faststructure
Link to section 'Introduction' of 'faststructure' Introduction
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 "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.
Link to section 'Versions' of 'faststructure' Versions
- 1.0-py27
Link to section 'Commands' of 'faststructure' Commands
- structure.py
- chooseK.py
- distruct.py
Link to section 'Module' of 'faststructure' Module
You can load the modules by:
module load biocontainers
module load faststructure
Link to section 'Example job' of '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