Merge branch 'main' into add-google-cloud-sdk

Author: dpark01

AGENTS.md

@@ -428,6 +428,8 @@ The `docs.yml` workflow builds Sphinx documentation. Key points:
 
 **Explicit requests**: Include agent attribution in commits or elsewhere when explicitly requested by a human reviewer or contributor.
 
+**Avoid amending pushed commits**: Do not use `git commit --amend` after a commit has been pushed to the remote. Amending pushed commits causes problems for collaboration. Instead, create a new commit with the fix. Amending is fine for local commits that haven't been pushed yet.
+
 ### Test-Driven Development
 
 1. Write tests first

docker/Dockerfile.assemble

@@ -18,6 +18,10 @@ LABEL org.opencontainers.image.source="https://github.com/broadinstitute/viral-n
 # Enable conda environment activation for RUN commands
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
+# 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
+
 # Copy requirements and dependency installation script
 COPY docker/requirements/baseimage.txt docker/requirements/core.txt docker/requirements/assemble.txt /tmp/requirements/
 COPY docker/install-conda-deps.sh /tmp/
@@ -28,7 +32,6 @@ RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements
 
 # Copy source code (includes assembly module)
 COPY src/ /opt/viral-ngs/source/src/
-COPY scripts/ /opt/viral-ngs/source/scripts/
 COPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/
 
 # Install viral-ngs package

docker/Dockerfile.classify

@@ -30,7 +30,6 @@ RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements
 
 # Copy source code (includes classify module)
 COPY src/ /opt/viral-ngs/source/src/
-COPY scripts/ /opt/viral-ngs/source/scripts/
 COPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/
 
 # Install viral-ngs package

docker/Dockerfile.core

@@ -30,6 +30,9 @@ RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements
 COPY src/ /opt/viral-ngs/source/src/
 COPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/
 
+# Copy utility scripts
+COPY docker/scripts/ /opt/viral-ngs/scripts/
+
 # Install viral-ngs package
 # VERSION is passed from GitHub Actions via git describe
 WORKDIR /opt/viral-ngs/source

docker/Dockerfile.mega

@@ -31,7 +31,6 @@ RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements
 
 # Copy source code (includes all modules)
 COPY src/ /opt/viral-ngs/source/src/
-COPY scripts/ /opt/viral-ngs/source/scripts/
 COPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/
 
 # Install viral-ngs package

docker/Dockerfile.phylo

@@ -30,7 +30,6 @@ RUN /tmp/install-conda-deps.sh /tmp/requirements/baseimage.txt /tmp/requirements
 
 # Copy source code (includes phylo module)
 COPY src/ /opt/viral-ngs/source/src/
-COPY scripts/ /opt/viral-ngs/source/scripts/
 COPY pyproject.toml README.md LICENSE /opt/viral-ngs/source/
 
 # Install viral-ngs package