We may want to consider fixing the versions of the installed software in our container. I know that this has been mentioned by @JeffAndBailey a couple of times in conversation. I am not sure that we need to fix the versions for every piece of software installed in the container but it may be useful to fix the versions for larger pieces of software.
Currently, we install software using apt-get, conda, mamba, git, wget, and some packages through R via the use of install.packages(). Of these, my initial thought would be to update system packages (installed via apt-get) on build but fix all other software.
The software we install with each system can be found below...
We may want to consider fixing the versions of the installed software in our container. I know that this has been mentioned by @JeffAndBailey a couple of times in conversation. I am not sure that we need to fix the versions for every piece of software installed in the container but it may be useful to fix the versions for larger pieces of software.
Currently, we install software using
apt-get,conda,mamba,git,wget, and some packages throughRvia the use ofinstall.packages(). Of these, my initial thought would be to update system packages (installed viaapt-get) on build but fix all other software.The software we install with each system can be found below...
### `conda` - `mamba` ### `mamba` - `r` - `python` - `bcftools` - `samtools` - `vcftools` - `freebayes` - `gatk4` - a ton of other packages... ### `git` - `msa2vcf` (through [`jvarkit`](https://github.com/lindenb/jvarkit)) - [`vt`](https://github.com/atks/vt) - [`MIPWrangler`](https://github.com/bailey-lab/MIPWrangler) - [`elucidator`](https://github.com/nickjhathaway/elucidator) ### `wget` - [basespace CLI](https://launch.basespace.illumina.com/CLI/latest/latest.html) - `conda` (via `miniconda`) ### `install.packages()` - [`magrittr`](https://magrittr.tidyverse.org/) - [`McCOILR`](https://github.com/OJWatson/McCOILR) - [`rehh`](https://cran.r-project.org/web/packages/rehh/index.html)