Circos is a program for the generation of publication-quality, circularly composited renditions of genomic data and related annotations. Circos is particularly suited for visualizing alignments, conservation and intra and inter-chromosomal relationships. Also, Circos is useful to visualize any type of information that benefits from a circular layout. Thus, although it has been designed for the field of genomics, it is sufficiently flexible to be used in other data domains.
References:
- Module Name: circos (see the modules page for more information)
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 circos [user@cn3144 ~]$ circos commands... [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. batch.sh). For example:
#!/bin/bash set -e module load circos circos commands
Submit this job using the Slurm sbatch command.
sbatch [--mem=#] batch.sh
Create a swarmfile (e.g. job.swarm). For example:
cd dir1; circos commnads... cd dir2; circos commnads... cd dir3; circos commnads... cd dir4; circos commnads...
Submit this job using the swarm command.
swarm -f job.swarm [-g #] --module circoswhere
| -g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
| --module | Loads the module for each subjob in the swarm |