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Author

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1		-XWiki.pierstanpaolucci
	1	+XWiki.robing

Content

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26	26
27	27	=== in the collab (beta) ===
28	28
	29	+* **Copy the collab drive to your drive space**
	30	+** Open the Drive from the left menu
	31	+** Select the folders 'pipeline' and 'datasets'
	32	+** Select 'Copy', and then 'My Library' from the dropdown 'Other Libraries'
	33	+
	34	+* **Start a Jupyter Hub instance **
	35	+copy the URL to another browser page: 'jupyterhub-preview.apps-dev.hbp.eu'
	36	+
29	29	* **Edit the config files**
30	30	Each stage has a config file to specify which analysis/processing blocks to execute and which parameters to use. General and specific information about the blocks and parameters can found in the README and config files. The default values are set for an example dataset (ECoG, anesthetized mouse, IDIBAPS [ref]).
31	31	** stage01_data_entry: [README.md](), [config.yaml]()
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34	34	** stage04_wavefront_detection: [README.md](), [config.yaml]()
35	35	** stage05_wave_characterization: [README.md](), [config.yaml]()
36	36
37		-* **Start a Jupyter Hub instance (copy the URL below in a separate browser page)**
38		-[[jupyterhub-preview.apps-dev.hbp.eu>>jupyterhub-preview.apps-dev.hbp.eu]]
	45	+* **Run the notebook**
	46	+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.
	47	+* Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
39	39
40		-* **Follow the notebook**
41		-In the jupyter hub, navigate to `drive/Shared with groups/Slow Wave Analysis Pipeline/pipeline/showcase_notebooks/run_snakemake_in_collab.ipynb`.
42		-Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
43	43	* **Coming soon**
44	44	** Use of KnowledgeGraph API
45	45	** Provenance Tracking
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52	52
53	53	* **Build the Python environment**
54	54	In the wavescalephant repository, there is an environment file (`pipeline/envs/wavescalephant_env.yaml`) specifying the required packages and versions. To build the environment, we recommend using *conda* ([how to get started with conda]()).
55		-`conda env create ~-~-file /envs/wavescalephant_env.yaml`.
	61	+`conda env create ~-~-file /envs/wavescalephant_env.yml`.
56	56
57	57	* **Edit the settings**
58	58	The settings file specifies the path to the output folder, where results are saved to. Open the template file `pipeline/settings_template.py`, set the `output_path` to the desired path, and save it as `pipeline/settings.py`.