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). - BioContainers: https://biocontainers.pro/tools/faststructure - Home page: https://rajanil.github.io/fastStructure/ ]]) whatis(“Name: fastStructure”) whatis(“Version: 1.0”) whatis(“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.”) whatis(“BioContainers: https://biocontainers.pro/tools/faststructure”) whatis(“Home page: https://rajanil.github.io/fastStructure/”) if not (os.getenv(“BIOC_SINGULARITY_MODULE”) “none”) then local singularity_module os.getenv(“BIOC_SINGULARITY_MODULE”) or “Singularity” if not (isloaded(singularity_module)) then load(singularity_module) end end conflict(myModuleName(), “fastStructure”) local image “quay.io_biocontainers_faststructure:1.0–py27h813d008_3.sif” local uri “docker://quay.io/biocontainers/faststructure:1.0–py27h813d008_3” local programs {“structure.py”, “chooseK.py”, “distruct.py”} local entrypoint_args “” – The absolute path to Singularity is needed so it can be invoked on remote – nodes without the corresponding module necessarily being loaded. – Trim off the training newline. local singularity capture(“which singularity | head -c -1”) if (os.getenv(“BIOC_IMAGE_DIR”)) then image pathJoin(os.getenv(“BIOC_IMAGE_DIR”), image) if not (isFile(image)) then – The image could not be found in the container directory if (mode() “load”) then LmodMessage(“file not found: “ .. image) LmodMessage(“The container image will be pulled upon first use to the Singularity cache”) end image uri – Alternatively, this could pull the container image and – save it in the container directory –if (mode() “load”) then – subprocess(singularity .. “ pull “ .. image .. “ “ .. uri) –end end else – Look for the image in the Singularity cache, and if not found – download it when “singularity run” is invoked. image uri end – Determine Nvidia and/or AMD GPUs (to pass coresponding flag to Singularity) local run_args {} if (capture(“nvidia-smi -L 2>/dev/null”) ~ “”) then if (mode() “load”) then LmodMessage(“BIOC: Enabling Nvidia GPU support in the container.”) end table.insert(run_args, “–nv”) end if (capture(“/opt/rocm/bin/rocm-smi -i 2>/dev/null | grep ^GPU”) ~ “”) then if (mode() “load”) then LmodMessage(“BIOC: Enabling AMD GPU support in the container.”) end table.insert(run_args, “–rocm”) end – And assemble container command local container_launch singularity .. “ run “ .. table.concat(run_args, “ “) .. “ “ .. image .. “ “ .. entrypoint_args – Programs to setup in the shell for i,program in pairs(programs) do set_shell_function(program, container_launch .. “ “ .. program .. “ "$@"”, container_launch .. “ “ .. program .. “ $*”) end – Additional commands or environment variables, if any – Set Matplotlib backend (see help text). local filler string.gsub(myModuleName(), ‘.’, ‘ ‘) if (mode() “load”) then LmodMessage(myModuleName() .. “: “ .. “Setting MPLBACKEND"agg" for PNG output in distruct.py.”) LmodMessage(filler .. “ “ .. “See ‘module help “ .. myModuleUsrName() .. “’ for details and alternatives.”) LmodMessage() end pushenv(“MPLBACKEND”, “agg”)
Note
Please follow the recommended citation guidelines from the developers when you use the tool in research.
Versions
Cluster |
Version(s) |
|---|---|
ANVIL |
1.0-py27 |
BELL |
1.0-py27 |
GAUTSCHI |
1.0-py27 |
NEGISHI |
1.0-py27 |
SCHOLAR |
1.0-py27 |
Commands
structure.py
chooseK.py
distruct.py
Module
You can load the modules by:
module load biocontainers
module load faststructure
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 faststructure on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -p wholenode # Partition 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
module biocontainers faststructure
# Your faststructure workflow...
#!/bin/bash
#SBATCH -A mygroup # Group name
#SBATCH -p cpu # Partition name
#SBATCH -q normal # QOS name (optional)
#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
module biocontainers faststructure
# Your faststructure workflow...
#!/bin/bash
#SBATCH -A mygroup # Group name
#SBATCH -p ai # Partition name
#SBATCH --gres=gpu:1 # Number of GPUs
#SBATCH -q normal # QOS name (optional)
#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
module biocontainers faststructure
# Your faststructure workflow...
#!/bin/bash
#SBATCH -A mygroup # Group name
#SBATCH -p a100 # Partition name
#SBATCH --gres=gpu:1 # Number of GPUs
#SBATCH --mem=2G # Memory
#SBATCH -q normal # QOS name (optional)
#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
module biocontainers faststructure
# Your faststructure workflow...
#!/bin/bash
#SBATCH -A queue # Queue 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
module biocontainers faststructure
# Your faststructure workflow...