Last modified by robing on 2022/03/25 09:55
From version 39.1
edited by robing
on 2020/04/17 12:14
Change comment: There is no comment for this version
To version 40.1
edited by robing
on 2020/04/21 12:36
Change comment: There is no comment for this version

Summary

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... ... @@ -50,19 +50,20 @@
50 50  **Copy the collab drive to your personal drive space**
51 51  
52 52  * Open the Drive from the left menu
53 -* Select the folders //pipeline// and //datasets//
53 +* Select the folders //pipeline// and //datasets,//
54 +and the notebook// run_snakemake_in_collab.ipynb//
54 54  * Select 'Copy', and then 'My Library' from the dropdown 'Other Libraries'
55 55  
56 56  )))
57 57  * **Start a Jupyter Hub instance **
58 58  In another browser tab, open [[https:~~/~~/lab.ebrains.eu>>https://lab.ebrains.eu]]
59 -
60 +
60 60  * **Edit the config files**
61 -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 of each stage. The default values are set for an example dataset (ECoG, anesthetized mouse, [[IDIBAPS>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=sanchez-vives#Dataset/2ead029b-bba5-4611-b957-bb6feb631396]]]).
62 +Each stage has a config file (//pipeline/<stage_name>/config.yaml//) 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 of each stage. The default values are set for an example dataset (ECoG, anesthetized mouse, [[IDIBAPS>>https://kg.ebrains.eu/search/?facet_type[0]=Dataset&q=sanchez-vives#Dataset/2ead029b-bba5-4611-b957-bb6feb631396]]]).
62 62  
63 63  * **Run the notebook**
64 64  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.
65 -* Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
66 +Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
66 66  
67 67  * **Coming soon**
68 68  ** Use of KnowledgeGraph API