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Software: fastStructure

Description

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.

Available Versions

Unspecified: 1.0-py27

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

Note: This containers lacks X11 libraries, so GUI plots with 'distruct.py' 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" distruct.py --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: https://biocontainers.pro/tools/faststructure and its home page on Github.

Commands

  • structure.py
  • chooseK.py
  • distruct.py

Module

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:

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

module --force purge
ml biocontainers faststructure