2023-08-26 | #Assembly #GenBank #NCBI
Recently, I wanted to download all genome assemblies of fungi from NCBI GenBank and RefSeq for making a Kraken database. I used my download-refseq-genomes program for downloading assemblies from RefSeq, which worked just fine:
2023-07-06 | #conda #R #RStudio
Again, I encountered shenanigans when running RStudio using base R and packages installed via conda-forge! This time, the error message is: TTY detected. Printing informational message about logging configuration. Logging configuration loaded from '/etc/xdg/xdg-mate:/etc/xdg/rstudio/logging.
2023-03-21 | #Conda #Docker #R #Shiny
There are many ways of running a Shiny Server in a Docker container, for example using the rocker/shiny images. However, this approach becomes more involved when one wants to run the Shiny server and apps with base R and additional packages from a conda environment using the conda-forge channel.
2023-03-07 | #conda #R #RStudio
I usually install R and the packages required for a project through conda and the conda-forge channel and do not use a system-wide R installation through the Linux package manager. However, RStudio is not installed via conda, but using the deb-package file provided by Posit, which means it cannot be run without first activating a conda environment that at least contains the r-base package.
2023-01-23 | #conda #GitHub Actions
When experimenting with GitHub Actions, I made workflow called check-conda-envs for checking conda environment definition files (in YAML format) for available package upgrades. The action will create a table in the workflow summary page containing the current and latest version number for each package, and also a link to the changelog for many bioinformatics packages.
