Singularity

Transforming Mirrors

This operation requires root privileges,we suggest transforming on your privite Linux environment.

$singularity pull docker://humanlongevity/hla
Building Singularity image...
...
Singularity container built: ./hla.simg
Cleaning up...
Done. Container is at: ./hla.simg

After done it,uploading mirror to PI HPC.

SLURM Sample

#!/bin/bash

#SBATCH --job-name=Hello_OpenMP
#SBATCH --partition=cpu
#SBATCH --output=%j.out
#SBATCH --error=%j.err
#SBATCH -n 1
#SBATCH --exclusive

ulimit -l unlimited
ulimit -s unlimited

singularity run  /lustre/singularity/hla/hla.simg \
xhla \
--sample_id test --input_bam_path HLA/tests/test.bam \
--output_path test_run

Reference