1. Installation

Note: we do not guarantee that these instructions will work on all operating systems.

General installation instructions

Download and install Anaconda or Miniconda
Via the command line/terminal, navigate to the folder you wish to install TALLSorts and execute
```
git clone https://github.com/Oshlack/TALLSorts.git
```
or
```
git clone git@github.com:Oshlack/TALLSorts.git
```
(Alternatively, you can use GitHub to directly download the files in a .zip. Extract these files in a folder of your choosing.)
In the folder containing TALLSorts (you should see an env folder in there), create a new environment by executing
```
conda env create -f env/tallsorts.yml
```
This will create a new conda environment called tallsortsenv.
Depending on your conda version, activate this environment using either
```
conda activate tallsortsenv
```
or
```
source activate tallsortsenv
```
(Optional) Download the pyensembl annotation files by running
```
pyensembl install --release 110 --species human
```
This helps TALLSorts convert gene symbols to Ensembl IDs. This installation step is not required if you plan on providing a counts matrix with Ensembl IDs instead of gene symbols.
Install TALLSorts by executing
```
pip install .
```
To ensure your installation works nicely, you should run a test.