Hi

I am new to docker and Bioconductor. I plan to create a container that uses DESeq2 and runs in AnVIL. I noticed while building a prototype on my local machine that installing DESeq caused a lot of files to be compiled. I do not think this container is going to work in other cloud environments.

I assume all I need to do was. start the container using the image bioconductor/bioconductor_docker:devel . connect to the server. and install DESeq2 as outlined on the https://bioconductor.org/packages/release/bioc/html/DESeq2.html

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DESeq2")

The tag and the commit the running container to save my changes.

Will this work on different hardware?

Is there a better way to create a portable container?

Andy

Hi,

You cannot launch the bioconductor_docker image on the AnVIL. There are some settings that need to be changed be to launch it. I also want to know why you are using the devel image to launch on the AnVIL?

If you want to use the RELEASE_3_12 image, then please use the image us.gcr.io/anvil-gcr-public/anvil-rstudio-bioconductor:0.0.10 as the image to inherit from.

FROM us.gcr.io/anvil-gcr-public/anvil-rstudio-bioconductor:0.0.10

RUN R -e 'BiocManager::install("DESeq2")'

But also, why do you want to install this ?? just launch the image available on the AnVIL and install DESeq2 on the fly.

Best,

Nitesh