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Galaxy interfacing with Django

Project description

Build Status (Travis) Py versions

Django interfacing with Galaxy. Backend using the bioblend API.

Galaxy is a web based workflow platform that can be used to perform bioinformatics in a reproducible and sharable environment.

Further documentation available on ReadTheDocs

Quick start

  1. Add “galaxy” and django application dependencies to your INSTALLED_APPS setting like this (galaxy should come before gfiles):

    INSTALLED_APPS = [
        ...
        'galaxy',
        'gfiles',
    
    
        'django_tables2',
        'bootstrap3',
        'django_tables2_column_shifter',
        'django_sb_admin',
        'django_filter'
    ]
    
  2. Include the polls URLconf in your project urls.py like this:

    url(r'^', include('gfiles.urls')),
    url('galaxy/', include('galaxy.urls')),
    
  3. Run python manage.py migrate to create the models.

  4. Start the development server and visit http://127.0.0.1:8000

  5. Register http://127.0.0.1:8000/register/ and login http://127.0.0.1:8000/login/

  6. View summary of Galaxy instances and options http://127.0.0.1:8000/galaxy/galaxy_summary/

  7. Register Galaxy instance http://127.0.0.1:8000/galaxy/addgi/

  8. Register Galaxy user http://127.0.0.1:8000/galaxy/addguser/

  9. Upload file(s) to Django (for bulk upload of files see django-misa and django-mogi) http://127.0.0.1:8000/upload_gfile/

  10. Upload file(s) to Galaxy data library (for bulk upload of files see django-misa and django-mogi) http://127.0.0.1:8000/galaxy/files_to_galaxy_datalib/

  11. Run workflow (for running workflows with ISA data see django-misa and django-mogi) http://127.0.0.1:8000/galaxy/workflow_summary/

  12. View histories http://127.0.0.1:8000/galaxy/history_status/

Project details


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