Add hg38 pre-installed in the docker image

[KyriakisDimitrios]

Hi ,

I’m running into an issue with Docker. When I try to run my container, I get an error about a missing package: "BSgenome.Hsapiens.UCSC.hg38".

Here’s the error message:

BSgenome for hg38 not installed! Now installing by the following:
        BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://p3m.dev/cran/__linux__/jammy/2024-10-30
Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Installing package(s) 'BSgenome.Hsapiens.UCSC.hg38'
Warning in install.packages(...) :
  'lib = "/usr/local/lib/R/site-library"' is not writable

Additionally, since I’m running this on an HPC node without internet access, installing the package on the fly isn’t an option.

With hg19 running fine.

Thanks in advance!

[immanuelazn]

Hi @KyriakisDimitrios , thanks for the message. We try not to bundle hg38 and other genomic sequences, to prevent the images from becoming even larger than they already are. What I would recommend just creating a new dockerfile based on a previous one that has ArchR preinstalled. You can then do the following,

FROM greenleaflab/archr:latest
RUN R -e 'BiocManager::install("BSgenome.Hsapiens.UCSC.hg38")

Then run docker build on your dockerfille, which you can just push to your personal/org account.

However, I acknowledge that ArchR has a ton of dependencies in general. Perhaps the best way to get around this is with creating a very large image with every reference genome we refer to. The image size would be massive, but would this be preferable on your end?