Installation

Note

Platform compatibility:

Selenoprofiles4 is officially supported on Linux and macOS systems. It is not compatible with Windows.

Docker installation

The docker image of selenoprofiles contains a complete installation, including all optional dependencies (see below). To use Docker for running Selenoprofiles, you should follow the next steps:

Pull the Docker image:

You can find the Docker image for Selenoprofiles on Docker Hub. To pull the image, run the following command:

docker pull maxtico/selenoprofiles_container:latest

For more information on using selenoprofiles Docker, refer to the documentation: https://hub.docker.com/r/maxtico/selenoprofiles_container/

Note

When using Docker, the way you run Selenoprofiles commands differs slightly. For detailed usage instructions and advanced options, see Using selenoprofiles in Docker.

Conda installation

We recommend to use the conda package manager to install selenoprofiles4 (check this page to install conda).

We recommend to create a new dedicated enviroment, e.g. called sp4, then activate it. In a terminal, run:

conda create -yn sp4
conda activate sp4

Then install selenoprofiles4 and its dependencies in the sp4 environment:

conda install -c mmariotti -c anaconda  -c bioconda -c biobuilds selenoprofiles4

If everything worked correctly, the selenoprofiles command is now available, but it is still not setup. Run this and follow instructions:

selenoprofiles -setup

Finally, run this to automically download the latest built-in profiles to search for known selenoproteins and selenium markers:

selenoprofiles -download

A couple of notes:

  • the -setup command creates the config file: ~/.selenoprofiles_config.txt – you may edit this to change default options

  • the -download command downloads data in the folder ~/selenoprofiles_data/. If necessary, you may move it to another location and change the value of selenoprofiles_data_dir in the config file.

You’re ready to go! Remember to activate the sp4 environment everytime you run selenoprofiles.

At any time, run this to access the help page:

selenoprofiles -h

Check the Getting started page to start using selenoprofiles.

Warning

Note for Mac users (Apple Silicon, M1/M2/M3/M4):

Some bioconda packages required by selenoprofiles4 (such as mafft) are not yet available for the ARM64 (Apple Silicon) architecture. If you see an error such as:

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides mafft needed by selenoprofiles4-4.x.x-py_0

This happens because Conda is searching only for ARM64 builds. To solve this, use Rosetta, which allows Conda to run Intel (x86_64) packages on your Mac:

  1. Make sure Rosetta is installed (only once per system). See: https://support.apple.com/en-us/102527

  2. Create and activate the environment as Intel (osx-64)

CONDA_SUBDIR=osx-64 conda create -n sp4
conda activate sp4

  1. Install selenoprofiles4 using Intel packages

CONDA_SUBDIR=osx-64 conda install -c mmariotti -c anaconda -c bioconda -c biobuilds selenoprofiles4

After this, installation should succeed and selenoprofiles4 will work normally on Apple Silicon.