InstallationInstructions.txt

##For the lecuters:
#Please install ZOOM: https://zoom.us/download
#Please join the slack channel: <See email>
#Optionally: install the slack app: https://slack.com/intl/en-de/

##For the tutorials (day1-day2): 

##Step 0.
#Install Anaconda or miniconda
#(information see: https://docs.anaconda.com/anaconda/install/)

##Step 1.
#After installation you will automatically load the base enviroment.
#These instructions will install software in the "base" enviroment but you can also make a specific enviroment for the course.
# To do so use: "conda create --name myenv" & "conda activate myenv" (myenv can be replaced with a name of choice)

##Step 2.
#Install R 4 (conda forge)
conda install -c conda-forge r-base=4 r-curl r-rgeos

##Step 3.
##install other dependancies within R!
#Start R
R
(within R)
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.14")

install.packages("R.utils")
BiocManager::install("knitr")
BiocManager::install("umap")
BiocManager::install("Rtsne")
BiocManager::install("dplyr")
BiocManager::install("ggplot2")
BiocManager::install("data.table")
BiocManager::install("biomaRt")
BiocManager::install("SingleCellExperiment")
BiocManager::install("MOFA2")
install.packages("Seurat")

##Step 4.
#Please try and load the packages in R. 
#Specifically for "Seurat" make sure you load the library at least once "library("Seurat")" and install the remaining dependancies via miniconda.

#Also please check if mofa is installed correctly by running the following in R:
#This runs mofa with test data and makes sure that the environment is set up correctly (warnings are fine here)

library(MOFA2)
data <- make_example_data(n_views = 2, n_samples = 200, n_features = 1000, n_factors = 10)[[1]]
MOFAobject <- create_mofa(data)
MOFAobject <- prepare_mofa(object = MOFAobject)
run_mofa(MOFAobject)


##Step 5.
# To install the dependencies for the day3 please follow the instructions here: https://github.com/PMBio/SingleCellCourse/blob/master/day3/installation.md