/doc/tutorials/simple_tutorial/step4_run_pipeline_graphically_code.rst
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1.. include:: ../../global.inc 2.. _Simple_Tutorial_4th_step_graphical_code: 3 4 5################################################################### 6Code for Step 4: Displaying the pipeline visually 7################################################################### 8* :ref:`Simple tutorial overview <Simple_Tutorial>` 9* :ref:`pipeline functions <pipeline_functions>` in detail 10* :ref:`Back to Step 4 <Simple_Tutorial_4th_step_graphical>` 11 12************************************ 13Code 14************************************ 15 :: 16 17 from ruffus import * 18 import time 19 20 #--------------------------------------------------------------- 21 # 22 # first task 23 # 24 task1_param = [ 25 [ None, 'job1.stage1'], # 1st job 26 [ None, 'job2.stage1'], # 2nd job 27 ] 28 29 @files(task1_param) 30 def first_task(no_input_file, output_file): 31 open(output_file, "w") 32 33 34 #--------------------------------------------------------------- 35 # 36 # second task 37 # 38 task2_param = [ 39 [ 'job1.stage1', "job1.stage2", " 1st_job"], # 1st job 40 [ 'job2.stage1', "job2.stage2", " 2nd_job"], # 2nd job 41 ] 42 43 @follows(first_task) 44 @files(task2_param) 45 def second_task(input_file, output_file, extra_parameter): 46 open(output_file, "w") 47 print extra_parameter 48 49 #--------------------------------------------------------------- 50 # 51 # Show flow chart and tasks before running the pipeline 52 # 53 print "Show flow chart and tasks before running the pipeline" 54 pipeline_printout_graph ( open("flowchart_before.png", "w"), 55 "png", 56 [second_task], 57 no_key_legend=True) 58 59 #--------------------------------------------------------------- 60 # 61 # Run 62 # 63 pipeline_run([second_task]) 64 65 66 # modify job1.stage1 67 open("job1.stage1", "w").close() 68 69 70 #--------------------------------------------------------------- 71 # 72 # Show flow chart and tasks after running the pipeline 73 # 74 print "Show flow chart and tasks after running the pipeline" 75 pipeline_printout_graph ( open("flowchart_after.png", "w"), 76 "png", 77 [second_task], 78 no_key_legend=True) 79 80 81************************************ 82Resulting Flowcharts 83************************************ 84 +-------------------------------------------------------------+-----------------------------------------------------------------------+ 85 | .. image:: ../../images/simple_tutorial_stage4_before.png | .. image:: ../../images/simple_tutorial_stage4_after.png | 86 | :alt: Before running the pipeline | :alt: After running the pipeline | 87 | :scale: 50 | :scale: 50 | 88 | :align: center | :align: center | 89 | | | 90 | .. centered:: Before | .. centered:: After | 91 | | | 92 +-------------------------------------------------------------+-----------------------------------------------------------------------+ 93 94 +-------------------------------------------------------------------------------------------------------------------------------------+ 95 | .. image:: ../../images/tutorial_key.jpg | 96 | :alt: Legend key | 97 | :scale: 75 | 98 | :align: center | 99 | | 100 | .. centered:: Legend | 101 | | 102 +-------------------------------------------------------------------------------------------------------------------------------------+ 103 104