eXFrame

eXFrame is a reusable framework for building genomics experiments repositories.

CONTENTS OF THIS FILE

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• Introduction
• Requirements
• Recommended Modules
• Installation
• Configuration
• Support
• Contributing
• Maintainers
• License
• Citations

INTRODUCTION

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• For a full description, please visit:
  • http://www.jbiomedsem.com/content/5/S1/S3
  • http://www.biomedcentral.com/1471-2105/12/452
• To submit bug reports or feature suggestions:
  • http://github.com/mindinformatics/exframe/issues

REQUIREMENTS

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• R (>= {Version?}) - https://www.r-project.org/
• Web Server (Apache,Nginx)
• Database Server (MySQL / MariaDB {Version?}, postgreSQL {???}, SQLite {???})
• PHP (>= 5.2)
• Drush - http://www.drush.org

RECOMMENDED MODULES

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INSTALLATION

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1. Verify installation dependencies have been installed (R, Drush, Database Server, PHP)
2. https://www.drupal.org/documentation/install
3. Log in
4. Enable eXFrame modules (Administer -> Modules) * Check the box next to each module that starts with "exframe_". Click "Save Configuration" at the bottom of the page.
5. Create Content * Import Taxonomies * Create Users
   • Administer -> People -> Add Users
   • (Or import CSV) * Create Group(s)
   • Administer -> Content -> Add Content -> Group * Create Project(s)
   • Administer -> Content -> Add Content -> Project * Create Experiment(s)
   • Administer -> Content -> Add Content -> Experiment * Create Sample(s)
   • Administer -> Content -> Add Content -> Sample * Create Sample Group(s)
   • Administer -> Content -> Add Content -> Sample Group

CONFIGURATION

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SUPPORT

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TROUBLESHOOTING

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FAQ

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• Q:
  • A:

CONTRIBUTING

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ROADMAP

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• [] Generate "install profile"
• [] Update code (style) to meet Drupal coding standards
• [] Create installation script (drush)
• [] Create demo installation (eXFrame example module / sub-profile)
• [] Improve documentation
  • [] Installation
  • [] Configuration
  • [] Customization
• [] Continuous Integration (Jenkins, Travis)
  • [] Regression Testing
• [] Create "Official" Drupal project

LICENSE

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This is licensed under GPL v2 See LICENSE.txt for the full text

MAINTAINERS (CONTRIBUTORS)

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Current Maintainers:

• First M. Last (uname) - webpage_link
• ... This project has been sponsored by / funded through:
• ...

CITATION

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Sinha, A., Merrill, E., Armstrong, S., Clark, T., & Das, S. (2011). EXframe: Reusable framework for storage, analysis and visualization of genomics experiments. BMC Bioinformatics, 12, 452-452. doi:10.1186/1471-2105-12-452

http://www.biomedcentral.com/1471-2105/12/452

Merrill, E., Corlosquet, S., Ciccarese, P., Clark, T., & Das, S. (2014). Semantic Web repositories for genomics data using the eXframe platform. Journal of Biomedical Semantics, 5(Supplement 1), S3-S3. doi:10.1186/2041-1480-5-S1-S3

http://www.jbiomedsem.com/content/5/S1/S3