Fix container build

Dockerfile

@@ -1,10 +1,12 @@
+# syntax=docker/dockerfile:1.4
+
 FROM ubuntu:rolling as base
 
 ENV LC_ALL="C.UTF-8" \
     LANG="C.UTF-8" \
     DEBIAN_FRONTEND="noninteractive" \
     DEBCONF_NOWARNINGS="yes" \
-    PATH="/usr/local/mambaforge/bin:$PATH"
+    PATH="/opt/conda/bin:$PATH"
 
 RUN apt-get update && \
     apt-get install --yes --no-install-recommends \
@@ -26,7 +28,7 @@ FROM base as conda
 RUN curl --silent --show-error --location \
     "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" \
     --output "conda.sh" &&  \
-    bash conda.sh -b -p /usr/local/mambaforge && \
+    bash conda.sh -b -p /opt/conda && \
     rm conda.sh && \
     conda config --system --append channels "bioconda" && \
     conda config --system --prepend channels "conda-forge/label/cython_dev" && \
@@ -40,53 +42,49 @@ FROM conda as builder
 RUN mamba install --yes "boa" "conda-verify"
 COPY recipes/conda_build_config.yaml /root/conda_build_config.yaml
 
-COPY recipes/bolt-lmm bolt-lmm
-RUN conda mambabuild --no-anaconda-upload "bolt-lmm" && \
-    conda build purge
-
-COPY recipes/dosage-convertor dosage-convertor
-RUN conda mambabuild --no-anaconda-upload "dosage-convertor" && \
+RUN --mount=source=recipes/bolt-lmm,target=/bolt-lmm \
+    conda mambabuild --no-anaconda-upload "bolt-lmm" && \
     conda build purge
 
-COPY recipes/gcta gcta
-RUN conda mambabuild --no-anaconda-upload "gcta" && \
+RUN --mount=source=recipes/dosage-convertor,target=/dosage-convertor \
+    conda mambabuild --no-anaconda-upload "dosage-convertor" && \
     conda build purge
 
-COPY recipes/qctool qctool
-RUN conda mambabuild --no-anaconda-upload "qctool" && \
+RUN --mount=source=recipes/gcta,target=/gcta \
+    conda mambabuild --no-anaconda-upload "gcta" && \
     conda build purge
 
-COPY recipes/raremetal raremetal
-RUN conda mambabuild --no-anaconda-upload "raremetal" && \
+RUN --mount=source=recipes/qctool,target=/qctool \
+    conda mambabuild --no-anaconda-upload "qctool" && \
     conda build purge
 
-COPY recipes/r-gmmat r-gmmat
-RUN conda mambabuild --no-anaconda-upload "r-gmmat" && \
+RUN --mount=source=recipes/raremetal,target=/raremetal \
+    conda mambabuild --no-anaconda-upload "raremetal" && \
     conda build purge
 
-COPY recipes/r-saige r-saige
-RUN conda mambabuild --no-anaconda-upload "r-saige" && \
+RUN --mount=source=recipes/r-gmmat,target=/r-gmmat \
+    conda mambabuild --no-anaconda-upload "r-gmmat" && \
     conda build purge
 
-COPY recipes/python-blosc2 python-blosc2
-RUN conda mambabuild --no-anaconda-upload "python-blosc2" && \
+RUN --mount=source=recipes/r-saige,target=/r-saige \
+    conda mambabuild --no-anaconda-upload "r-saige" && \
     conda build purge
 
-COPY src/gwas gwas-protocol/src/gwas
-COPY recipes/gwas gwas-protocol/recipes/gwas
-# copy .git folder too for setuptools_scm
-COPY .git gwas-protocol/.git
-RUN cd gwas-protocol/recipes && \
+# mount .git folder too for setuptools_scm
+RUN --mount=source=recipes/gwas,target=/gwas-protocol/recipes/gwas \
+    --mount=source=src/gwas,target=/gwas-protocol/src/gwas \
+    --mount=source=.git,target=/gwas-protocol/.git \
+    cd gwas-protocol/recipes && \
     conda mambabuild --no-anaconda-upload "gwas" && \
     conda build purge
 
-RUN conda index /usr/local/mambaforge/conda-bld
+RUN conda index /opt/conda/conda-bld
 
 # Install packages
 # ================
 FROM conda as install
 
-COPY --from=builder /usr/local/mambaforge/conda-bld /usr/local/mambaforge/conda-bld
+COPY --from=builder /opt/conda/conda-bld /opt/conda/conda-bld
 RUN mamba install --yes --use-local \
     "python=3.11" \
     "pytorch=*=cpu*" \
@@ -110,14 +108,14 @@ RUN mamba install --yes --use-local \
     "r-gmmat" \
     "r-saige" && \
     sync && \
-    rm -rf /usr/local/mambaforge/conda-bld && \
+    rm -rf /opt/conda/conda-bld && \
     mamba clean --yes --all --force-pkgs-dirs && \
     sync && \
-    find /usr/local/mambaforge/ -follow -type f -name "*.a" -delete && \
+    find /opt/conda/ -follow -type f -name "*.a" -delete && \
     sync
 
 
 # Final
 # =====
 FROM base
-COPY --from=install /usr/local/mambaforge /usr/local/mambaforge
+COPY --from=install /opt/conda /opt/conda

recipes/conda_build_config.yaml

@@ -4,3 +4,5 @@ numpy:
   - 1.24
 zlib:
   - 1.2
+pin_run_as_build:
+  python: x.x

recipes/gwas/meta.yaml

@@ -9,24 +9,24 @@ requirements:
   build:
     - {{ compiler("c") }}
     - {{ compiler("cxx") }}
-    - {{ compiler('rust') }}
+    - {{ compiler("rust") }}
     - "sysroot_linux-64>=2.17"
   host:
+    - python
     - "cython>=3b1"
     - mkl
     - mkl-include
     - "numpy>=1.22"
-    - "python>=3.11"
+    - "python"
     - pip
     - "setuptools>=62"
     - "setuptools_scm>=6.2"
     - "setuptools-rust"
     - wheel
     - zlib
   run:
-    - mkl
+    - python
     # Python dependencies
-    - "python=3.11"
     - "numpy>=1.22"
     - scipy
     - pandas
@@ -40,6 +40,7 @@ requirements:
     - pyyaml
     - more-itertools
     - typing_extensions
+    - mkl
     # Compression tools
     - zstd
     - htslib