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lpbio provides scripts and modules for computational biology

Project description

lpbio

Scripts, tools and modules for computational biology

Scripts

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

Modules

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

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

$ pwd
lpbio/
$ pytest --cov

Project details


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