installation.md

Installation

Python 3.10, 3.11 or 3.12 is required.

Requirements

The ST Pipeline requires STAR installed in the system (minimum version 2.5.4 if you use a ST Pipeline version >= 1.6.0). The ST Pipeline requires samtools installed in the system.

If you use anaconda you can install STAR and samtools with:

conda install -c bioconda star samtools

The ST Pipeline needs a computer with at least 32GB of RAM (depending on the size of the genome) and 8 cpu cores.

Dependencies

The ST Pipeline depends on some Python packages that will be automatically installed during the installation process. You can see them in the file requirements.txt

From source

The source for ST Pipeline can be downloaded from the Github repo.

You can either clone the public repository:

git clone https://github.com/jfnavarro/stpipeline

Or download the tarball:

curl -OJL https://github.com/jfnavarro/stpipeline/tarball/master

Once you have a copy of the source, you can install it with:

Using Poetry

If you don't have Poetry installed you can use the following command:

curl -sSL https://install.python-poetry.org | python -

Install the package:

poetry install

Now you can run the ST Pipeline:

poetry run st_pipeline_run --help

Using Pip

If you don't have pip installed, this Python installation guide can guide you through the process.

Install the package:

pip install .

You can also use the official PyPy repositories:

pip install stpipeline

Now you can run ST Pipeline:

st_pipeline_run --help

Using Docker

Before installing, ensure that Docker is installed in your environment.

First, build a Docker image:

docker buildx build --platform linux/amd64 -t stpipeline .

Then, you can run ST Pipeline using Docker:

To run ST Pipeline commands:

docker run --rm stpipeline st_pipeline_run --help

Using Anaconda

Before installing, ensure you have either Anaconda or Miniconda installed in your environment.

First, create the environment:

conda env create -n stpipeline python=3.10

Then, activate the environment:

conda activate stpipeline

Install the package:

pip install .

Now you can run ST Pipeline:

st_pipeline_run --help