Merge pull request #58 from alneberg/johannes_test

Adapt Dockerfile for arm64 and some requirements changes

Dockerfile

@@ -5,12 +5,47 @@ LABEL author="Remi-Andre Olsen" \
       maintainer="[email protected]"
 
 USER root
+
+# Check for arm64 architecture to install minimap2
+ARG TARGETARCH
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      # Install compliation tools for minimap2
+      apt-get update;\
+      apt-get install -y curl build-essential libz-dev;\
+    fi
+
+ENV MINIMAP_VERSION=2.26
+
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      # Download minimap2
+      curl -L https://github.com/lh3/minimap2/archive/refs/tags/v${MINIMAP_VERSION}.tar.gz | tar -zxvf - ;\
+    fi
+
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      # Compile minimap2
+      cd minimap2-${MINIMAP_VERSION};\
+      make arm_neon=1 aarch64=1; \
+      # Add to path
+      mv minimap2 /usr/local/bin/;\
+    fi
+
 COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /
-RUN micromamba env create -n anglerfish && micromamba install -y -n anglerfish -f /environment.yml && micromamba clean --all --yes 
-ENV PATH /opt/conda/envs/anglerfish/bin:$PATH
+COPY --chown=$MAMBA_USER:$MAMBA_USER requirements.txt /
+
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      grep -v 'minimap2' /environment.yml > /environment.tmp.yml ;\
+    else \
+      cp /environment.yml /environment.tmp.yml ;\
+    fi ;\
+    chown $MAMBA_USER:$MAMBA_USER /environment.tmp.yml
 
 # Add source files to the container
 ADD . /usr/src/anglerfish
 WORKDIR /usr/src/anglerfish
-RUN eval "$(micromamba shell hook --shell bash)" && micromamba activate anglerfish && python -m pip install .[dev]
+
+# Activate the environment
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+RUN micromamba install -y -f /environment.tmp.yml && micromamba clean --all --yes
+
+RUN eval "$(micromamba shell hook --shell bash)" && python -m pip install .[dev]
 USER $MAMBA_USER

environment.yml

@@ -4,10 +4,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::biopython=1.79
-  - conda-forge::python-levenshtein=0.23.0
-  - conda-forge::numpy>=1.22.0
-  - bioconda::minimap2=2.20
-  - conda-forge::pyyaml=6.0
+  - bioconda::minimap2=2.26
+  - pip
+  - pip:
+      - -r requirements.txt
   - conda-forge::pre-commit
   - conda-forge::prettier

requirements.txt

@@ -0,0 +1,4 @@
+numpy==1.26.3
+biopython==1.83
+levenshtein==0.23.0
+pyyaml==6.0.1

setup.py

@@ -32,12 +32,8 @@
     python_requires=">=3.10",
     packages=find_packages(),
     package_data={"": ["config/adaptors.yaml"]},
-    install_requires=[
-        "python-levenshtein==0.23.0",
-        "biopython==1.79",
-        "numpy>=1.22.0",
-        "pyyaml==6.0",
-    ],
+    # Read requirements.txt
+    install_requires=[x.strip() for x in open("requirements.txt").readlines()],
     extras_require={"dev": ["ruff", "mypy", "editorconfig-checker"]},
     entry_points={
         "console_scripts": [