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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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batch processing compatibility #45

Closed stolarczyk closed 3 years ago

stolarczyk commented 3 years ago

hi @mikelove,

I'm writing a vignette that calls tximeta function and discovered there's no way to make the prompt decisions upfront. Therefore the knitting process hangs once it gets to this function call.

Is batch processing compatibility something you are willing to enable for tximeta? I expect this might be useful outside of my use case.

mikelove commented 3 years ago

Do you mean the question about where to store the cache? I believe we have two solutions.

You can either do setTximetaBFC:

https://rdrr.io/bioc/tximeta/man/getTximetaBFC.html

Or you could use the environmental variable solution proposed by Charlotte:

https://github.com/mikelove/tximeta/issues/31

stolarczyk commented 3 years ago

thanks! yes, setTximetaBFC eliminates one of the prompts I've been getting. There's another one concerning AnnotationHub cache directory creation, in case it does not exist. For my use case I can set useHub=FALSE, though.

mikelove commented 3 years ago

The other one can be avoided also with the AHub environmental variable (see AnnotationHub man pages).