Installation

Please follow the guide below to install orthomap and its dependent software.

If a containerised option is available to you (docker or singularity) it will help you to either isolate it from the host environment or deals with the situation of broken conde dependencies (with only limited control on our side to resolve these issues). We of course try to support conda and other issues, but if you want to avoid conda issues, the suggestion is to use either docker or singularity.

Docker image

Pre-built docker image is available through Docker Hub .

docker pull kkuweb/orthomap_ubuntu:latest

  • This docker image was built based on Ubuntu 22.04.

  • Python dependent packages and orthomap are installed in an anaconda environment, orthomap_env. This environment will be activated automatically when you log in.

  • See additional information

Singularity image

  • Pre-built docker image is available through Docker Hub .

singularity pull kkuweb/orthomap_ubuntu:latest

  • This docker image was built based on Ubuntu 22.04.

  • Python dependent packages and orthomap are installed in an anaconda environment, orthomap_env. This environment needs to be activated when you log in.

  • See additional information

Install orthomap

Python Requirements

  • orthomap was developed using Python 3.8. We do not support Python 2.7x or Python <=3.7.

orthomap installation using conda and pip

We recommend installing orthomap in an independent conda environment to avoid dependent software conflicts. Please make a new python environment for orthomap and install dependent libraries in it.

The environment is created with conda create in which orthomap is installed.

If you do not have a working installation of Python 3.8 (or later), consider installing Anaconda or Miniconda. Then run:

git clone https://github.com/kullrich/orthomap.git
cd orthomap
conda env create --file environment.yml
conda activate orthomap_env

Install orthomap via PyPI:

pip install orthomap

Development Version

To work with the latest version on GitHub: clone the repository and cd into its root directory.

git clone kullrich/orthomap
cd orthomap

Install orthomap into your current python environment:

pip install .

Installing Miniconda

After downloading Miniconda, in a unix shell (Linux, Mac), run

cd DOWNLOAD_DIR
chmod +x Miniconda3-latest-VERSION.sh
./Miniconda3-latest-VERSION.sh