How I use Bioconductor with Docker (part 2): More memory, faster Bioconductor with Docker

Step 1: Go to Preferences on docker desktop (Image 1)

Image 1

Step 2: Go to the Advanced option (Image 2)

Image 2

Step 3: Run your image

docker run \
-rm \ ## Automatically remove the container when it exits
--memory=6g \ ## memory limit
--cpus=1.5 \ ## number of CPUs
-v /shared/data-store:/home/rstudio/data \
-v /shared/library-store:/usr/local/lib/R/host-site-library \
-e PASSWORD=bioc \
-p 8787:8787 \
bioconductor/bioconductor_full:devel
Image 3

References on customizations

  • Read about container resources and what each flag means.

TL;DR: Increase the memory limit to get the R/Bioconductor containers to run faster.

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