/doc/tutorials/simple_tutorial/step4_run_pipeline_graphically_code.rst

https://code.google.com/p/ruffus/ · ReStructuredText · 104 lines · 84 code · 20 blank · 0 comment · 0 complexity · adcd2f32dca5923f637c2130840f98f6 MD5 · raw file 

    

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

  2. .. _Simple_Tutorial_4th_step_graphical_code:
    3. 

  3. 

  4. 

  5. ###################################################################
    6. 

  6. Code for Step 4: Displaying the pipeline visually
    7. 

  7. ###################################################################
    8. 

  8. * :ref:`Simple tutorial overview <Simple_Tutorial>` 
    9. 

  9. * :ref:`pipeline functions <pipeline_functions>` in detail
    10. 

  10. * :ref:`Back to Step 4 <Simple_Tutorial_4th_step_graphical>` 
    11. 

  11. 

  12. ************************************
    13. 

  13. Code
    14. 

  14. ************************************
    15. 

  15.     ::
    16. 

  16.         
    17. 

  17.         from ruffus import *
    18. 

  18.         import time
    19. 

  19.         
    20. 

  20.         #---------------------------------------------------------------
    21. 

  21.         #
    22. 

  22.         #   first task
    23. 

  23.         #
    24. 

  24.         task1_param = [
    25. 

  25.                             [ None, 'job1.stage1'], # 1st job
    26. 

  26.                             [ None, 'job2.stage1'], # 2nd job
    27. 

  27.                       ]
    28. 

  28.                                             
    29. 

  29.         @files(task1_param)
    30. 

  30.         def first_task(no_input_file, output_file):
    31. 

  31.             open(output_file, "w")
    32. 

  32. 

  33. 

  34.         #---------------------------------------------------------------
    35. 

  35.         #
    36. 

  36.         #   second task
    37. 

  37.         #
    38. 

  38.         task2_param = [
    39. 

  39.                             [ 'job1.stage1', "job1.stage2", "    1st_job"], # 1st job
    40. 

  40.                             [ 'job2.stage1', "job2.stage2", "    2nd_job"], # 2nd job
    41. 

  41.                       ]
    42. 

  42.         
    43. 

  43.         @follows(first_task)
    44. 

  44.         @files(task2_param)
    45. 

  45.         def second_task(input_file, output_file, extra_parameter):
    46. 

  46.             open(output_file, "w")
    47. 

  47.             print extra_parameter
    48. 

  48.         
    49. 

  49.         #---------------------------------------------------------------
    50. 

  50.         #
    51. 

  51.         #       Show flow chart and tasks before running the pipeline
    52. 

  52.         #
    53. 

  53.         print "Show flow chart and tasks before running the pipeline"
    54. 

  54.         pipeline_printout_graph ( open("flowchart_before.png", "w"),
    55. 

  55.                                  "png",
    56. 

  56.                                  [second_task],
    57. 

  57.                                  no_key_legend=True)
    58. 

  58.         
    59. 

  59.         #---------------------------------------------------------------
    60. 

  60.         #
    61. 

  61.         #       Run
    62. 

  62.         #
    63. 

  63.         pipeline_run([second_task])
    64. 

  64.     
    65. 

  65.    
    66. 

  66.         # modify job1.stage1
    67. 

  67.         open("job1.stage1", "w").close()
    68. 

  68.    
    69. 

  69.        
    70. 

  70.         #---------------------------------------------------------------
    71. 

  71.         #
    72. 

  72.         #       Show flow chart and tasks after running the pipeline
    73. 

  73.         #
    74. 

  74.         print "Show flow chart and tasks after running the pipeline"
    75. 

  75.         pipeline_printout_graph ( open("flowchart_after.png", "w"),
    76. 

  76.                                  "png",
    77. 

  77.                                  [second_task],
    78. 

  78.                                  no_key_legend=True)
    79. 

  79.         
    80. 

  80.         
    81. 

  81. ************************************
    82. 

  82. Resulting Flowcharts
    83. 

  83. ************************************
    84. 

  84.    +-------------------------------------------------------------+-----------------------------------------------------------------------+
    85. 

  85.    | .. image:: ../../images/simple_tutorial_stage4_before.png   | .. image::  ../../images/simple_tutorial_stage4_after.png             |
    86. 

  86.    |           :alt: Before running the pipeline                 |     :alt: After running the pipeline                                  |                           
    87. 

  87.    |           :scale: 50                                        |     :scale: 50                                                        |                           
    88. 

  88.    |           :align: center                                    |     :align: center                                                    |                           
    89. 

  89.    |                                                             |                                                                       |                           
    90. 

  90.    | .. centered:: Before                                        | .. centered:: After                                                   |                           
    91. 

  91.    |                                                             |                                                                       |                           
    92. 

  92.    +-------------------------------------------------------------+-----------------------------------------------------------------------+
    93. 

  93. 

  94.    +-------------------------------------------------------------------------------------------------------------------------------------+
    95. 

  95.    | .. image:: ../../images/tutorial_key.jpg                                                                                            |
    96. 

  96.    |           :alt: Legend key                                                                                                          |                           
    97. 

  97.    |           :scale: 75                                                                                                                |                           
    98. 

  98.    |           :align: center                                                                                                            |                           
    99. 

  99.    |                                                                                                                                     |                           
    100. 

  100.    | .. centered:: Legend                                                                                                                |                           
    101. 

  101.    |                                                                                                                                     |                           
    102. 

  102.    +-------------------------------------------------------------------------------------------------------------------------------------+
    103.