From dec1b39ecf0a460f27a9be324764f17df1ad9026 Mon Sep 17 00:00:00 2001 From: Guoying Qi Date: Wed, 5 Feb 2025 20:30:35 +0000 Subject: [PATCH] update workflow to build Docker from current checkout --- .github/workflows/docker-publish.yml | 3 ++- src/docker/Dockerfile | 10 ++++------ 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml index b428414..b6c9ea7 100644 --- a/.github/workflows/docker-publish.yml +++ b/.github/workflows/docker-publish.yml @@ -50,7 +50,8 @@ jobs: id: build-and-push uses: docker/build-push-action@v6 with: - context: src/docker + context: . + file: ./src/docker/Dockerfile tags: ${{ steps.meta.outputs.tags }} push: true labels: ${{ steps.meta.outputs.labels }} diff --git a/src/docker/Dockerfile b/src/docker/Dockerfile index 11adceb..db1153d 100644 --- a/src/docker/Dockerfile +++ b/src/docker/Dockerfile @@ -8,16 +8,14 @@ RUN mamba create -q -y -c conda-forge -c bioconda -n snakemake snakemake=6.10.0 RUN echo "source activate snakemake" > ~/.bashrc ENV PATH=/opt/conda/envs/snakemake/bin:$PATH -WORKDIR /Marker_pipeline - RUN apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get install -y \ locales \ libtbb2 \ unzip \ && rm -rf /var/lib/apt/lists/* -RUN git clone https://github.com/CobiontID/Marker-pipeline.git . && \ - sed -i 's/dependencies:/dependencies:\n - python=3.9/' envs/hifiasm.yaml && \ - sed -i '/- defaults/d' envs/hifiasm.yaml +WORKDIR /Marker_pipeline + +COPY . . -RUN snakemake -p --cores 1 --use-conda --conda-prefix /opt/conda/envs --conda-create-envs-only -s /MarkerScanPipeline/create-envs.smk +RUN snakemake -p --cores 1 --use-conda --conda-prefix /opt/conda/envs --conda-create-envs-only -s create-envs.smk