relink container added

Author: ypriverol

Dockerfile

@@ -0,0 +1,78 @@
+FROM python:3.12-slim
+
+# 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.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)
+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/*
+
+# Create directory for xiSEARCH
+RUN mkdir -p /opt/xisearch
+
+# Download and install xiSEARCH 1.8.11
+RUN wget --no-check-certificate \
+    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 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 \
+    pyopenms \
+    polars==1.35.1 \
+    polars-runtime-32==1.35.1 \
+    matplotlib==3.10.7 \
+    seaborn==0.13.2 \
+    numpy==2.3.4 \
+    pandas==2.3.3 \
+    contourpy==1.3.3 \
+    cycler==0.12.1 \
+    fonttools==4.60.1 \
+    kiwisolver==1.4.9 \
+    packaging==25.0 \
+    pillow==12.0.0 \
+    pyparsing==3.2.5 \
+    python-dateutil==2.9.0.post0 \
+    pytz==2025.2 \
+    psutil==7.1.3 \
+    pyarrow==22.0.0 \
+    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" && \
+    ls -lh /opt/xisearch/*.jar && \
+    python -c "import pyopenms; print(f'pyopenms {pyopenms.__version__}')" && \
+    python -c "import polars; print(f'polars {polars.__version__}')"