Genomedata

Introduction

Genomedata is a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/genomedata
Home page: http://pmgenomics.ca/hoffmanlab/proj/genomedata/

Versions

  • 1.5.0

Commands

  • python

  • python3

  • genomeCoverageBed

  • genomedata-close-data

  • genomedata-erase-data

  • genomedata-hardmask

  • genomedata-histogram

  • genomedata-info

  • genomedata-load

  • genomedata-load-assembly

  • genomedata-load-data

  • genomedata-load-seq

  • genomedata-open-data

  • genomedata-query

  • genomedata-report

Module

You can load the modules by:

module load biocontainers
module load genomedata

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run genomedata on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=genomedata
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers genomedata