DE-LIMP/Dockerfile.search at main · bsphinney/DE-LIMP · GitHub

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# =============================================================================
# Dockerfile.search — DE-LIMP with embedded DIA-NN for local searching
# =============================================================================
# Multi-stage build: copies DIA-NN from user's pre-built image into DE-LIMP.
# Requires: diann:2.0 image (build with build_diann_docker.sh first)
#
# Usage:
#   docker compose up          (recommended — uses docker-compose.yml)
#   docker build -f Dockerfile.search -t delimp-search .
# =============================================================================

# Stage 1: Get DIA-NN binaries from user's pre-built image
FROM diann:2.0 AS diann

# Stage 2: DE-LIMP app with DIA-NN embedded
FROM rocker/shiny:4.5.0

# 1. System dependencies (same as base Dockerfile + wget for .NET install)
RUN apt-get update && apt-get install -y \
    libcurl4-openssl-dev \
    libssl-dev \
    libxml2-dev \
    libfontconfig1-dev \
    libharfbuzz-dev \
    libfribidi-dev \
    libfreetype6-dev \
    libpng-dev \
    libtiff5-dev \
    libjpeg-dev \
    libcairo2-dev \
    libxt-dev \
    cmake \
    openssh-client \
    wget \
    && rm -rf /var/lib/apt/lists/*

# 2. CRAN packages
# Install arrow with full codec support (zstd needed for parquet files)
ENV LIBARROW_MINIMAL=false
RUN R -e "install.packages(c('bslib', 'readr', 'tibble', 'dplyr', 'tidyr', 'ggplot2', 'httr2', 'rhandsontable', 'DT', 'arrow', 'shinyjs', 'plotly', 'stringr', 'ggrepel', 'remotes', 'BiocManager', 'markdown', 'shinyFiles', 'jsonlite', 'processx', 'callr'), repos='https://cloud.r-project.org/')"

RUN R -e "install.packages(c('KSEAapp', 'ggseqlogo', 'ggdendro'), repos='https://cloud.r-project.org/')"
RUN R -e "install.packages(c('systemfonts', 'gdtools', 'Rcpp'), repos='https://cloud.r-project.org/')"
RUN R -e "install.packages(c('ggraph', 'graphlayouts', 'tidygraph', 'scatterpie', 'shadowtext', 'ggforce'), repos='https://cloud.r-project.org/')"

# Core Facility mode packages (SQLite, YAML, UUID, Quarto rendering)
RUN R -e "install.packages(c('DBI', 'RSQLite', 'yaml', 'uuid', 'quarto'), repos='https://cloud.r-project.org/')"

# 3. Bioconductor packages
RUN R -e "BiocManager::install(c('DOSE', 'GOSemSim', 'yulab.utils'), ask=FALSE, update=FALSE)"
RUN R -e "BiocManager::install(c('limma', 'limpa', 'ComplexHeatmap', 'AnnotationDbi', 'org.Hs.eg.db', 'org.Mm.eg.db', 'ggridges'), ask=FALSE, update=FALSE)"
RUN R -e "BiocManager::install(c('ggtree', 'ggtangle'), ask=FALSE, update=FALSE)"
RUN R -e "BiocManager::install(c('clusterProfiler', 'enrichplot'), ask=FALSE, update=FALSE)"

# MOFA2 + basilisk (Python env managed by basilisk for mofapy2)
RUN R -e "BiocManager::install(c('MOFA2', 'basilisk'), ask=FALSE, update=FALSE)"
# Pre-initialize basilisk env so first MOFA run doesn't need to download Python
RUN R -e "library(MOFA2); basilisk::basiliskStart(MOFA2:::mofa_env) |> basilisk::basiliskStop()" 2>/dev/null || true

# 4. Copy DIA-NN binaries + shared libraries from Stage 1
COPY --from=diann /opt/diann/ /opt/diann/
RUN chmod +x /opt/diann/diann-linux 2>/dev/null || true && \
    ln -sf /opt/diann/diann-linux /usr/local/bin/diann
ENV LD_LIBRARY_PATH="/opt/diann:${LD_LIBRARY_PATH}"

# 5. Install .NET SDK 8.0 (DIA-NN needs this for Thermo .raw file reading)
RUN wget -q https://dot.net/v1/dotnet-install.sh -O /tmp/dotnet-install.sh && \
    chmod +x /tmp/dotnet-install.sh && \
    /tmp/dotnet-install.sh --channel 8.0 --install-dir /usr/share/dotnet && \
    ln -s /usr/share/dotnet/dotnet /usr/bin/dotnet && \
    rm /tmp/dotnet-install.sh
ENV DOTNET_ROOT=/usr/share/dotnet
ENV PATH="$PATH:/usr/share/dotnet"

# 6. Copy DE-LIMP app
COPY app.R /srv/shiny-server/app.R
COPY R/ /srv/shiny-server/R/
COPY contaminants/ /srv/shiny-server/contaminants/
COPY VERSION /srv/shiny-server/VERSION
COPY stats/ /srv/shiny-server/stats/

# 7. Create data mount point with subdirectories
RUN mkdir -p /data/raw /data/fasta /data/output

# 8. Environment: signal to app.R that we're in Docker with local DIA-NN
ENV DELIMP_DATA_DIR=/data

EXPOSE 3838

# Entrypoint: fix SSH key permissions (Windows mounts give 777 which SSH rejects)
# then start the Shiny app
CMD ["bash", "-c", "\
  if [ -d /data/ssh ]; then \
    mkdir -p /tmp/.ssh && \
    cp /data/ssh/* /tmp/.ssh/ 2>/dev/null; \
    chmod 600 /tmp/.ssh/* 2>/dev/null; \
    export DELIMP_SSH_KEY=$(ls /tmp/.ssh/* 2>/dev/null | grep -v gitkeep | head -1); \
  fi && \
  R -e \"shiny::runApp('/srv/shiny-server/', host='0.0.0.0', port=3838)\""]