Skip to content
Snippets Groups Projects
README.md 1.05 KiB
Newer Older
### Run hands-on tutorial Jupyter notebook on Binder

Click on the below badge. Tested on Chrome web browser. IE might have some issues.

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.rc.uab.edu%2Fmcbios19_single_cell%2Fsingle_cell_rnaseq_hands-on_1.git/a20f707fc0b67f6eb4f9bf85a5daacc52c125df6?filepath=pbmc_small_case2.ipynb)
### Set up developer conda env on Cheaha
Min Gao's avatar
Min Gao committed

* Load Anaconda module.
  * We are testing with Anaconda3/5.2.0 right now.
  * Something like `module load Anaconda3/5.2.0` should do the trick.
* Create a conda env from the `dev-conda-env.yml` file.
  * See https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file.
  * `conda env create -f dev-conda-env.yml`
  * You can change the name of the conda env in the YAML file.
  * This takes about 5 minutes and is a one-time cost.

That's it!

Now you can load the conda env the usual way (e.g. `source activate`) at the shell or pick it as the Jupyter kernel for your notebook.