Skip to content

Added Scout and dependencies to Relink Dockerfile #4

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jBeale23 wants to merge 12 commits into
base: main
Choose a base branch
from
Open

Added Scout and dependencies to Relink Dockerfile #4

Changes from 1 commit
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
812ddf8
Added Scout and dependencies to Relink Dockerfile
jBeale23 Jan 9, 2026
cf5a767
Update relink-1.0.0/Dockerfile
jBeale23 Jan 12, 2026
54861d4
Update relink-1.0.0/Dockerfile
jBeale23 Jan 12, 2026
21b98c7
Update relink-1.0.0/Dockerfile
jBeale23 Jan 12, 2026
2b117e8
Update relink-1.0.0/Dockerfile
jBeale23 Jan 12, 2026
e948045
Changed scout dependencies to use the smaller libmpfr and libgmp rath…
jBeale23 Jan 12, 2026
f46cc69
Updated dotnet dependency to use Debian 12 repositories
jBeale23 Jan 12, 2026
bb02cc5
Conversion to multi-stage build
jBeale23 Jan 12, 2026
3be938b
Removed unnecessary build cleanup from build stage
jBeale23 Jan 12, 2026
80cf269
Updated MPFR and GMP path environmental variables for consistency wit…
jBeale23 Jan 12, 2026
7fa8102
Improved robustness of Scout validation as per qodo-code-review bot s…
jBeale23 Jan 12, 2026
f1112f2
Updated PPA installation to explicitly use /tmp/
jBeale23 Jan 12, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
34 changes: 31 additions & 3 deletions relink-1.0.0/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ 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"
Expand All @@ -26,6 +26,17 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
procps \
&& rm -rf /var/lib/apt/lists/*

# Install Dotnet runtime, MPFR, and GMP (required for Scout)
RUN wget https://packages.microsoft.com/config/debian/13/packages-microsoft-prod.deb \
-O packages-microsoft-prod.deb && \
dpkg -i packages-microsoft-prod.deb && \
rm packages-microsoft-prod.deb && \
apt-get update && apt-get install -y --no-install-recommends \
dotnet-runtime-9.0 \
libmpfr-dev \
libgmp-dev \
&& rm -rf /var/lib/apt/lists/*

# Create directory for xiSEARCH
RUN mkdir -p /opt/xisearch

Expand All @@ -38,6 +49,21 @@ RUN wget --no-check-certificate \
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

# Create directory for Scout
RUN mkdir -p /opt/scout

# Download and install Scout 2.0.0
RUN wget --no-check-certificate \
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

# 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 \
Expand All @@ -62,7 +88,7 @@ RUN pip install --no-cache-dir \
six==1.17.0 \
tzdata==2025.2

# Clean up build tools (keep Java runtime)
# Clean up build tools (keep Dotnet, MPFR, GMP, and Java runtime)
RUN apt-get remove -y wget unzip build-essential && \
apt-get autoremove -y && \
apt-get clean && \
Expand All @@ -72,7 +98,9 @@ RUN apt-get remove -y wget unzip build-essential && \
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 && \
dotnet /opt/scout/Scout_Unix.dll | grep -q "Scout - v. 2.0.0" && 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__}')"
Loading