GWAS Protocol (as a container)

Usage

The container comes with all the software needed to generate summary statistics.

You need to download the container file using one of the following commands. This will use approximately one gigabyte of storage.

Container platform	Version	Command
Singularity	3.x	`wget http://download.gwas.science/singularity/gwas-protocol-latest.sif`
Docker		`docker pull gwas.science/gwas-protocol:latest`

Next, start an interactive shell inside the container using one of the following commands.

Container platform	Command
Singularity	`singularity shell --hostname localhost --bind ${working_directory}:/data --bind /tmp gwas-protocol-latest.sif`
Docker	`docker run --interactive --tty --volume ${working_directory}:/data --bind /tmp gwas.science/gwas-protocol /bin/bash`

Development

To create a local development environment install Miniforge and create a .condarc file in your home directory with the following contents:

channels:
  - conda-forge
  - bioconda

Then update your .bashrc or .zshrc with mamba init. This will allow you to use the conda command.

Next, install mamba using conda install mamba and then create the environment using the following command:

mamba create --name "gwas" \
  "mamba" "boa" "conda-verify" \
  "python=3.11" "more-itertools" \
  "jupyterlab" "ipywidgets" \
  "numpy" "scipy" "pandas" "pytorch<2" "networkx" \
  "matplotlib" "seaborn" \
  "bzip2" "p7zip>=15.09" \
  "python-blosc2" "msgpack-python" "ndindex" \
  "bcftools>=1.17" "plink" "plink2" "tabix" \
  "cython>=3b1" "mkl-include" "zlib" \
  "mypy" "pytest-benchmark" "threadpoolctl" \
  "compilers" "rust" "sysroot_linux-64>=2.17"

Finally, install the gwas package using the following command:

pip install --no-deps --editable "src/gwas"

dominikgoeller/GWASProtocol

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