rcorces / archr_docker Goto Github PK

Hi @rcorces,

Is this repository still pre-release? I'm attempting to build a Singularity container - the script appears to have gotten as far as the install of RStudio before encountering the following problem:

Installing BiocManager [1.30.16] ...
OK [built from source]
Copying BiocManager [1.30.16] into the cache ...
OK [copied 25 files in 0.011 seconds]
Error: failed to determine Bioconductor repositories
Traceback (most recent calls last):
9: renv::restore(prompt = FALSE)
8: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
7: renv_retrieve(packages)
6: handler(package, renv_retrieve_impl(package))
5: renv_retrieve_impl(package)
4: renv_scope_bioconductor()
3: renv_bioconductor_repos()
2: stopf("failed to determine Bioconductor repositories")
1: stop(sprintf(fmt, ...), call. = call.)
Execution halted
FATAL: failed to execute %post proc: exit status 1
FATAL: While performing build: while running engine: while running /usr/local/libexec/singularity/bin/starter: exit status 255

Any ideas?

Hi @rcorces and @paupaiz

Building off our conversation from GreenleafLab/ArchR#1218 (comment), I am currently trying to set up a containerized ArchR analysis using Singularity on my institution's HPC system. Docker would be preferable, but as you may know, HPC systems typically do not support Docker. Therefore, I am also trying the Singularity route to run Docker images!

How do you envision this Singularity image running on an HPC system? Ideally, I would like to submit a bash script or snakemake command to run an ArchR analysis non-interactively. Thanks for your insights and help!