BamTools
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 holdersRRA
account holdersSC
account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
BamTools requires the following module file to run:
apps/bamtools/2.4.0
- See Modules for more information.
Running BamTools on CIRCE
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 $WORK directory!
- Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
Interactive Mode
Next, use srun
to enter an interactive shell. This example is for 48 hours using 1 cpu cores on 1 node:
srun --time=48:00:00 --nodes=1 --ntasks-per-node=1 --pty /bin/bash
Once you get dropped into an interactive shell on the execution host, you need to load the bamtools module.
You should now be able to execute one of the bamtools commands from the command line:
bamtools count -in NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
Batch Job submission
To run batch jobs on the CIRCE cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.
If, for example, you have wish to count the number of alignments in a BAM file, you would set up a submit script to use bamtools like this
#!/bin/bash # #SBATCH --job-name=bamtools-test #SBATCH --time=01:00:00 #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --output=output.%j.bamtools-test #### SLURM 1 processor bamtools test to run for 1 hours. # Load the bamtools module: module load apps/bamtools/2.4.0 # Start bamtools bamtools count -in NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
Next, you can change to your job’s directory, and run the sbatch command to submit the job:
[user@login0 ~]$ 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:
- BamTools Toolkit Documentation:
Use the following links for the bamtools documentation.
Benchmarks, Known Tests, Examples, Tutorials, and Other Resources
- BamTools API Documentation:
More Job Information
See the following for more detailed job submission information:
Reporting Bugs
Report bugs with BamTools to the IT Help Desk: rc-help@usf.edu