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davidaknowles / leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
http://davidaknowles.github.io/leafcutter/
Apache License 2.0
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Installation steps suggestion #95

Closed pcarbo closed 5 years ago

pcarbo commented 5 years ago

Hi Yang & David,

Briana & I are currently working on installing leafcutter. Unfortunately, your conda environment doesn't quite work---I didn't look into how you set it up, but we are having issues that the R packages under different versions of R than the R that was installed.

My suggestion is to make installation of rstan a separate installation step, and as early on as possible. This is by far the most difficult installation step (in particular, it requires installing C++14-compliant compilers, figuring out how to set up R to build packages from source, and perhaps rebuilding R from source depending on your OS); I suggest pointing to the rstan documentation. Once rstan is installed, everything else should be relatively smooth.

davidaknowles commented 5 years ago

Hi Peter - sorry for the super delayed response. Starting a lab isn't very conducive to fixing github issues it seems. This is a great idea, thanks.

And yeah, getting conda to work originally on my system was a struggle, maybe we should just deprecate that installation option for now.

davidaknowles commented 5 years ago

Ok I've linked to the rstan installation instructions and pointed out that you don't actually need to do this if you're just going to do sQTLs or something else with the raw count matrix.