Description

From the BamTools Home Page: BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.

Version

• 2.4.0

Authorized Users

• CIRCE account holders
• RRA account holders
• SC account holders

Platforms

• CIRCE cluster
• RRA cluster
• SC cluster

Modules

BamTools requires the following module file to run:

• apps/bamtools/2.4.0

• See Modules for more information.

Running BamTools on CIRCE/SC

The BamTools user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

• Note on CIRCE: Make sure to run your jobs from your $WORK directory!
• Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Interactive Mode

Next, use the following commands to open an SRUN Interactive Session, load the module for BamTools, and execute the BamTools binary:

[user@login0 ~]$ srun --time=48:00:00 --nodes=1 --cpus-per-task=1 --pty /bin/bash
[user@wh-520-4-1 ~]$ module load apps/bamtools/2.4.0
[user@wh-520-4-1 ~]$ bamtools count -in NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 30 minutes to run on a standard PC.

If, for example, you wish to count the number of alignments in a BAM file, you would set up a submit script to use bamtools like the following.

#!/bin/bash
#
#SBATCH --job-name=bamtools-test
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=output.%j.bamtools-test

#### SLURM 1 processor bamtools test to run for 1 hours.

# Load the bamtools module:
module load apps/bamtools/2.4.0

# Start bamtools
bamtools count -in NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./bamtools-test.sh

• You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

• BamTools Home Page:
  • https://github.com/pezmaster31/bamtools
• BamTools Toolkit Documentation:
  • https://github.com/pezmaster31/bamtools/wiki/Using-the-toolkit

Use the following links for the bamtools documentation.

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

• BamTools API Documentation:
  • https://github.com/pezmaster31/bamtools/wiki/Using-the-API

More Job Information

See the following for more detailed job submission information:

• SLURM User’s Guide
• Scheduling and Dispatch Policies
• Advanced Submit Techniques

Reporting Bugs

Report bugs with BamTools to the IT Help Desk: rc-help@usf.edu