diff --git a/Dockerfile b/Dockerfile index d7e7e19..b732444 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,8 +5,7 @@ FROM ubuntu:rolling as base ENV LC_ALL="C.UTF-8" \ LANG="C.UTF-8" \ DEBIAN_FRONTEND="noninteractive" \ - DEBCONF_NOWARNINGS="yes" \ - PATH="/opt/conda/bin:$PATH" + DEBCONF_NOWARNINGS="yes" RUN apt-get update && \ apt-get install --yes --no-install-recommends \ @@ -25,6 +24,7 @@ RUN apt-get update && \ # ============= FROM base as conda +ENV PATH="/opt/conda/bin:$PATH" RUN curl --silent --show-error --location \ "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" \ --output "conda.sh" && \ @@ -38,7 +38,6 @@ RUN curl --silent --show-error --location \ # Build packages # ============== FROM conda as builder - RUN mamba install --yes "boa" "conda-verify" COPY recipes/conda_build_config.yaml /root/conda_build_config.yaml @@ -112,12 +111,15 @@ RUN mamba install --yes --use-local \ "r-saige" && \ sync && \ rm -rf /opt/conda/conda-bld && \ - mamba clean --yes --all --force-pkgs-dirs && \ - sync && \ - find /opt/conda/ -follow -type f -name "*.a" -delete && \ - sync + mamba clean --yes --all --force-pkgs-dirs # Final # ===== FROM base COPY --from=install /opt/conda /opt/conda + +# Ensure that we can link to libraries installed via conda +ENV PATH="/opt/conda/bin:$PATH" \ + CPATH="/opt/conda/include:${CPATH}" +RUN echo /opt/conda/lib > /etc/ld.so.conf.d/conda.conf && \ + ldconfig diff --git a/recipes/conda_build_config.yaml b/recipes/conda_build_config.yaml index 3671e4b..16c3210 100644 --- a/recipes/conda_build_config.yaml +++ b/recipes/conda_build_config.yaml @@ -6,3 +6,5 @@ zlib: - 1.2 pin_run_as_build: python: x.x +gcc_version: + - 13.2.0 diff --git a/src/gwas/src/gwas/vcf/_read.cpp b/src/gwas/src/gwas/vcf/_read.cpp index 5adb471..6232892 100644 --- a/src/gwas/src/gwas/vcf/_read.cpp +++ b/src/gwas/src/gwas/vcf/_read.cpp @@ -77,7 +77,6 @@ struct RingBuffer { const ssize_t bytes_read = read(file_descriptor, data_.data() + actual_write_index, read_size); if (bytes_read < 0) { - // std::cerr << "Error reading from file descriptor" << std::endl; PyErr_SetString(PyExc_IOError, "Error reading from file descriptor"); throw error_already_set(); }