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Setting-up a conda environment

Only for advanced users.

This documentation contains installing instructions for advanced users that opt to setup a conda environment for the transcriptutorial.

Install miniconda3

NOTE: only done once (1st time) in your local machine

miniconda3 is the framework to create and manage envs. Before starting to work with virtual environments (envs), you need to install miniconda3.

Download the installer of miniconda3

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

Create a directory where you are going to install your SOFTWARE

mkdir /home/$USER/SOFTWARE/

Run the installer and define the installation path. See below.

bash Miniconda3-latest-Linux-x86_64.sh

# Press <ENTER> to continue an read Miniconda License
# Go down and enter 'yes' to accept Miniconda License
# Importantly! Miniconda3 will be installed into the default location,
# that is your $HOME. However, you could install it in another location
# Thus, specify another location. For instance:
#	/home/<username>/SOFTWARE/miniconda3
# run conda init when asked during the installation

If you didnt run conda init during the installation, this is a good time to do so. This will make changes into your ~/.bashrc file needed to setup the conda environment when needed.

Remove the installer

rm Miniconda3-latest-Linux-x86_64.sh

Setup of environment

The first time that you install conda, it is installed with a default configuration. You have to extend this configuration by adding essential channels that are required to install R, CRAN and BioConductor packages.

conda config --append channels conda-forge
conda config --append channels r
conda config --append channels bioconda

Then you can create the conda enviroment from scratch using:

conda create -p envs/transcriptutorial r-base=4.0 python=3.8 bioconductor-CARNIVAL r-cowplot r-dplyr bioconductor-viper \ 
	r-ggplot2 r-ggrepel r-gridExtra bioconductor-GSEABase r-hexbin bioconductor-limma r-network bioconductor-OmnipathR \
	r-pheatmap bioconductor-piano r-plyr bioconductor-progeny r-readr r-reshape r-reshape2 r-scales r-tibble r-tidyr \
	r-visNetwork bioconductor-vsn r-ggraph r-tidygraph r-rmarkdown

Finally, install manually dorothea and the latest devel version of OmnipathR:

# Terminal
conda activate ./envs/transcriptutorial
$CONDA_PREFIX/bin/R
# R session
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## dorothea
#NOTE: dorothea is included in bioconda, although installation fails due to wrong indexing to bioconductor URL 
#	with current version of recipe. We have reported the issue. It will be fixed soon.
BiocManager::install("dorothea")

## OmnipathR package
BiocManager::install("OmnipathR", version='devel')

Note: if the installation of any of the packages fails with the conda recipe, just install it manually as the last chunk above.