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dawneve/rstudio

By dawneve

•Updated over 5 years ago

R4.0.4, Seurat 4.0.0, monocle3 0.2.3 with an Rstudio web port. (2021.3.3)

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dawneve/rstudio repository overview

⁠Overview

This is an Rstudio with R 4.0.4, with ggplot2 3.3.3, Seurat 4.0.0. based on Ubuntu.

These images are based on rocker/rstudio, with R and Rstudio pre-installed.

Version control:

  • latest: the init and base image, only R and Rstudio. https://hub.docker.com/r/rocker/rstudio⁠
  • v1: add Seurat (need pkgs_forDocker_seurat.tar.gz)
  • v1.2: based on v1, add monocle3 (need pkgs_forDocker_seurat.tar.gz + pkgs_forDocker_monocle3_incre.tar.gz )
  • v3: add Jupyter notebook support // todo

⁠Preparation

You need download Seurat pkgs tar files on github before run :Seurat.

You need download Seurat + monocle3 pkgs tar file on github before run :monocle3.

$ cd ~/data/
$ wget https://github.com/DawnEve/scRNAseqCode/releases/download/scDocker-Seurat/pkgs_forDocker_seurat.tar.gz
$ tar zxvf pkgs_forDocker_seurat.tar.gz

## increasement tar on top of the above tar
$ wget https://github.com/DawnEve/scRNAseqCode/releases/download/scDocker-monocle3/pkgs_forDocker_monocle3_incre.tar.gz 
$ tar zxvf pkgs_forDocker_monocle3_incre.tar.gz

## move the corresponding files in the above tar files to the following dirs, can be modified, if you change the outer dir in the docker -v paras:
$ mkdir -p /home/wangjl/data/dockerRstudio
$ chmod 777 /home/wangjl/data/dockerRstudio

$ mkdir -p /home/wangjl/data/dockerRstudio/R_lib_4.0
$ chmod 777 /home/wangjl/data/dockerRstudio/R_lib_4.0

The content in dockerRstudio/ and dockerRstudio/R_lib_4.0/ can be found on github: https://github.com/DawnEve/scRNAseqCode/tags
|dockerRstudio/
|-- R_lib_4.0/

⁠Run a container

$ docker run -d -p 5000:8787 -v /home/wangjl/data/dockerRstudio:/home/rstudio \
	-v /home/wangjl/data/dockerRstudio/R_lib_4.0:/home/rstudio/R/x86_64-pc-linux-gnu-library/4.0 \
	-e ROOT=TRUE \
	-e PASSWORD=yourpasswordhere dawneve/rstudio:Seurat

⁠web port

## get your IP v4:
$ ifconfig

## Open a web browser, type
http://ipV4:5000

user: rstudio
passwd: yourpasswordhere 


## Put your inputs and outputs files at /home/wangjl/data/dockerRstudio/ on your physical machine.
## Then begin to analyse with the web browser.

⁠Help or Contact me

Github: https://github.com/DawnEve/scRNAseqCode/releases⁠

Email: jimmyMall at 163 dot com

QQ: 314649593

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539.1 MB

Last updated

over 5 years ago

docker pull dawneve/rstudio