Gadma

Introduction

GADMA is a command-line tool. Basic pipeline presents a series of launches of the genetic algorithm folowed by local search optimization and infers demographic history from the Allele Frequency Spectrum of multiple populations (up to three).

For more information, please check:

BioContainers: https://biocontainers.pro/tools/gadma

Home page: https://github.com/ctlab/GADMA

Versions

• 2.0.0rc21

Commands

• gadma

• python

• python3

Module

You can load the modules by:

module load biocontainers
module load gadma

Interactive job

To run GADMA 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 gadma
(base) UserID@bell-a008:~ $ python
Python 3.8.13 |  packaged by conda-forge |  (default, Mar 25 2022, 06:04:10)
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from gadma import *

Batch job

Warning

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 gadma on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gadma
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers gadma

gadma -p params_file