Last modified by robing on 2022/03/25 09:55
From version 18.1
edited by robing
on 2020/01/21 00:14
Change comment: There is no comment for this version
To version 10.1
edited by robing
on 2020/01/20 09:33
Change comment: There is no comment for this version

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... ... @@ -34,13 +34,12 @@
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 **
38 -copy the URL below in a separate browser page
39 -[[jupyterhub-preview.apps-dev.hbp.eu>>jupyterhub-preview.apps-dev.hbp.eu]]
37 +* **Start a Jupyter Hub instance**
40 40  
41 41  * **Follow the notebook**
42 -In the jupyter hub, navigate to `drive/Shared with groups/Slow Wave Analysis Pipeline/pipeline/showcase_notebooks/run_snakemake_in_collab.ipynb`.
40 +In the jupyter hub, navigate to `drive/Shared with groups/Slow Wave Analysis Pipeline/pipeline/showcase_notebooks/snakemake_collab_test.ipynb`.
43 43  Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
42 +
44 44  * **Coming soon**
45 45  ** Use of KnowledgeGraph API
46 46  ** Provenance Tracking
... ... @@ -53,7 +53,7 @@
53 53  
54 54  * **Build the Python environment**
55 55  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]()).
56 -`conda env create ~-~-file /envs/wavescalephant_env.yml`.
55 +`conda env create ~-~-file /envs/wavescalephant_env.yaml`.
57 57  
58 58  * **Edit the settings**
59 59  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`.