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Let us take a  look at the files inside the directory "tutorial-pegasus-vina".  The following are vina input files. 

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2gutreceptor_config.txt   ### Configuration file (input)
2gutreceptor.pdbqt        ### Receptor pdbqt file that contains coordinates and charges of atoms(input)

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$ ls input_ligands   ### There are 4640 ligands inside this directory. 

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languageactionscript3
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line 9 ./dax-generator-vina.py ### Execution of "dax-generator-vina.py" script. Generates dax.xml. 
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line 14 ./sites-generator.bash   ### Execution of "sites-generator.bash" script. Generates sites.xml.
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line 17 pegasus-plan \               ###  Executes the pegasus-plan with the following arguments
line 18    --conf pegasusrc \             ###   pegasus configuration file
line 19    --sites condorpool \           ###   jobs are executed in condorpool
line 20    --dir $PWD/workflows \         ###   The path of the workflow directory
line 21    --output-site local \          ###   Outputs are directed to the local site.
line 22    --cluster horizontal \         ###   Cluster the jobs horizontally
line 23    --dax dax.xml \                ###   Name of the dax file
line 2324    --submit                       ###   Type of action is submit

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languageactionscript3
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line 8 dax = ADAG("vina-ligand-receptor") ###   Name of dax. You canmay change any interesting name you like.
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line 10 base_dir = os.getcwd()   ### The path of the reference base directory defined as the current working directory
line 11 
...     ###  Adds "vina_wrapper.bash" file path to the dax.xml file
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line 18  
...     ###  Adds "2gutreceptor_config.txt" file path to the dax.xml file
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...     ###  Adds "2gutreceptor.pdbqt" file path to the dax.xml file
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line 31 input_ligands_dir = base_dir + "/input_ligands"   ### Defines the path of the input ligands directory
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line 35 ### Loops over the ligand files inside the "input_ligands" directory. 
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line 36
...     ###  Adds each ligand file path to dax.xml
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line 40
...     ### Name and information of output files
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line 45
...    ### Define a job with the description about input and output files.
line 53 

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