Installation¶
Install using conda¶
MiniAn is available on conda-forge and this is the recommended way to get MiniAn. Before you start though, we highly recommend creating an empty environment for MiniAn:
conda create -y -n minian
conda activate minian
See conda start guide for more detail.
After you have created and activated an environment, you can install MiniAn with:
conda install -y -c conda-forge minian
and Done!
Install from source¶
You can install MiniAn directly using github repo. This is helpful if you want to checkout latest development, or to contribute to MiniAn. Run the following to obtain a full copy of MiniAn repo and setup necessary dependencies.
git clone https://github.com/DeniseCaiLab/minian.git
cd minian/
conda env create -n minian -f environment.yml
You can then activate the environment and start running the notebooks. Note that if you install in this way you will have a local copy of MiniAn scripts, and any modification made to those scripts will be reflect in your pipeline.
Getting notebooks and demos¶
The main features of Minian are exposed through pipeline.ipynb and cross-registration.ipynb notebooks. You can use the following links to get the latest version of the two notebooks:
Download pipeline.ipynb
Download cross-registration.ipynb
If you’d prefer specific version of them, head to github release page to see all the released versions.
Alternatively, MiniAn also come with convenient scripts to help you download notebooks and demos into your current folder. Run the following (in your activated environment if any) to get the notebooks:
minian-install --notebooks
Additionally, we also hosted some small demo data that works with the notebooks. Once you obtained these data, you should be able to run the two notebooks locally without modifying anything. Run the following script to get demo data:
minian-install --demo
The script can also help you get files from different branchs.
See minian-install --help for more detail.
Note that if you choose to Install from source you would already have a local copy of everything and you can also checkou different version of them using git. You can skip this step altogether.
Start the pipeline¶
And that’s it! Once you have installed MiniAn and obtained a copy of notebooks through any methods above, you can then start the jupyter notebook interface with:
jupyter notebook
(Remeber to activate the environment if your computer complain about command not found)
You can then either run the notebook, or refer to Pipeline and Cross-registration for some ideas about expected outcomes when running with demo data.