fwdpy11
Link to section 'Introduction' of 'fwdpy11' Introduction
Fwdpy11 is a Python package for forward-time population genetic simulation.
Docker hub: https://hub.docker.com/r/molpopgen/fwdpy11
Home page: https://github.com/molpopgen/fwdpy11
Link to section 'Versions' of 'fwdpy11' Versions
- 0.18.1
Link to section 'Commands' of 'fwdpy11' Commands
- python3
- python
Link to section 'Module' of 'fwdpy11' Module
You can load the modules by:
module load biocontainers
module load fwdpy11
Link to section 'Interactive job' of 'fwdpy11' Interactive job
To run fwdpy11 interactively on our clusters:
(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers fwdpy11
(base) UserID@bell-a008:~ $ python
Python 3.8.10 (default, Mar 15 2022, 12:22:08)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import fwdpy11
>>> pop = fwdpy11.DiploidPopulation(100, 1000.0)
>>> print(f"N = {pop.N}, L = {pop.tables.genome_length}")
Link to section 'Batch job' of 'fwdpy11' Batch job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run fwdpy11 on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=fwdpy11
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers fwdpy11
python script.py