Grabix

Description

From the Grabix Home Page: grabix leverages the fantastic BGZF library in samtools to provide random access into text files that have been compressed with bgzip. grabix creates it’s own index (.gbi) of the bgzipped file. Once indexed, one can extract arbitrary lines from the file with the grab command. Or choose random lines with the, well, random command.

Version

  • 0.1.6

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Grabix requires the following module file to run:

  • apps/grabix/ 0.1.6

Running Grabix on CIRCE/SC

The Grabix 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 Grabix, and execute the Grabix binary:

[user@login0 ~]$ srun --time=48:00:00 --nodes=1 --ntasks-per-node=1 --pty /bin/bash
[user@wh-520-4-1 ~]$ module load apps/grabix/0.1.6
[user@wh-520-4-1 ~]$ grabix index simrep.chr1.bed.gz

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 20 minutes to run on a standard PC.

If, for example, you have wish to create a grabix index file, you would set up a submit script to use grabix like this

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

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

# Load the grabix module:
module load apps/grabix/0.1.6

# Start grabix
grabix index simrep.chr1.bed.gz

 
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 ./grabix-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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