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Snakemake library for all kinds of tasks, with a focus on bioinformatics and next-generation sequencing. See the documentation for more information.

snakemakelib is still not on PyPI but you can still install from github using pip in several ways. I recommend using the user installation scheme by making use of the --user flag.

By default, user site-packages are placed in ~/.local. If you choose to install in a different location, you need to set the environment variable PYTHONUSERBASE to e.g. $HOME/lib/python. Then, with this setting, set PYTHONPATH to $HOME/lib/python/lib/python3.4/site-packages to access the package. The examples below show the user installation scheme.

Alternatively, install the package into a virtual environment.

You can install as an editable install by invoking

pip3 install -e git+https://github.com/percyfal/snakemakelib.git@master#egg=snakemakelib --user

The previous command currently fails to install bokehutils (see issue 16). As a workaround, you can manually clone the repo

git clone git@github.com:percyfal/snakemakelib.git

and invoke (standing in the cloned repo)

pip3 install -r requirements.txt --user -e .

Probably the best way to get started is to run a real example. See the repaper repository for workflows that should work out of the box.