Merge branch 'main' of https://github.com/bigbio/quantms-containers

Author: ypriverol

relink-1.0.0/Dockerfile

@@ -1,43 +1,75 @@
-FROM python:3.12-slim
+FROM python:3.12-slim AS build
 
 # Metadata
 LABEL base_image="python:3.12-slim"
 LABEL version="1"
 LABEL software="relink"
 LABEL software.version="1.0.0"
-LABEL about.summary="Container for relink pipeline: xiSEARCH, xiFDR, and Python dependencies for crosslinking mass spectrometry analysis"
+LABEL about.summary="Container for relink pipeline: xiSEARCH, xiFDR, Scout, and Dotnet / Python dependencies for crosslinking mass spectrometry analysis"
 LABEL about.home="https://github.com/bigbio/relink"
 LABEL about.documentation="https://github.com/bigbio/relink"
 LABEL about.license="Apache-2.0"
 LABEL about.tags="Proteomics,Crosslinking,Mass Spectrometry"
 LABEL maintainer="Yasset Perez-Riverol <ypriverol@gmail.com>"
 
 ENV DEBIAN_FRONTEND=noninteractive
-ENV PYTHONUNBUFFERED=1
-ENV PYTHONDONTWRITEBYTECODE=1
 
-# Install Java runtime (required for xiSEARCH and xiFDR)
+# Build dependencies
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    openjdk-21-jre \
-    wget \
-    unzip \
-    build-essential \
-    libgomp1 \
-    procps \
-    && rm -rf /var/lib/apt/lists/*
+	wget \
+	unzip \
+	ca-certificates \
+	&& rm -rf /var/lib/apt/lists/* && \
+	wget https://packages.microsoft.com/config/debian/12/packages-microsoft-prod.deb \
+	-O packages-microsoft-prod.deb
 
-# Create directory for xiSEARCH
-RUN mkdir -p /opt/xisearch
-
-# Download and install xiSEARCH 1.8.11
-RUN wget --no-check-certificate \
+# Install xiSEARCH 1.8.11 and xiFDR
+RUN mkdir -p /opt/xisearch && wget -q \
     https://www.rappsilberlab.org/wp-content/uploads/2025/12/xiSEARCH_1.8.11.zip \
     -O /tmp/xiSEARCH.zip && \
     unzip /tmp/xiSEARCH.zip -d /opt/xisearch && \
     rm /tmp/xiSEARCH.zip && \
     cp /opt/xisearch/xiSEARCH_1.8.11/xiSEARCH.jar /opt/xisearch/xiSEARCH.jar && \
     cp /opt/xisearch/xiSEARCH_1.8.11/xiFDR-2.3.10.jar /opt/xisearch/xiFDR.jar
 
+# Install Scout 2.0.0
+RUN mkdir -p /opt/scout && wget -q \
+	https://github.com/diogobor/Scout/releases/download/2.0.0/Scout_Linux64.zip \
+	-O /tmp/Scout.zip && \
+	unzip /tmp/Scout.zip -d /opt/scout && \
+	rm /tmp/Scout.zip && \
+	mv /opt/scout/Scout_Linux64/* /opt/scout && \
+	rmdir /opt/scout/Scout_Linux64
+
+FROM python:3.12-slim AS runtime
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV PYTHONUNBUFFERED=1
+ENV PYTHONDONTWRITEBYTECODE=1
+
+# Copy necessary package for dotnet-runtime from build stage
+COPY --from=build packages-microsoft-prod.deb /tmp/packages-microsoft-prod.deb
+
+# Install Java runtime (required for xiSEARCH and xiFDR) Dotnet runtime, MPFR, and GMP (required for Scout)
+RUN dpkg -i /tmp/packages-microsoft-prod.deb && \
+	rm /tmp/packages-microsoft-prod.deb && \
+	apt-get --allow-insecure-repositories --allow-unauthenticated update && apt-get install --allow-unauthenticated -y --no-install-recommends \
+	dotnet-runtime-9.0 && \
+	apt-get install -y --no-install-recommends \
+	libmpfr6 \
+	libgmp10 \
+	openjdk-21-jre \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy xiSEARCH 1.8.11 and xiFDR from build stage
+COPY --from=build /opt/xisearch /opt/xisearch
+
+# Copy Scout 2.0.0 from build stage
+COPY --from=build /opt/scout /opt/scout 
+
+# Set necessary env for scout
+ENV MPFR_PATH=/usr/lib/x86_64-linux-gnu GMP_PATH=/usr/lib/x86_64-linux-gnu
+
 # Install Python packages for mass recalibration
 # Using versions from pycross requirements.txt (pyopenms version left open for pip to resolve)
 RUN pip install --no-cache-dir \
@@ -62,17 +94,21 @@ RUN pip install --no-cache-dir \
     six==1.17.0 \
     tzdata==2025.2
 
-# Clean up build tools (keep Java runtime)
-RUN apt-get remove -y wget unzip build-essential && \
-    apt-get autoremove -y && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
-
 # Set working directory
 WORKDIR /data/
 
 # Verify installation
-RUN java -jar /opt/xisearch/xiSEARCH.jar --help || echo "xiSEARCH installed" && \
+RUN java -jar /opt/xisearch/xiSEARCH.jar --help 1>/dev/null && echo "xiSEARCH installed" && \
     ls -lh /opt/xisearch/*.jar && \
+	set -e; \
+    test -s /opt/scout/Scout_Unix.dll; \
+    dotnet --info >/dev/null; \
+    test -e /usr/lib/x86_64-linux-gnu/libgmp.so.10; \
+    test -e /usr/lib/x86_64-linux-gnu/libmpfr.so.6; \
+    out="$(timeout 5s dotnet /opt/scout/Scout_Unix.dll 2>&1 || true)"; \
+    echo "$out" | head -n 20; \
+    echo "$out" | grep -qvE "It was not possible to find any compatible framework version|Could not execute because the specified command or file was not found|A fatal error was encountered" && \
+	echo "Scout installed" && \
+	ls -lh /opt/scout/Scout_Unix.dll && \
     python -c "import pyopenms; print(f'pyopenms {pyopenms.__version__}')" && \
     python -c "import polars; print(f'polars {polars.__version__}')"