Nathan Weeks

#384 proposes adding the vim-extra package to the Cloud Shell base image to resolve this issue. In the interim, one could manually install vim runtime files in their Cloud Shell...

I've deployed Rocker containers on Kubernetes as non-root; the protocol is similar to that for running [Rocker using Singularity](https://www.rocker-project.org/use/singularity/) on a (multi-user) HPC cluster: set the `PASSWORD` environment variable to...

Yes. A couple caveats I forgot to mention: 1. `ADD=shiny` won't work (can't install Debian packages as an unprivileged user) 2. R_LIBS_USER is hard-coded in /usr/local/lib/R/etc/Renviron : ``` R_LIBS_USER='/usr/local/lib/R/site-library' ```...

It looks like the hardcoded-R_LIBS_USER issue was resolved in r-ver:3.6.1: https://github.com/rocker-org/rocker-versioned/blob/master/r-ver/3.6.1.Dockerfile#L112

When installing umap-learn=0.5.4 with `reticulate::py_install()`, there is now a problem with numpy (which recently had a major 2.0 release): ``` > library(Seurat) ... > data("pbmc_small") > pbmc_small reticulate::py_list_packages() package version...

The `unknown compression algorithm value 6` error also occurs when mounting a [SquashFS image file](https://apptainer.org/docs/user/main/bind_paths_and_mounts.html#squashfs-image-files) that was compressed using the mksquashfs `-comp zstd` option.

> I can imagine making apptainer flexible enough to recognize other compression algorithms but I'm not sure it's a good idea to make it easy for people to generate non-backward...

This would be helpful for providing additional data storage headroom in GitHub Codespaces (where CUDA isn't very useful anyway, except for the select users that have access to [codespaces with...

I can look into submitting a pull request---hopefully before someone wants `-best_hit_overhang` or `-best_hit_score_edge`! I'll hold off on starting this until galaxy_blast incorporates BLAST 2.7.1+, which fixes a `-culling_limit` bug...

It looks like the `makeblastdb -max_file_sz` limit was [increased to 4GB in BLAST+ 2.8.0](https://www.ncbi.nlm.nih.gov/books/NBK131777/): > * The 2GB output file size limit for makeblastdb has been increased to 4 GB.