Purdue University

Commands

• python3

Module

You can load the modules by:

module load biocontainers
module load hail

Interactive job

To run Hail 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 hail
(base) UserID@bell-a008:~ $ python3
Python 3.7.13 (default, Apr 24 2022, 01:05:22)  
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.  
>>> import hail as hl
>>>  print(hl.citation())
Hail Team. Hail 0.2.94-f0b38d6c436f. https://github.com/hail-is/hail/commit/f0b38d6c436f.

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 hail on our clusters:

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

module --force purge
ml biocontainers hail
python3 script.py