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updating documentation
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docs/source/generating_workflows_recipe.rst

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@@ -63,20 +63,21 @@ less tasks. This is a useful flag to use when there is trust that all
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possible patterns present in this application can be already found in the
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smaller instances.
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Workflow recipes are automatically installed and can be used throughout the system. WfCommons creates a Python package in the directory
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specified by the flag :code:`--out` in which the :file:`setup.py` and :file:`recipe.py` files are stored. If the flag :code:`--no-install` is set
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when creating a package for a specific application, the user will need to install the package before using it. The code
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bellow is an example of how to install/uninstall a package for an application in WfCommons: ::
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Workflow recipes are automatically installed and can be used throughout the
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system. WfCommons creates a Python package in the directory specified by the
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flag :code:`--out` in which the :file:`setup.py` and :file:`recipe.py` files
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are stored. If the flag :code:`--no-install` is set when creating a package
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for a specific application, the user will need to manually install the package
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before using it. The code bellow is an example of how to install/uninstall a
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package for an application in WfCommons: ::
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# installing the package
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$ pip install path/to/the/package
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$ pip install /path/to/the/package
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# uninstalling a package
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$ pip uninstall wfcommons.wfchef.recipes.appication_name_workflow
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The snippet below show an example of how to import the recipes: ::
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The snippet below shows an example of how to import the recipes: ::
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# creating an Epigenomics workflow recipe
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from wfcommons.wfchef.recipes import EpigenomicsRecipe
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To check which recipes are installed in a system and how to import them use: ::
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$ wfchef ls
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Examples
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--------
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The following example generates 10 *Epigenomics* synthetic workflow instances
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based on the number of tasks entered by the user (1000), builds the synthetic workflow instances, and writes the
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synthetic instances to JSON files. ::
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from wfcommons.wfchef.recipes import EpigenomicsRecipe
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from wfcommons.generator import WorkflowGenerator
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generator = WorkflowGenerator(EpigenomicsRecipe.from_num_tasks(1000))
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for i, workflow in enumerate(generator.build_workflows(10)):
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workflow.write_json(f'epigenomics-workflow-{i}.json')
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The example below generates a *Cycles* (agroecosystem) synthetic workflow instance based on the number
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of tasks entered by the user (250), builds the synthetic workflow instance, and writes the synthetic
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instance to a JSON file. ::
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from wfcommons.wfchef.recipes import CyclesRecipe
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from wfcommons.generator import WorkflowGenerator
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generator = WorkflowGenerator(CyclesRecipe.from_num_tasks(250))
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workflow = generator.build_workflow()
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workflow.write_json(f'cycles-workflow.json')
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..
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maybe we should pout examples only on generator, because we need it

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