Bioinformatics Learn

Создание окружения

Miniforge3:

wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh
~/mambaforge/bin/conda init bash
exec bash

mamba env create -f bioinformatics-learn.yml
conda activate bioinformatics-learn

Обновление окружения при добавлении зависимостей:

conda env update -f bioinformatics-learn.yml --prune

Тесты:

python -m pytest -q

Обновление conda base:

conda update -n base -c conda-forge conda

Installing R:

Note: that r-essentials installs a lot of R packages, including ggplot2,

conda install rpy2 r-essentials r-gridextra

Базовые пакеты R (rpy2)

conda install r-ggplot2 r-lazyeval r-gridextra rpy2

Dataset

wget -nd http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/20130502.phase3.sequence.index -O /datasets/sequence.index