Purdue University

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

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