albicans2021/rstudio-rnaseq repository overview

http://<server-IP>:18787

Username: rstudio
Password: (defined in the .env file)

FROM bioconductor/bioconductor_docker:RELEASE_3_19

ENV LANG=ja_JP.UTF-8 \
    LC_ALL=ja_JP.UTF-8 \
    TZ=Asia/Tokyo

# ---- Japanese locale + fonts ----
RUN apt-get update && apt-get install -y --no-install-recommends \
      locales \
      fonts-ipaexfont \
      fonts-noto-cjk \
      libxt6 \
      liblzma-dev \
      libz-dev \
      libbz2-dev \
    && sed -i '$d' /etc/locale.gen \
    && echo "ja_JP.UTF-8 UTF-8" >> /etc/locale.gen \
    && locale-gen ja_JP.UTF-8 \
    && ln -sf /usr/share/zoneinfo/Asia/Tokyo /etc/localtime \
    && apt-get clean && rm -rf /var/lib/apt/lists/*

# ---- Install R packages at build time ----
COPY install_packages.R /tmp/install_packages.R
RUN R -q -e 'if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager", repos="https://cloud.r-project.org")' \
  && R -q -f /tmp/install_packages.R \
  && rm -f /tmp/install_packages.R

# Remove legacy PhantomJS stack (security)
RUN R -q -e 'if ("webshot" %in% rownames(installed.packages())) remove.packages("webshot")'

RUN rm -rf \
    /usr/lib/node_modules/casperjs \
    /usr/local/lib/node_modules/casperjs \
    /opt/phantomjs \
    /usr/bin/phantomjs \
    /usr/bin/casperjs 2>/dev/null || true

services:
  rstudio:
    image: albicans2021/rstudio-rnaseq:tagname
    build:
      context: .
      dockerfile: Dockerfile
    container_name: rstudio_bioc_jp_319
    restart: always
    ports:
      - 18787:8787
    environment:
      ROOT: TRUE
      PASSWORD: ${RSTUDIO_PASSWORD}
      TZ: Asia/Tokyo
    volumes:
      - /home/main/analysis/rstudio:/home/rstudio

docker compose up -d

docker compose up -d --build

RSTUDIO_PASSWORD=your_password

# install_packages.R (for Docker build)

# Fix repository sources to official Bioconductor and CRAN cloud for reproducibility
repos <- BiocManager::repositories()
repos["CRAN"] <- "https://cloud.r-project.org"
options(repos = repos)

# 2) CRAN packages
cran_pkgs <- c(
  "pheatmap",
  "matrixStats",
  "tidyverse",
  "knitr",
  "kableExtra",
  "ggrepel",
  "pathview"
)

install.packages(cran_pkgs, dependencies = TRUE)

# 3) Bioconductor packages
bioc_pkgs <- c(
  "biomaRt",
  "DESeq2",
  "clusterProfiler",
  "org.Hs.eg.db",
  "enrichplot",
  "ReactomePA",
  "ggtree"
)

BiocManager::install(bioc_pkgs, ask = FALSE, update = FALSE)