Running a simulation:
run.sh /PATH/Singularity.sif Simulation_output seed Parameters/zombi_parameters Parameters/sim_parameters
Exemple:
run.sh sim.sif sim_1 8059 Parameters/zombi_parameters Parameters/sim_parameters
If seed = 0, then a random seed is used for each set, else the same seed is used for the tree simulation and the rest of the pipeline.
You can use singularirty to build a container with all the required dependency for this work. You need to be sudo to perform this task.
sudo singularity build singularity.sif ~/GitHub/abba_baba/singularity/singularity.def
ZOMBi version in the singularity container is up to the commit 21d562cc380fafca58a7068913f4a17f52c60451 If you are using an up to date ZOMBI you will have to use ZOMBI/Partameters/SpeciesTreeParameters.tsv instead of abba_baba/Parameters/zombi_parameters. This can lead to unforeseen bugs!