Bcbio-nextgen

Description

From the bcbio web site: bcbio is a python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.

Version

1.0.5

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

Bcbio-nextgen requires the following module file to run:

apps/bcbio/1.0.5

See Modules for more information.

Running Bcbio-nextgen on CIRCE/SC

The Bcbio-nextgen 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.

How to Submit Jobs

Provided are batch scripts for running 'bcbio' as a single processor or multi-processor job. These scripts can be copied into your work directory (the folder with your input files and database files) so that you can submit batch processes to the queue. .

Batch Job Submit Script

Single-end assembly

Assemble short reads in a file named reads.fa into contigs in a file named contigs.fa with the following script:

#!/bin/bash
#
#SBATCH --job-name=bcbio-test
#SBATCH --nodes=1
#SBATCH --ntasks=10
#SBATCH --output=output.%j.bcbio-test
#SBATCH --time=24:00:00

#### SLURM 10 processor / single node bcbio-nextgen test to run for 24 hours.

module purge
module load apps/bcbio/1.0.5

bcbio_nextgen.py ../config/cancer-dream-syn3.yaml -n 1

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 ./bcbio-test.sh

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

Documentation

Home Page, User Guides, and Manuals

bcbio Home Page
- https://bcbio-nextgen.readthedocs.io/en/latest/index.html

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

bcbio Examples
- https://bcbio-nextgen.readthedocs.io/en/latest/contents/testing.html#example-pipelines

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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