bripipetools (i.e., BRI Pipeline Tools) is a collection of packages for managing the operation of processing workflows — as well as the input and output data for these workflows — within the Genomics and Bioinformatics Cores at the Benaroya Research Institute.
WARNING: These tools are designed with very strong assumptions about data structure and formats, as well as available resources (e.g., file system, database). While bits and pieces of the code may be useful in other contexts, as a general rule, if you try to install/use this package somewhere other than one of a handful of properly configured BRI servers, you're going to have a bad time.
Currently, there are three primary functions served by package modules:
- Generation of workflow instructions and submission of data processing batches
- Collection and organization of output data from bioinformatics processing workflows
- Annotation and import of pipeline input & output data into the Genomics Core Mongo database — i.e., GenLIMS
These features are continuing to expand and evolve over time.
bripipetools can be installed by cloning this repository and running:
$ pip install .
For development, the recommended setup is the following:
$ conda env create -n bripipetools environment.yml $ source activate bripipetools $ pip install -e .
To test that the application was installed:
$ python setup.py test # for production $ py.test # for development $ bripipetools --help
The documentation for bripipetools is available here (courtesy of ReadTheDocs).
- Issue tracker: github.com/BenaroyaResearch/bripipetools/issues
- Source code: github.com/BenaroyaResearch/bripipetools/bripipetools
The project is licensed under the MIT license.