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73	73	Each stage has config files (//pipeline/<stage_name>/configs/config_<profile>.yaml//) to specify which analysis/processing blocks to execute and which parameters to use. General and specific information about the blocks and parameters can be found in the README and config files of each stage. There are preset configuration profiles for the benchmark datasets IDIBAPS ([[ECoG, anesthetized mouse>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=sanchez-vives#Dataset/2ead029b-bba5-4611-b957-bb6feb631396]]) and LENS ([[Calcium Imaging, anesthetized mouse>>https://kg.ebrains.eu/search/instances/Dataset/71285966-8381-48f7-bd4d-f7a66afa9d79]]).
74	74
75	75	* **Run the notebook**
76		-In the jupyter hub, navigate to //drive/My Libraries/My Library/pipeline/showcase_notebooks/run_snakemake_in_collab.ipynb//, or where you copied the //pipeline// folder to.
77		-Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake
	76	+In the jupyter hub, navigate to //drive/My Libraries/My Library/run_snakemake_in_collab.ipynb//, or where you copied the file to.
	77	+Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
78	78
79	79	=== ii) Local execution ===
80	80
81		-//tested only with Linux!//
	81	+//tested only with Mac OS and Linux!//
82	82
83	83	* **Get the code**
84	84	The source code of the pipeline is available via Github: [[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]] and can be cloned to your machine ([[how to get started with Github>>https://guides.github.com/activities/hello-world/]]).
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88	88	In the wavescalephant git repository, there is an environment file ([[pipeline/environment.yaml>>https://drive.ebrains.eu/smart-link/1a0b15bb-be87-46ee-b838-4734bc320d20/]]) specifying the required packages and versions. To build the environment, we recommend using conda ([[how to get started with conda>>https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html]]).
89	89	##conda env create ~-~-file environment.yaml
90	90	conda activate wavescalephant_env##
	91	+
	92	+Make sure that neo and elephant were installed as their Github development version, and if necessary add them manually to the environment.
	93	+##pip install git+https:~/~/github.com/NeuralEnsemble/elephant.git
	94	+pip install git+https:~/~/github.com/NeuralEnsemble/python-neo.git##
91	91
92	92	)))
93	93	* **Edit the settings**