initial Dockerfile

Dockerfile

@@ -0,0 +1,35 @@
+FROM continuumio/miniconda3
+RUN apt-get update
+
+#NOTE: I don't know whether the --fix-broken is actually needed
+RUN apt-get -y install gcc libdeflate-dev libcurl4-openssl-dev --fix-broken
+
+WORKDIR /cgr-dev
+
+RUN mkdir GwasQcPipeline
+
+WORKDIR /cgr-dev/GwasQcPipeline
+
+ENV PYTHONPATH=${PYTHONPATH}:${PWD}
+
+COPY . .
+
+#NOTE: I don't think we need a special env inside the container
+#RUN conda create -n cgr-dev python=3.8 poetry make -y
+#RUN echo "conda activate cgr-dev" >> ~/.bashrc
+#RUN conda init bash && conda activate cgr-dev
+
+RUN conda install poetry make -y
+RUN conda install -c conda-forge mamba
+RUN poetry config virtualenvs.create false
+RUN poetry install --without dev
+
+#NOTE: Aren't these also not needed? Unless somehow the docs adds the help for the CLI...
+#RUN make -C docs html
+#RUN pytest -v
+#RUN pre-commit install
+#RUN pre-commit run
+
+WORKDIR /cgr-dev
+
+ENTRYPOINT [ "cgr" ]

pyproject.toml

@@ -23,7 +23,7 @@ python = "^3.8"
 typer = "^0.3.2"
 pandas = "^1.2.4"
 snakemake = "~6.15.5"
-pysam = "^0.16.0"
+pysam = "^0.21.0"
 ryd = "^0.4.1"
 pydantic = "^1.8.2"
 networkx = "^2.5"