gadma
Link to section 'Introduction' of 'gadma' Introduction
GADMA is a command-line tool. Basic pipeline presents a series of launches of the genetic algorithm followed by local search optimization and infers demographic history from the Allele Frequency Spectrum of multiple populations (up to three).
BioContainers: https://biocontainers.pro/tools/gadma
Home page: https://github.com/ctlab/GADMA
Link to section 'Versions' of 'gadma' Versions
- 2.0.0rc21
Link to section 'Commands' of 'gadma' Commands
- gadma
- python
- python3
Link to section 'Module' of 'gadma' Module
You can load the modules by:
module load biocontainers
module load gadma
Link to section 'Interactive job' of '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 *
Link to section 'Batch job' of 'gadma' 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 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