Metadata-Version: 1.1
Name: trailblazer
Version: 0.0.1
Summary: Track analyses.
Home-page: https://github.com/Clinical-Genomics/analysis
Author: Robin Andeer
Author-email: robin.andeer@scilifelab.se
License: MIT
Description: # Trailblazer [![Build Status][travis-image]][travis-url] [![Coverage Status][coveralls-image]][coveralls-url]
        
        _Trailblazer_ is a tool to keep track of analyses.
        
        ## Concerns
        
        For now we are only concerned with the MIP pipeline even thought in the future we'd like to support additional tools.
        
        1. keep track of analyses on the cluster and their status
        2. return references to analyses to be rerun or processed downstream
        3. remove data once it's no longer needed
        
        Future concerns will include **starting up analyses** as well as **automatically restarting** failed ones under certain conditions.
        
        ### Setup
        
        The first thing is setting up a database. It will simply setup the tables.
        
        ```bash
        $ trailblazer init sqlite:///path/to/store.sqlite3
        ```
        
        ### Adding new analyses
        
        You can add individual analyses by pointing to the "qc sample info" file or scan for analyses under customer directories.
        
        ```bash
        $ trailblazer add /path/to/familyId_qc_sampleInfo.yaml
        $ trailblazer scan /path/to/cust003
        ```
        
        ### Deleting an existing analysis
        
        When you are sure you no longer need the analysis output or would like to clean up before a rerun you can remove the reference to said analysis and the actual files.
        
        ```bash
        $ trailblazer delete [customer]-[family]
        Are you sure? [Y/n]
        ```
        
        ## API structure and architecture
        
        This section will describe the implementation.
        
        ### Store
        
        SQL(ite) database containing references to the analyses and in which state they belong. It should have a straight-forward API.
        
        ### CLI
        
        Likely the main entry point for accessing the API. However, it should to do the least possible. Abstract away anything that isn't directly concerning parsing command line arguments etc. Uses the Click-framework.
        
        ### Web interface
        
        Built using the Flask-framework. Barebones. Should provide overviews for analyses in different states.
        
        
        [travis-url]: https://travis-ci.org/Clinical-Genomics/analysis
        [travis-image]: https://img.shields.io/travis/Clinical-Genomics/analysis.svg?style=flat-square
        
        [coveralls-url]: https://coveralls.io/r/Clinical-Genomics/analysis
        [coveralls-image]: https://img.shields.io/coveralls/Clinical-Genomics/analysis.svg?style=flat-square
        
Keywords: analysis development
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Environment :: Console
