Requirements

Snakevir requires , and .

Snakevir is developed to work on an slurm HPC.

Install Snakevir from pypi

First, install the Snakevir python package with github and pip.

python3 -m pip install snakevir
snakevir --help

Update Snakevir from pypi

python3 -m pip install -U snakevir
snakevir --version

Warning

After updating Snakevir please re-use the snakevir install_cluster command on the same tools directory and then re-run the edit_cluster command with you’re account and partition.

Steps for HPC distributed cluster installation

Snakevir uses any available snakemake profiles to cluster installation and resources management. Run the command snakevir install_cluster to install tools and most databases needed by snakevir. We tried to make cluster installation as easy as possible, but it is somehow necessary to adapt a few files according to your cluster environment.

snakevir install_cluster

This function allow to install tools with conda and dowload database needed by snakevir except nt & nr database

snakevir install_cluster [OPTIONS]

Options

-p, --path <path>: Required Give the installation PATH for conda environment that contains all the necessary tools for snakevir.

-s, --skip: Skip all install and download if it’s already existing

-t, --tool: Update conda environment (Re-install conda environment even if it’s already install)

-d, --database: Update database (Re-download files even if it’s already download)

1. Adapt your cluster configuration

Now that Snakevir is installed, it proposes default configuration files, but they can be modified. Please check and adapt these files to your own system architecture.

For adapt the cluster configuration ou can use the snakevir edit_cluster command.

snakevir edit_cluster

The command make_config is used for create config fime at yaml format for snakevir. You have 2 choice, you can use arguement for write all information needed in config or you can only use some argument (-o is mandatory) and wirte in the file after the missing information.

snakevir edit_cluster [OPTIONS]

Options

-p, --partition <partition>: Name of the default partition.

-a, --account <account>: Name of you’re account for launch job in cluster

-e, --edit: Edit cluster config for less/more ressources