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MonashBioinformaticsPlatform / RNAsik-pipe

RNAsik - more than just a pipeline
https://monashbioinformaticsplatform.github.io/RNAsik-pipe/
Apache License 2.0
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Only check for existence of executables if the run requires it #13

Open pansapiens opened 6 years ago

pansapiens commented 6 years ago

Version: 1.4.8

RNAsik fails to run if bwa or hisat2 are missing, even if run won't use them based on the given commandline parameters.

eg, if -align star is specified, don't check for the existence of bwa or hisat2 executables unless they are actually required.

serine commented 6 years ago

yes, this is an issue. Sort of working on that issue, also put it on the road map for 1.4.10. However this is also a little bit related to @stu2 PR #6 should have it all cleaned by 1.4.10.

Thanks

pansapiens commented 6 years ago

A hacky workaround in the meantime is to specify, in sik.config:

hisat2Exe = false
bwaExe = false

This way it finds the false executable to keep it happy.

serine commented 6 years ago

that's not gonna fix it, problem is in sikLog.bds file here basically I simply take a log of all dependencies irrespective whether those tools are going to be used or not.. Like I said working on making this better fix_logger branch

this isn't a bad idea trying to use false there. I'll have to think about how its going to work, just not in this case

pansapiens commented 6 years ago

I'm aware of where the executable checks happen. Just a quick workaround users can implement easily themselves if they happen to stumble upon this issue in the meantime vs. proper fix.

serine commented 6 years ago

Comment to myself, I started fix_logger branch, going to work there to fix these issues