fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.

Note: programs “”, “” and “” are standalone executable and should be called by name directly (“”, etc). DO NOT invoke them as “python”, or as “python /usr/local/bin/”, this will not work!

Note: This containers lacks X11 libraries, so GUI plots with ‘’ do not work. Instead, we need to tell the underlying Matplotlib to use a non-interactive plotting backend (to file). The easiest and most flexible way is to use the MPLBACKEND environment variable: env MPLBACKEND=”svg” –output myplot.svg …….

Available backends in this container:

Backend Filetypes Description agg png raster graphics – high quality PNG output ps ps eps vector graphics – Postscript output pdf pdf vector graphics – Portable Document Format svg svg vector graphics – Scalable Vector Graphics

Default MPLBACKEND=”agg” (for PNG format output).

For more information, please check its website: and its home page on Github.


  • 1.0-py27






You can load the modules by:

module load biocontainers
module load faststructure

Example job


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 fastStructure on our clusters:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -n 1
#SBATCH --job-name=faststructure
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers faststructure