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Fix CVE-2026-41316: upgrade Ruby erb gem to >=6.0.4 #1060

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Merged
dpark01 merged 1 commit into from
Apr 27, 2026
Merged

Fix CVE-2026-41316: upgrade Ruby erb gem to >=6.0.4 #1060

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7 changes: 6 additions & 1 deletion docker/Dockerfile.assemble
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Expand Up @@ -20,7 +20,7 @@

# Workaround: add sequip lib directory to PERL5LIB
# NOTE: sequip version here must match the version in requirements/assemble.txt
ENV PERL5LIB=$PERL5LIB:/opt/conda/share/sequip-0.11/lib

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GitHub Actions / build-assemble-amd64

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$PERL5LIB'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/

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GitHub Actions / build-assemble-amd64

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$PERL5LIB'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/

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GitHub Actions / build-assemble-arm64

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$PERL5LIB'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/

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GitHub Actions / build-assemble-arm64

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$PERL5LIB'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/

# Copy requirements and dependency installation script
COPY docker/requirements/baseimage.txt docker/requirements/core.txt docker/requirements/assemble.txt docker/requirements/assemble-x86.txt /tmp/requirements/
Expand All @@ -32,12 +32,17 @@
# - mafft's dash_client: Go 1.22.1 binary with Go stdlib CVEs; we never use --dash mode
# - Ruby json gem: mummer4/sequip pull in Ruby (via yaggo), whose bundled json gem
# has CVE-2026-33210; remove the old default gem and install patched version (>=2.19.2)
# - Ruby erb gem: same chain (mummer4 → yaggo → ruby), CVE-2026-41316 (Marshal
# deserialization bypass via ERB#def_module); remove default gem and install >=6.0.4
RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/assemble.txt \
--x86-only:/tmp/requirements/assemble-x86.txt && \
rm -f /opt/conda/libexec/mafft/dash_client && \
find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \
gem install json --version '>=2.19.2' --no-document
gem install json --version '>=2.19.2' --no-document && \
find /opt/conda/lib/ruby -maxdepth 3 -name 'erb*' -exec rm -rf {} + && \
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/erb-*.gemspec && \
gem install erb --version '>=6.0.4' --no-document

# Copy source code (includes assembly module)
COPY src/ /opt/viral-ngs/source/src/
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7 changes: 6 additions & 1 deletion docker/Dockerfile.mega
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Expand Up @@ -29,14 +29,19 @@ COPY docker/install-conda-deps.sh /tmp/
# - mafft's dash_client: Go 1.22.1 binary with Go stdlib CVEs; we never use --dash mode
# - Ruby json gem: mummer4 → yaggo → Ruby, whose bundled json gem has CVE-2026-33210;
# remove the old default gem and install patched version (>=2.19.2)
# - Ruby erb gem: same chain (mummer4 → yaggo → ruby), CVE-2026-41316 (Marshal
# deserialization bypass via ERB#def_module); remove default gem and install >=6.0.4
RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/assemble.txt /tmp/requirements/classify.txt /tmp/requirements/phylo.txt \
--x86-only:/tmp/requirements/assemble-x86.txt \
--x86-only:/tmp/requirements/classify-x86.txt \
--x86-only:/tmp/requirements/phylo-x86.txt && \
rm -f /opt/conda/libexec/mafft/dash_client && \
find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \
gem install json --version '>=2.19.2' --no-document
gem install json --version '>=2.19.2' --no-document && \
find /opt/conda/lib/ruby -maxdepth 3 -name 'erb*' -exec rm -rf {} + && \
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/erb-*.gemspec && \
gem install erb --version '>=6.0.4' --no-document

# Copy source code (includes all modules)
COPY src/ /opt/viral-ngs/source/src/
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7 changes: 6 additions & 1 deletion docker/Dockerfile.phylo
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Expand Up @@ -29,12 +29,17 @@ COPY docker/install-conda-deps.sh /tmp/
# - mafft's dash_client: Go 1.22.1 binary with Go stdlib CVEs; we never use --dash mode
# - Ruby json gem: mummer4 pulls in yaggo → Ruby, whose bundled json gem has
# CVE-2026-33210; remove the old default gem and install patched version (>=2.19.2)
# - Ruby erb gem: same chain (mummer4 → yaggo → ruby), CVE-2026-41316 (Marshal
# deserialization bypass via ERB#def_module); remove default gem and install >=6.0.4
RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements/core.txt /tmp/requirements/phylo.txt \
--x86-only:/tmp/requirements/phylo-x86.txt && \
rm -f /opt/conda/libexec/mafft/dash_client && \
find /opt/conda/lib/ruby -maxdepth 3 -name 'json*' -not -path '*/psych/*' -exec rm -rf {} + && \
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/json-*.gemspec && \
gem install json --version '>=2.19.2' --no-document
gem install json --version '>=2.19.2' --no-document && \
find /opt/conda/lib/ruby -maxdepth 3 -name 'erb*' -exec rm -rf {} + && \
rm -f /opt/conda/lib/ruby/gems/*/specifications/default/erb-*.gemspec && \
gem install erb --version '>=6.0.4' --no-document

# Copy source code (includes phylo module)
COPY src/ /opt/viral-ngs/source/src/
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