PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program
GNU General Public License v3.0
45 stars 9 forks source link

The option -m does not recognize the method #90

Closed PaulaPrietoOliveira closed 1 month ago

PaulaPrietoOliveira commented 1 month ago

Hello! I am trying to run the openrdp with only one method with the option -m, but it is running all the methods. How can I solve this, please?

time cat test_neisseria.fasta | docker run -i --rm openrdp -m bootscan > neisseria_result.csv && docker stats --no-stream

GopiGugan commented 1 month ago

Hi @PaulaPrietoOliveira, you need to update the Dockerfile and add the -m option:

https://github.com/PoonLab/OpenRDP/blob/bb0200092d6245cfd11784a1e7fd081a59507de1/Dockerfile#L51-L54

For example, if you want to run bootscan, you would update the instruction as follow:

RUN echo 'cat - > /app/in.fa && openrdp /app/in.fa -m bootscan --outfile=/app/out.csv --cfg=/app/cfg.ini 1>&2 && cat /app/out.csv' > /app/driver.sh