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lpbio provides scripts and modules for computational biology

Project description


Scripts, tools and modules for computational biology


When installed, the lpbio package provides the following scripts, available at the command-line:


The lpbio package provides the following modules for use in Python applications and scripts

  • pysge: a module that writes job files compatible with SGE-like schedulers, and runs them.
  • swarm: a module for interacting with the Swarm clustering tool and its output.

Development notes

Create a local environment, e.g. in conda, and install with pip install -e .:

$ conda create --name lpbio
$ source activate lpbio
$ pip install -e .


Tests are intended to be run with pytest from the repository root (using coverage and pytest-cov):

$ pwd
$ pytest --cov

Project details

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