Closed inodb closed 4 years ago
Awesome, @inodb! A couple comments:
BiocManager::install("waldronlab/cBioPortalData", update = FALSE, ask = FALSE)
(avoiding any other available updates)Thanks for the prompt review @lwaldron!
I believe this is what installdev.sh does. I assume BiocManager will try pull the latest code from the master branch on GitHub?
Is this the line you're referring to?
Rscript --vanilla -e 'devtools::install(pkg=".",dependencies=FALSE)'
in which case "." refers to the currently checked-out repo, and yes you're right. BiocManager
would have installed from the Bioconductor repository (devel or release) if there isn't a "repo/pkgname" style package used.
@lwaldron correct. That's the command I've been using to install a package from a local dir while developing (not sure if there's a more canonical way to do this, but that seemed to work)
I see, thanks for the clarification re BiocManager
!
Use anaconda base image + the existing cbioportaldata conda dependency to build the image. Then re-install cBioPortalData using the code in the repo. This is much faster than compiling all dependencies from source (compare <5m of GitHub action vs >20m for Travis)