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Last modified by robing on 2022/03/25 09:55
From version 15.2
edited by epastorelli
on 2020/01/20 14:08
Change comment: There is no comment for this version
To version 13.1
edited by robing
on 2020/01/20 13:37
Change comment: There is no comment for this version

Summary

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1 -XWiki.epastorelli
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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)**
37 +* **Start a Jupyter Hub instance**
38 38  [[jupyterhub-preview.apps-dev.hbp.eu>>jupyterhub-preview.apps-dev.hbp.eu]]
39 39  
40 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`.
41 +In the jupyter hub, navigate to `drive/Shared with groups/Slow Wave Analysis Pipeline/pipeline/showcase_notebooks/snakemake_collab_test.ipynb`.
42 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 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.yml`.
56 +`conda env create ~-~-file /envs/wavescalephant_env.yaml`.
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`.