Merlin on HPC
MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around (Abecasis et al, 2002).
Documentation
- Module Name: merlin (see the modules page for more information)
- Example files: /usr/local/apps/merlin/version/examples/
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load merlin [user@cn3144 ~]$ merlin -d x.dat -p x.ped -m x.map [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. batch.sh). For example:
#!/bin/bash set -e module load merlin merlin -d x.dat -p x.ped -m x.map
Submit this job using the Slurm sbatch command.
sbatch batch.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.
Create a swarmfile (e.g. job.swarm). For example:
cd dir1; merlin -d x.dat -p x.ped -m x.map cd dir2; merlin -d x.dat -p x.ped -m x.map cd dir3; merlin -d x.dat -p x.ped -m x.map
Submit this job using the swarm command.
swarm -f job.swarm --module merlin