To install with pip:
$ pip install swiftseq
Or to get the latest development version:
$ pip install git+https://github.com/PittGenomics/SwiftSeq@dev
The development version may not be stable
Once SwiftSeq is install, software dependencies can be installed with Bioconda:
$ swiftseq install-env
This will produce an
executables.config file that the user can pass directly into a SwiftSeq run.
The above command will only work if the user has Anaconda/Miniconda installed. It’s provided as a convenience; if
the user would rather install software dependencies manually, Swiftseq only needs an
runtime and is indifferent to where it comes from.
The user can then run Swiftseq:
swiftseq run --exe-config /path/to/executables.config [options]