My R(Cellchat) environment

Cellchat.md

Cellchat R environment

build

docker-compose up --build

contains

• Cellchat
• xterm for plotting
• pandoc for Rmarkdowns

docker-compose.yml

version: '3'

services:
    r-housing:
        build: .
        cap_add:
            - SYS_PTRACE #but i want gdb
        security_opt:
            - seccomp:unconfined
        tty: true
        stdin_open: true
        ports:
            - "1337:1337"
        hostname: envi-r-on

Dockerfile

FROM ubuntu:latest

RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -qy \
    openssh-server \
    vim \ 
    python3 \
    python3-pip \
    python-is-python3 \
    gcc \
    gdb \
    lrzsz \ 
    xterm \
    software-properties-common \
    dirmngr \ 
    htop \
    sudo \
    libxml2-dev \
    libssl-dev \ 
    libcurl4-openssl-dev \
    libfontconfig1-dev \
    libcairo2-dev \
    libxt-dev \
    git \
    pandoc \ 
    texlive-latex-base \
    texlive-fonts-recommended \ 
    texlive-fonts-extra \ 
    texlive-latex-extra \
    libharfbuzz-dev \
    libfribidi-dev \
    libfreetype6-dev \
    libpng-dev \
    libtiff5-dev \
    libjpeg-dev 
    
#install R & radian for quality life
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

RUN apt-get install -qy r-base

RUN python -m pip install radian umap-learn


#R littler for more efficient scripting
RUN R -e "install.packages('littler')"
RUN ln -s /usr/local/lib/R/site-library/littler/bin/r /usr/bin


#install tidyverse, Cellchat & its dependencies
RUN r -e "install.packages('tidyverse')"
RUN r -e "install.packages('shiny')"
RUN r -e "install.packages('BiocManager')"
RUN r -e "BiocManager::install('Biobase')"
RUN r -e "BiocManager::install('ComplexHeatmap')"
RUN r -e "install.packages('devtools')"
RUN r -e "install.packages('httpgd')"
RUN r -e "devtools::install_github('sqjin/CellChat')"
RUN r -e "install.packages('Seurat')"

#global setup script
COPY setup.sh /root/setup.sh

CMD ["/bin/sh", "/root/setup.sh"]

setup.sh

#!/bin/sh

echo "[\033[1;32m+\033[0m] adding user"
echo "[edit here to add user]"; exit || echo "[\033[1;33m!\033[0m] failed to add user"
echo "[\033[1;32m+\033[0m] setting user password"
echo "[edit here to change password]"; exit || echo "[\033[1;33m!\033[0m] failed to set user password"

# Set SSHD option and start SSH service
echo "[\033[1;32m+\033[0m] starting sshd"
#sed -ri 's/^#?PermitRootLogin\s+.*/PermitRootLogin yes/' /etc/ssh/sshd_config
sed -ri 's/^#*?Port\s+.*/Port 1337/' /etc/ssh/sshd_config
sed -ri 's/^#?X11UseLocalhost\s+.*/X11UseLocalhost no/' /etc/ssh/sshd_config
service ssh start

echo "[\033[1;32m+\033[0m] Ready"
exec bash