chore: use tools from virtool/tools

Author: igboyes

.mise.toml

@@ -21,11 +21,6 @@ description = "Interactive shell in test container"
 depends = ["test-setup"]
 run = "./scripts/test-docker.sh --shell"
 
-[tasks.test-rust]
-description = "Run Rust tests only"
-depends = ["test-setup"]
-run = "docker run --rm -v \"$(pwd):/app\" -w /app pathoscope:dev cargo test"
-
 [tasks.test-clean]
 description = "Clean up test Docker resources"
 run = "docker rmi pathoscope:dev 2>/dev/null || true"

Dockerfile

@@ -1,27 +1,9 @@
-FROM debian:bookworm AS bowtie2
-WORKDIR /build
-RUN apt-get update && apt-get install -y build-essential cmake wget zlib1g-dev
-RUN wget https://github.com/BenLangmead/bowtie2/archive/refs/tags/v2.5.4.tar.gz
-RUN tar -xvf v2.5.4.tar.gz
-WORKDIR bowtie2-2.5.4
-RUN make
-RUN mkdir /build/bowtie2
-RUN cp bowtie2* /build/bowtie2/
-
-FROM debian:bookworm AS pigz
-WORKDIR /build
-RUN apt-get update && apt-get install -y gcc make wget zlib1g-dev
-RUN wget https://zlib.net/pigz/pigz-2.8.tar.gz && \
-    tar -xzvf pigz-2.8.tar.gz && \
-    cd pigz-2.8 && \
-    make
-
 FROM python:3.12.3-bookworm AS deps
 WORKDIR /app
-COPY --from=bowtie2 /build/bowtie2/* /usr/local/bin/
-COPY --from=ghcr.io/virtool/workflow-tools:2.0.1 /opt/fastqc /opt/fastqc
-COPY --from=ghcr.io/virtool/workflow-tools:2.0.1 /opt/hmmer /opt/hmmer
-COPY --from=ghcr.io/virtool/workflow-tools:2.0.1 /usr/local/bin/pigz /usr/local/bin/
+COPY --from=ghcr.io/virtool/tools:1.0.0 /tools/bowtie2/2.5.4/bowtie* /usr/local/bin/
+COPY --from=ghcr.io/virtool/tools:1.0.0 /tools/hmmer/3.2.1 /opt/hmmer
+COPY --from=ghcr.io/virtool/tools:1.0.0 /tools/fastqc/0.11.9 /opt/fastqc
+COPY --from=ghcr.io/virtool/tools:1.0.0 /tools/pigz/2.8/pigz /usr/local/bin/
 RUN apt-get update && \
     apt-get install -y --no-install-recommends default-jre && \
     rm -rf /var/lib/apt/lists/* && \

scripts/test-docker.sh

@@ -74,6 +74,6 @@ case $MODE in
             -v "$(pwd):/app" \
             -w /app \
             "$IMAGE_NAME" \
-            bash -c "echo 'Running Rust tests...' && cargo test && echo 'Running Python tests...' && poetry install --no-root && poetry run maturin develop --release && poetry run pytest$PYTEST_ARGS"
+            bash -c "echo 'Running Python tests...' && poetry install --no-root && poetry run maturin develop --release && poetry run pytest$PYTEST_ARGS"
         ;;
 esac