phamidko / rstudio-mofa2

Base Rstudio docker container for Multi-Omics Factor Analysis V2 (MOFA+)

Rstudio docker container for MOFA+

Multi-Omics Factor Analysis V2 (MOFA+) https://biofam.github.io/MOFA2/index.html

Docker image

docker pull phamiducla/rstudio_mofa2:latest

From your host data directory,

docker run  --rm -v ${PWD}:/data -d -p 3787:8787 -p 8888:8888 -e PASSWORD=rstudio1 --name rstudio phamiducla/rstudio_mofa2:latest

The command mounts the current directory to the container [/data]. Windows User must run this command line in Powershell command.

For Linux user, clone this repository and build docker image. It prevents file premission issue when you attempt to save files inside container or rstudio.

docker build --pull --no-cache -t <INSERT_IMAGE_TAG> \
  --build-arg USER_ID=$(id -u) --build-arg GROUP_ID=$(id -g) .

Rstudio Login

Go to localhost:3787 in browser and login with rstudio (username) and rstudio1 (password from command argument)

In Rstudio script

setRepositories(ind=1:2)
sapply(c('BSgenome.Hsapiens.UCSC.hg38'),BiocManager::install)

library(Seurat)
library(ggplot2)
library(MOFA2)

List all R packages installed in the image

List R packages (Console R prompt)

ip = as.data.frame(installed.packages()[,c(1,3:4)])
ip = ip[is.na(ip$Priority),1:2,drop=FALSE]
ip

Check mofapy2 version (Terminal command prompt)

pip show mofapy2

Root user

Enter root user passoword from command argument which is rstudio1

rstudio@6929df934634:~$ sudo -i
[sudo] password for rstudio:
root@6929df934634:~#

Jupyter Notebook

From terminal prompt or docker commandline, launch jupyter lab and access python notebook at http://127.0.0.1:8888/rstudio/lab

jupyter lab --notebook-dir=/home/rstudio --ip=0.0.0.0 --no-browser --allow-root \
  --port=8888 --NotebookApp.token='' --NotebookApp.password='' --NotebookApp.allow_origin='*' \
  --NotebookApp.base_url=rstudio"