diff --git a/README.md b/README.md index a8b1f20cdc5e9c9a434606bf0f5c049cfce75a86..48a1ae056c50397ff959a58c86992bea500fea5a 100644 --- a/README.md +++ b/README.md @@ -3,12 +3,13 @@ Linux/Unix Python (>= 3.7) ## Install Scanpy through conda: -The Miniconda3 package management system can be used to harmonize all of the software packages. We can install Scanpy using the conda environment. -Use the following commands to install Miniconda3: -$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh +The Miniconda3 package management system can be used to harmonize all of the software packages. We can install Scanpy using the following commands to install Miniconda3: +``` +$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh $ bash Miniconda3-latest-Linux-x86_64.sh - +``` We can create an isolated environment for Scanpy and install through the following commands: +``` $ conda config --add channels defaults $ conda config --add channels bioconda $ conda config --add channels conda-forge @@ -18,10 +19,10 @@ $ conda install seaborn scikit-learn statsmodels numba pytables $ conda install -c conda-forge python-igraph leidenalg $ conda install -c bioconda scanpy $ conda install -c anaconda ipykernel - +``` ## Clone the repository: +``` $ git clone git@gitlab.rc.uab.edu:attis2021/single_cell_rnaseq_scanpy.git - +``` ## Tutorial: A more detailed tutorial of how to analyze PBMC data use Scanpy can be found in file scanpy_pbmc_tutorial.ipynb. -