- make a github user github
- download and install Anaconda version 3.7, command line version
- download and install github desktop
- (optional) download and install atom
Set up access to Norstore first:
Then follow the installation instructions for your operating system:
(old) See the wiki or the documentation for more information on how to use expipe.
(new)
First we need to clone the cinpla-base repository.
Open Github Desktop, hit Clone Repository --> URL --> paste https://github.com/CINPLA/cinpla-base and choose the folder in which you want to save this repository (you will need it later).
It is reccommended to create a new folder called apps in your local disk (not kant!).
Open the Anaconda prompt and navigate to the cinpla-base folder (cd path-to-cinpla-base - e.g. cd C:\\apps\cinpla-base)
Now we need to create a new anaconda environment:
conda create -n expipe python=3.5
source activate expipe
If you plan to use electrophysiology and spike sorting also run this:
conda install pyqt=4
Then we can get all the python packages needed by:
pip install -r requirements.txt
Now run expipe:
expipe
(in Windows, if it fails, run:
pip uninstall numpy
pip install numpy
and try again!)
Templates are used to create modules in expipe actions. Use github desktop to clone https://github.com/CINPLA/expipe-templates-cinpla.git. This is a collection of templates used by the group that can be loaded into each project's templates folder.
The project will contain the data and relative information. You can make a folder called data or projects, for example, and create you projects there.
First change directory to your projects directory
cd path-to-data (or path-to-projects)
Then create a new project:
expipe create project_name
Now we can interact with the project by running:
jupyter notebook
This will open a browser window (e.g. in Chrome). To create a new notebook (used to write and run code) press New-->Python 3. This will create an ipython notebook file (.ipynb).
In the first cell type and import the expipe packages:
from expipe_plugin_cinpla.widgets import browser
import expipe
In the second cell type:
browser.display('project_name')
This will display an interactive widget to register actions (such as surgery, adjustment, perfusion, recordings, analysis), entities (such as animals) and process them, and saving them in exdir format.
In order to process extracellular data
Gitea allows to handle large file sizes (LFS). We use NIRD to store those files at https://gitea.expipe.sigma2.no/ If you don't have an account contact Mikkel Lepperød.
If you already created a project following the previous information, from the terminal go into the repository and type:
cd path-to-project
git init
Then you have to create a repository on Gitea with the same name by Add repository. Once this is done, you have to tell Gitea that the repository you created needs to be connected to your local repository. Copy the gitea url of your repository (e.g. https://gitea.expipe.sigma2.no/your-user-name/your-project-name.git) and run:
git remote add origin https://gitea.expipe.sigma2.no/your-user-name/your-project-name.git
Then we have to add the files that expipe created (actions, templates, modules, etc.).
expipe init-lfs
git add -A
git commit -m "loading first files (or any other message)"
git pull
git branch --set-upstream-to=origin/master master
git push