PhyloSoC:Galaxy phylogenetics pipeline development

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Abstract

Galaxy is a popular web based interface for integrating biological tools and analysis pipelines. HyPhy provides a popular package for molecular evolution and sequence statistical analysis. Integrating those tools will make Galaxy even more powerful and useful. Hence probably increase its popularity.

The goal of this project is to integrate the relevant tools into Galaxy. Functional tests will be developed for tools and workflows, along with high level documentation for end users.

Student

Filip Balejko

Mentors

Next TODO

Here I present a detailed plan for every next 2-3 weeks. It can change due to decisions made with mentors and community.

(Analyses are shortly described on the homepage of http://www.datamonkey.org/)

Week 1

  • Creating a general implementation pattern for integrating analyses
  • Integrating Data Reader (input validation tool)

Week 2

  • Finish integrating Data Reader
  • Creating a general implementation pattern for integrating analyses
  • Integrating SLAC analysis

Week 3

  • Creating implementation pattern
  • Integrating SLAC (with simplified output)
  • Creating documentation and tests for Data Reader and SLAC

Week 4

  • Finish creating implementation pattern
  • Finish integrating SLAC (with simplified output)
  • Composite Datatype (some problems here)
  • Render html with mako templates
  • Template Runner tool

Week 5

  • Creating on-demand requests generating details of SLAC analysis. This include:
    • Creating controllers for handling requests
    • Generating images and PDFs for SLAC analysis
    • Creating controllers for accessing this static files
  • Creating JavaScript based feature allowing unfolding details of each row of the result table (and implementing it in SLAC)

Week 6

  • Finish creating JavaScript based feature allowing unfolding details of each row of the result table (and implementing it in SLAC)
  • Finish creating documentation for Data Reader and SLAC
  • Improving SLAC HTML output

Week 7

  • Improving SLAC HTML output:
    • Filtering sites without substitutions
    • Adding inferred substitution report to site's details
  • Starting implementing PARRIS analysis

Week 8

  • Implementing PARRIS analysis
  • Creating jobs for on demand computation

Week 9

  • Creating documentation for PARRIS
  • Improving documentation for Data Reader and SLAC
  • Creating tests for Data Reader and SLAC
  • Creating sniffer for PhyloSequence datatype

Week 10

  • Implementing PARRIS analysis
  • Creating tests for PARRIS analysis
  • Improving the implementation pattern

Week 11

  • Creating tests for PARRIS analysis
  • Expanding the documentation
  • Creating a how-to guide for adding new hyphy based analyses
  • Improving tests for SLAC

Week 12

  • Improving tests and documentation
  • Creating patch

Resources

Source Code

Documentation

Project Blog