Only check for existence of executables if the run requires it

[pansapiens]

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]

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]

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]

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]

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]

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