Last modified by robing on 2022/03/25 09:55
From version 19.1
edited by robing
on 2020/01/21 00:20
Change comment: There is no comment for this version
To version 20.1
edited by robing
on 2020/01/21 00:34
Change comment: There is no comment for this version

Summary

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29 29  * **Copy the collab drive to your drive space**
30 30  ** Open the Drive from the left menu
31 31  ** Select the folders 'pipeline' and 'datasets'
32 -** Select 'Copy', and 'My Library' from the dropdown 'Other Libraries'
32 +** Select 'Copy', and then 'My Library' from the dropdown 'Other Libraries'
33 33  
34 34  * **Start a Jupyter Hub instance **
35 -copy the URL below in a separate browser page: 'jupyterhub-preview.apps-dev.hbp.eu'
35 +copy the URL to another browser page: 'jupyterhub-preview.apps-dev.hbp.eu'
36 36  
37 37  * **Edit the config files**
38 38  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]).
... ... @@ -42,9 +42,10 @@
42 42  ** stage04_wavefront_detection: [README.md](), [config.yaml]()
43 43  ** stage05_wave_characterization: [README.md](), [config.yaml]()
44 44  
45 -* **Follow the notebook**
46 -In the jupyter hub, navigate to `drive/Shared with groups/Slow Wave Analysis Pipeline/pipeline/showcase_notebooks/run_snakemake_in_collab.ipynb`.
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 47  * Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
48 +
48 48  * **Coming soon**
49 49  ** Use of KnowledgeGraph API
50 50  ** Provenance Tracking