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README.txt

README.txt 2.6 KB
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  1. What is Tripal?
    2. 

  2. --------------
    3. 

  3. Tripal is a collection of open-source freely available Drupal modules 
    4. 

  4. and is a member of the GMOD family of tools. Tripal serves as a web 
    5. 

  5. interface for the GMOD Chado database and is designed to allow anyone 
    6. 

  6. with genomic data to quickly create an online genomic database using 
    7. 

  7. community supported tools.
    8. 

  8. 

  9. 

  10. Features
    11. 

  11. --------------
    12. 

  12.  - a Chado installer
    13. 

  13.  - Data loaders for ontologies (controlled vocabularies), GFF files, 
    14. 

  14.    and FASTA files
    15. 

  15.  - Generic Data Loader Modules allows for creation of custom loading 
    16. 

  16.    templates
    17. 

  17.  - Drupal nodes (web pages) are automatically generated for organisms,
    18. 

  18.    genomic features, biological libraries, and stocks
    19. 

  19.  - Web pages can be enriched with analysis results from BLAST, 
    20. 

  20.    KAAS/KEGG, InterProScan, and Gene Ontology (GO)
    21. 

  21.  - Views Integration allows for custom listings of data
    22. 

  22.  - Content pieces exposed as blocks allowing the use of Panels for 
    23. 

  23.    custom layouts of Tripal Nodes
    24. 

  24. 

  25. 

  26. Required Modules
    27. 

  27. --------------
    28. 

  28.  - Drupal 6.x (work is currently underway for a 7.x compatible 
    29. 

  29.    version)
    30. 

  30.  - Drupal Core Modules: Search and Path
    31. 

  31.  - Database containing GMOD Chado Schema (can be installed by the 
    32. 

  32.    Tripal Core module)
    33. 

  33. NOTE: A PostgreSQL database is required for installation of the 
    34. 

  34. Chado Schema
    35. 

  35. 

  36. Highly Recommended Modules
    37. 

  37.  - Views 2.x (Views 3.x compatible version already exists in 6.x-0.4-dev)
    38. 

  38.  - Views Data Export
    39. 

  39. 

  40. 

  41. Installation
    42. 

  42. --------------
    43. 

  43. Please follow the online tutorial for installation instructions:
    44. 

  44. http://www.gmod.org/wiki/Tripal_Tutorial_v1.1
    45. 

  45. 

  46. 

  47. Customization
    48. 

  48. --------------
    49. 

  49. Tripal can be used “as is” but also allows for complete customization.
    50. 

  50. PHP-based template files are provided for all data types to allow for 
    51. 

  51. precise customizations as required by the community. A well-developed 
    52. 

  52. Tripal API provides a uniform set of variables and functions for 
    53. 

  53. accessing any and all data within the Chado database.
    54. 

  54. 

  55. 

  56. Future Work
    57. 

  57. --------------
    58. 

  58. Currently, Tripal only supports a large subset of the 
    59. 

  59. current Chado schema, but further development is underway. Meanwhile, 
    60. 

  60. others can use the Tripal API to develop their own extensions. Those 
    61. 

  61. extensions can in turn be made available for anyone to use. These 
    62. 

  62. custom extensions, the Tripal package, and access to support resource 
    63. 

  63. such as an active mailing list can be found on the Tripal website 
    64. 

  64. (http://tripal.sourceforge.net).
    65. 

  65. 

  66. For more information, see the recent publication:
    67. 

  67. 

  68. Stephen P. Ficklin, Lacey-Anne Sanderson, Chun-Huai Cheng, Margaret 
    69. 

  69. Staton, Taein Lee, Il-Hyung Cho, Sook Jung, Kirstin E Bett, Dorrie 
    70. 

  70. Main. Tripal: a construction Toolkit for Online Genome Databases. 
    71. 

  71. Database, Sept 2011. Vol 2011. 
    72.