Galaxy tools and wrappers for sequence analysis
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README.rst

README.rst

Linux testing with TravisCI Landscape Code Metrics

Introduction

Galaxy is a web-based platform for biological data analysis, supporting extension with additional tools (often wrappers for existing command line tools) and datatypes. See http://www.galaxyproject.org/ and the public server at http://usegalaxy.org for an example.

This repository is for the development of several of my Galaxy tools and wrappers for use within Galaxy, with a focus on sequence analysis. These Galaxy tools are released on the Galaxy Tool Shed here:

Previews of works in progress are often on the Galaxy Test Tool Shed, but these should not be used in a production Galaxy server:

Most of these Galaxy tools and wrappers were originally developed on the 'tools' branch of my BitBucket hosted mercurial (hg) repository, https://bitbucket.org/peterjc/galaxy-central - the old commit history has been preserved were possible, and/or the releases made to the Galaxy Tool Shed were used as snapshots. Some of the content was first developed on https://github.com/peterjc/picobio and also moved here.

See also https://github.com/peterjc/galaxy_blast for my repository for the Galaxy wrappers for the NCBI BLAST+ suite and other related tools like Blast2GO.

The repository name (pico_galaxy) is a play on pico meaning small (10^-12), and the Japanense phonetics of my name (romaji).

Folder Structure

Within the tools folder is one folder for each Tool or Tool Suite released on the Galaxy Tool Shed, similarly for the workflows folder.

Additionally there is a shared test-data folder used for functional test sample data, and a shared tool-data folder used for configuration files.

Testing

Most of these Galaxy tools include a <tests> section in the tool XML files, which defines one or more functional tests - listing sample input files and user parameters, along with the expected output. If you install the tools, you can run these tests via Galaxy's run_functional_tests.sh script - and/or do this automatically if installing the tools via the Tool Shed.

The Galaxy team run nightly tests on all the tools which have been uploaded to the main Tool Shed and the Test Tool Shed, simulating how they would behave in a local Galaxy instance once installed via the Tool Shed.

In addition we are running the same functional tests via TravisCI whenever this GitHub repository is updated:

Current status of TravisCI build for master branch

This TravisCI integration is still somewhat experimental, but simulates a manual install of these Galaxy Tools and their dependencies. See the special .travis.yml file for more technical details.

Bug Reports

You can file an issue here https://github.com/peterjc/pico_galaxy/issues or for more general Galaxy Tool Shed problems please ask on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev

License

Please see the README file in each folder, but by default the MIT license is being used.