Installation Instructions

We recommend installing pipemake using mamba. This is the simplest and most reliable installation method to ensure that all dependencies are installed correctly.

To obtain mamba, we currently recommend using Miniforge, a lightweight package that includes both conda and mamba. Miniforge may be installed from the Miniforge GitHub page.

mamba

To install pipemake with all currently available pipelines, you may run the following command:

mamba create -c conda-forge -c bioconda -c kocherlab -n pipemake pipemake

Note

The pipelines directory may be found within the share directory of the conda environment.

If you wish to maintain the pipelines in a separate directory, you may install the pipemake without the pipelines using the following command:

mamba create -c conda-forge -c bioconda -c kocherlab -n pipemake pipemake-minimal

You may then used the environmental variable PM_SNAKEMAKE_DIR to specify the location of the pipelines directory. For example:

export PM_SNAKEMAKE_DIR=/path/to/pipelines

pip

Caution

While pipemake may also be installed using pip, Snakemake will have limited functionality and this method is not recommended. Instead we only recommend using pip if an environment with Snakemake already exists.

pip install pipemake

Note

We recommend Snakemake 8 or greater and require python 3.8 or greater.

Snakemake,

Singularity containers

pipemake also includes the option to store Singularity containers in a predefined directory. This is useful for groups that wish to maintain a single set of containers. This can be done by setting the environmental variable PM_SINGULARITY_DIR to the desired directory. For example:

export PM_SINGULARITY_DIR=/path/to/singularity

Note

It’s also possible to use the argument --singularity-dir when running the pipemake command to specify the desired directory.