This is a Dockerfile based on Ubuntu22.04 to run Phyloskims, it it a modified version of the original recipe from https://gricad-gitlab.univ-grenoble-alpes.fr/eric.coissac/phyloskim to sort out ambiguities and resolve conflicts so that it could still be built in 2024/06/15.

Only the recipe has been updated, the source code for the software itself was not modified in any way, and users will still find that the executables are located in /org-assembler and /bin.

docker pull quay.io/jeani/phyloskims:main

apptainer pull docker://quay.io/jeani/phyloskims:main

Warning: this container was not tested and if you want to contribute with an example of usage (including all the necessary inputs and command lines), please get in touch.

A sample command might look like:

apptainer shell --bind ./inputdata:/opt/uio/inputdata,./results:/opt/uio/results phyloskims_main.sif

phyloskim --input /opt/uio/inputdata/sequences.fasta --output /opt/uio/results/phylogeny.tre

where the inputdata is located in a folder called inputdata in the current directory, and the output results will be stored in another local directory called results on the host, however from inside the container these will be referred to as /opt/uio/inputdata and /opt/uio/results, respectively.

Should you use this modified recipe and/or the corresponding container image, please cite:

Iaquinta, J. (2024). j34ni/Phyloskims_container: Version 1.0.2 (1.0.2). Zenodo. https://doi.org/10.5281/zenodo.12806246