Fastspar

Introduction

FastSpar is a C++ implementation of the SparCC algorithm which is up to several thousand times faster than the original Python2 release and uses much less memory. The FastSpar implementation provides threading support and a p-value estimator which accounts for the possibility of repetitious data permutations.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/fastspar
Home page: https://github.com/scwatts/fastspar

Versions

  • 1.0.0

Commands

  • fastspar

  • fastspar_reduce

  • fastspar_bootstrap

  • fastspar_pvalue

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 fastspar on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=fastspar
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load fastspar/XXXX ### you can run *module avail fastspar* to check all available versions