The MuG GitHub repos contains the code that has been developed. Listed below are links to all of the code and documentation for each of the repositories. Each set of documents contains details about the installation and usage both for an end user and for developers creating pipelines.
Development APIs
- Data Management API
GitHub ReatheDocs
This API track files within the MuGVRE and contains meta data about how the file was generated with access to the file genealogy.
- MuG Tool API
GitHub ReatheDocs
This API provides the interface between the pyCOMPSs architecture and the tool. It provides a standard way for all tools to be wrapped to allow for a common interface layer.
Pipelines
- Pipelines for processing FASTQ data
GitHub ReatheDocs
These pipelines can handle ChIP-seq, MNase-Seq, RNA-Seq and Whole Genome BiSulphate Sequencing (WGBS). There are also scripts for generating the initial set of indexes for given genome assemblies. There are also pipelines for processing Hi-C data to generate adjacency matrices and calculate TAD regions
- Pipelines for processing indexed data
GitHub ReatheDocs
Pipelines for processing results files into an indexed form for use in a RESTful interface.
RESTful APIs
- RESTful server ReadtheDocs
GitHub ReadtheDocs
The root RESTful server. This provides links to the main root end points. Each endpoint is a provides a unique function within the defined URL so that the service as a whole appears seamless to the end user.
- DM RESTful interface
GitHub ReadtheDocs
RESTful interface to the DM API along with endpoints to servicing out regions from basic file based data, such as Bed, Wig and TSV files.
- Adjacency matrices RESTful interface
Github ReadtheDocs
Interface for RESTfully querying adjacency matrices generated by the TADbit pipelines developed in mg-process-fastq.
- 3D models RESTful interface
Github ReadtheDocs
Interface for RESTfully querying 3D models generated by the TADbit pipelines developed in mg-process-files.
- RESTful utilities
Github ReadtheDocs
Set of common functions that are required by the RESTful interfaces for interacting with the DM API.
Developers