fastspar.rst

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