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

• CLONET Main Site: http://demichelislab.unitn.it/doku.php?id=public:clonet

• 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/

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 ~]$

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

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 CLONET