Cannoli on Biowulf

Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools.

Documentation
Important Notes

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 --mem 20g -c 8
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 cannoli

[user@cn3144 ~]$ cannoli-submit \
                    -- \
                    bwa \
                    sample.unaligned.fragments.adam \
                    sample.bwa.hg38.alignments.adam \ 
                    sample \
                    -index hg38.fa \
                    -sequence_dictionary hg38.dict \
                    -fragments \
                    -add_indices 

[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. cannoli.sh). For example:

#!/bin/bash
module load cannoli
cannoli-submit -- bwa sample.unaligned.fragments.adam sample.bwa.hg38.alignments.adam sample \
-index hg38.fa -sequence_dictionary hg38.dict -fragments -add_indices

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=16g cannoli.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. cannoli.swarm). For example:

cannoli-submit -- bwa sample1.adam [...]
cannoli-submit -- bwa sample2.adam [...]
cannoli-submit -- bwa sample3.adam [...]

Submit this job using the swarm command.

swarm -f cannoli.swarm -g 20 -t 8 --module cannoli
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module cannoli Loads the cannoli module for each subjob in the swarm