sequintools 0.11.1

A suite of tools for manipulating and reporting on NGS data that has sequins added to the sample.
Documentation 
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# Use multi-stage builds to reduce the size of the final image
# https://docs.docker.com/build/building/multi-stage/#use-multi-stage-builds

# Stage 1: Build the rust app
FROM mcr.microsoft.com/devcontainers/rust:2-1-bookworm AS builder

RUN apt-get update && apt-get install -y --no-install-recommends \
  cmake=3.25.1-1 \
  clang=1:14.0-55.7~deb12u1 \
  && rm -rf /var/lib/apt/lists/*

WORKDIR /usr/sequins

# Accept version string from build context (fallback handled in build.rs)
ARG SEQUINTOOLS_GIT_VERSION
ENV SEQUINTOOLS_GIT_VERSION=${SEQUINTOOLS_GIT_VERSION}

# Copy the Cargo.toml and Cargo.lock files first
COPY ./Cargo.toml ./Cargo.toml
COPY ./Cargo.lock ./Cargo.lock
COPY ./build.rs ./build.rs
COPY ./src ./src

# Build with locked deps; build.rs will embed version using SEQUINTOOLS_GIT_VERSION if provided
RUN cargo build --locked --release

# Stage 2: Create final Docker image with debian-slim.
FROM debian:13.3-slim

# Augment debian-slim with tools needed to run in nextflow
RUN apt-get update && \
  apt-get --no-install-recommends install -y \
  procps=2:4.0.4-9 \
  samtools=1.21-1 && \
  apt-get clean && \
  apt-get autoremove -y && \
  rm -rf /var/lib/apt/lists/*

# Copy app and test data.
COPY --from=builder /usr/sequins/target/release/sequintools /usr/local/bin/sequintools

CMD [ "sequintools" ]