Installation¶

The recommended way to install SeqNado is via a combination of conda and pip, this will ensure that all dependencies are installed correctly in a virtual environment. Using the recommended method, the main dependencies of the pipeline are accessed from a singularity container, so it is not necessary to install these manually. If required, conda can be used to install the dependencies locally, but this is not recommended.

Set-up¶

Check conda|mamba is installed¶

Ideally, ensure that mamba is installed and is working correctly.

which mamba

You should see something like:

/ceph/project/milne_group/asmith/software/mambaforge/condabin/mamba

Install mamba (if required)¶

If mamba is not installed, install it using the following command:

Warning

Ensure that this is installed in your /project directory, not your home directory! These environments can be very large and will fill up your home directory very quickly.

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

Install from bioconda (recommended)¶

mamba install seqnado

Quick installation¶

Use the following command to install SeqNado and all dependencies:

bash <(curl -s https://raw.githubusercontent.com/alsmith151/SeqNado/master/install_seqnado.sh)

Detailed installation for advanced users or troubleshooting¶

Create a conda environment¶

Create a basic conda environment (with pip to install python packages) and activate it.

mamba create -n seqnado pip "python>=3.12"
conda activate seqnado

Install the pipeline¶

Install the package from pip¶

pip install seqnado

Ensure that Environment variables are set¶

Ensure that the environment variables are set correctly. This can be done by adding the following to your .bashrc or .bash_profile. Run this command to add the environment variables to your .bashrc:

echo 'export APPTAINER_BINDPATH="/ceph:/ceph, /project:/project, /databank:/databank"' >> ~/.bashrc

Reload the .bashrc file:

source ~/.bashrc

Alternatively, start a new terminal session.

Install from GitHub directly¶

To install the latest version of the pipeline from GitHub (master branch), use the following command:

pip install git+https://github.com/alsmith151/SeqNado.git

You can also install a specific branch e.g. develop:

pip install git+https://github.com/alsmith151/SeqNado.git@develop

Install from a local copy of the repository¶

Clone the repositry and install directly.

git clone https://github.com/alsmith151/SeqNado.git
cd SeqNado
pip install .

Install the dependencies (if required)¶

Assuming the conda environment is activated, install the dependencies using the following command:

wget https://raw.githubusercontent.com/alsmith151/SeqNado/master/environment.yml
mamba env update -f environment.yml