Iphop's default predict doesnt run all steps

[Chris]

Hi Simon,

I’ve noticed that although ‘iphop predict' has the default ‘steps’ option listed as ‘all’ when I run ‘iphop predict’ without setting the ‘steps’ option it skips the initial two blast steps of the predict pipeline. If ‘predict’ is ran with the ‘steps’ flag set to ‘all’ as part of the command this does get iphop to run all the steps though, so that is a fix.

Just thought I’d pass this on in case anyone comes across this issue/to give you a heads-up.

PS. this was with the conda install, haven’t tried with the docker though.

Thanks,

Chris

[Simon Roux]

Hi Chris,

Thanks for reporting ! Does this behavior happens when running from scratch on an empty directory, or when running on an existing iPHoP result directory ? And if the former, what is the content of “Wdir” ? The default behavior should be to run all tools, so I’m not sure exactly what happens here.

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Thanks,

Simon