CLONET on Biowulf
Description
CLONET is a collection of R scripts that allows:
- computing global DNA admixture (1-purity) and ploidy of tumor DNA samples(each with matched normal sample) from sequencing data (WGS, WES, targeted)
- computing clonality of each somatic aberration, including somatic copy number aberrations, point mutations, and structural rearrangements
- nominating the temporal relation among somatic aberrations and building evolution maps
Documentation
- CLONET Main Site: http://demichelislab.unitn.it/doku.php?id=public:clonet
Important Notes
- Module Name: CLONET(see the modules page for more information)
- CLONET.R is the main R script required to compute global DNA admixture, ploidy and clonality of segmented data.
- Example files are in $CLONET_HOME/Examples/CLONETv2/
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ 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 CLONET [user@cn3144 ~]$ CLONET.R [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. runClonet.sh), which uses the input file 'CLONET.in'. For example:
#!/bin/bash module load CLONET CLONET.R < CLONET.in > CLONET.out
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] runClonet.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. CLONET.swarm). For example:
CLONET.R < CLONET.in > CLONET.out CLONET.R < CLONET.in > CLONET.out CLONET.R < CLONET.in > CLONET.out CLONET.R < CLONET.in > CLONET.out
Submit this job using the swarm command.
swarm -f CLONET.swarm [-g #] [-t #] --module CLONETwhere
-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 CLONET | Loads the CLONET module for each subjob in the swarm |