This course covers the installation and use of SAMAP for single-cell cross-species alignment. In addition, some introductory materials for the 2019 course are also saved here. These introductory materials come from Casey Dunn, Cat Munro, Francesco Lamanna, Jonathan Landry, and Jacob Musser.
If you don't already have Anaconda or Miniconda installed, download Miniconda here: Miniconda
Download SAMap github directory: SAMap Github
- click
Code, thenDownload ZIP, save zip file to an easy-to-remember location - unzip directory
In Mac/Linux, open a Terminal Window. In Windows click on start and open "Anaconda Prompt (miniconda)#. Then, change directory to the SAMap github directory that you just saved and unzipped.
Create a new conda environment for installing SAMap using the following command:
conda create -n SAMap2 -c conda-forge python=3.7 pip pybind11 h5py=2.10.0 leidenalg python-
igraph texttable jupyterlab=1.2.0
Activate the new conda environment:
conda activate SAMap
Install SAMap with the command pip install .
Open the jupyter lab notebook with the command jupyter lab
Install additional python libraries:
conda install -c conda-forge -c plotly ipywidgets plotly=4.0.0 colorlover ipyevents
For using SAM GUI in jupyterlab (vs. the classic jupyter notebook), there is one more installation step:
conda install nodejs
Enable ipythonwidgets in Jupyter Lab:
jupyter labextension install @jupyter-widgets/jupyterlab-manager@1.0 --no-build
jupyter labextension install plotlywidget@1.1.0 --no-build
jupyter labextension install jupyterlab-plotly@1.1.0 --no-build
jupyter lab build