Last modified by robing on 2022/03/25 09:55
From version 74.1
edited by robing
on 2020/05/08 16:06
Change comment: There is no comment for this version
To version 80.1
edited by robing
on 2020/05/26 09:41
Change comment: There is no comment for this version

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74 74  
75 75  * **Run the notebook**
76 76  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.
77 -Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake
77 +Follow the notebook to install the required packages into your Python kernel, set the output path, and execute the pipeline with snakemake.
78 78  
79 79  === ii) Local execution ===
80 80  
81 +//tested only with Mac OS and Linux!//
82 +
81 81  * **Get the code**
82 82  The source code of the pipeline is available via Github: [[INM-6/wavescalephant>>https://github.com/INM-6/wavescalephant]] and can be cloned to your machine ([[how to get started with Github>>https://guides.github.com/activities/hello-world/]]).
83 83  
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86 86  In the wavescalephant git repository, there is an environment file ([[pipeline/environment.yaml>>https://drive.ebrains.eu/smart-link/1a0b15bb-be87-46ee-b838-4734bc320d20/]]) specifying the required packages and versions. To build the environment, we recommend using conda ([[how to get started with conda>>https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html]]).
87 87  ##conda env create ~-~-file environment.yaml
88 88  conda activate wavescalephant_env##
91 +
92 +Make sure that neo and elephant were installed as their Github development version, and if necessary add them manually to the environment.
93 +##pip install git+https:~/~/github.com/NeuralEnsemble/elephant.git
94 +pip install git+https:~/~/github.com/NeuralEnsemble/python-neo.git##
89 89  
90 90  )))
91 91  * **Edit the settings**
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