Installation

Docker installation

Docker installation contains all information available from selenoprofiles, including optional dependencies (see below). To use Docker for running Selenoprofiles, you should follow the next steps:

  1. 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/container_selenoprofiles:latest

  2. Run the Docker container:

    Once you’ve pulled the Docker image, you can run the Selenoprofiles package inside the Docker container. Use the following command:

    docker run maxtico/container_selenoprofiles:latest <selenoprofiles_command>

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

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.

Optional dependencies for selenoprofiles utilities

Selenoprofiles comes with some utilities: join, build, drawer, database. Some of them have additional dependencies which are not strictly required for selenoprofiles and are not automatically installed:

  • selenoprofiles drawer requires ete3. Install it with:

    conda install -c etetoolkit ete3

  • selenoprofiles assess requires pyranges and pyfaidx. Install them with:

    pip install pyranges

conda install -c bioconda pyfaidx

  • selenoprofiles build offers a graphical interface which requires pylab. Install it with:

    conda install matplotlib