/doc/tutorials/simple_tutorial/step2_files_code.rst

https://code.google.com/p/ruffus/ · ReStructuredText · 69 lines · 57 code · 12 blank · 0 comment · 0 complexity · 535fd28ca0126f92fa897112f49ec7bb MD5 · raw file 

    

  1. .. include:: ../../global.inc
    2. 

  2. .. _Simple_Tutorial_2nd_step_code:
    3. 

  3. 

  4. ###################################################################
    5. 

  5. Code for Step 2: Passing parameters to the pipeline
    6. 

  6. ###################################################################
    7. 

  7. * :ref:`Up <Simple_Tutorial>` 
    8. 

  8. * :ref:`Back <Simple_Tutorial_2nd_step>` 
    9. 

  9. * :ref:`@files syntax <decorators.files>` in detail
    10. 

  10. 

  11. ************************************
    12. 

  12. Code
    13. 

  13. ************************************
    14. 

  14.     ::
    15. 

  15.         
    16. 

  16.         from ruffus import *
    17. 

  17.         import time
    18. 

  18.         
    19. 

  19.         #---------------------------------------------------------------
    20. 

  20.         #
    21. 

  21.         #   first task
    22. 

  22.         #
    23. 

  23.         task1_param = [
    24. 

  24.                             [ None, 'job1.stage1'], # 1st job
    25. 

  25.                             [ None, 'job2.stage1'], # 2nd job
    26. 

  26.                       ]
    27. 

  27.                                             
    28. 

  28.         @files(task1_param)
    29. 

  29.         def first_task(no_input_file, output_file):
    30. 

  30.             open(output_file, "w")
    31. 

  31. 

  32. 

  33.         #---------------------------------------------------------------
    34. 

  34.         #
    35. 

  35.         #   second task
    36. 

  36.         #
    37. 

  37.         task2_param = [
    38. 

  38.                             [ 'job1.stage1', "job1.stage2", "    1st_job"], # 1st job
    39. 

  39.                             [ 'job2.stage1', "job2.stage2", "    2nd_job"], # 2nd job
    40. 

  40.                       ]
    41. 

  41.         
    42. 

  42.         @follows(first_task)
    43. 

  43.         @files(task2_param)
    44. 

  44.         def second_task(input_file, output_file, extra_parameter):
    45. 

  45.             open(output_file, "w")
    46. 

  46.             print extra_parameter
    47. 

  47.         
    48. 

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

  49.         #
    50. 

  50.         #       Run
    51. 

  51.         #
    52. 

  52.         pipeline_run([second_task], multiprocess = 5)
    53. 

  53.        
    54. 

  54. 

  55. ************************************
    56. 

  56. Resulting Output
    57. 

  57. ************************************
    58. 

  58.     ::
    59. 

  59.         
    60. 

  60.         Start Task = first_task
    61. 

  61.             Job = [None -> job1.stage1] completed
    62. 

  62.             Job = [None -> job2.stage1] completed
    63. 

  63.         Completed Task = first_task
    64. 

  64.         Start Task = second_task
    65. 

  65.             1st_job
    66. 

  66.             Job = [job1.stage1 -> job1.stage2,     1st_job] completed
    67. 

  67.             2nd_job
    68. 

  68.             Job = [job2.stage1 -> job2.stage2,     2nd_job] completed
    69. 

  69.         Completed Task = second_task
    70.