Move dependencies to environment.yaml

Dockerfile

@@ -6,31 +6,9 @@ COPY --chown=$MAMBA_USER:$MAMBA_USER dist/*.whl /tmp/
 WORKDIR /app
 
 RUN micromamba install -y -n base -f /tmp/environment.yml && \
-    micromamba install -c conda-forge -n base gcc gxx_impl_linux-64 gxx_linux-64 binutils_impl_linux-64 && \
-    micromamba install -c conda-forge -n base binutils && \
     micromamba clean --all --yes
 
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 RUN WHEEL=$(ls /tmp/*.whl) && pip install ${WHEEL}
 
 RUN pip install petasus
-
-# FROM mambaorg/micromamba:latest
-# MAINTAINER William E Fondrie <[email protected]>
-# COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
-# COPY --chown=$MAMBA_USER:$MAMBA_USER dist/*.whl /tmp/
-
-# WORKDIR /app
-
-# RUN micromamba install -y -n base -f /tmp/environment.yml && \
-#     micromamba install -c conda-forge -n base gcc gxx_impl_linux-64 gxx_linux-64 binutils_impl_linux-64 && \
-#     micromamba install -c conda-forge -n base binutils && \
-#     micromamba clean --all --yes
-
-# ARG MAMBA_DOCKERFILE_ACTIVATE=1
-# RUN WHEEL=$(ls /tmp/*.whl) && pip install ${WHEEL}
-
-# RUN echo "conda activate petasus" >> ~/.bashrc
-# SHELL ["/bin/bash", "--login", "-c"]
-
-# RUN pip install git+https://github.com/TalusBio/petasus

environment.yml

@@ -13,10 +13,17 @@ dependencies:
   - pyteomics
   - pip
   - wheel
-  - procps-ng
   - git
   - spectrum_utils
   - pyarrow
   - polars
   - psims
   - hdf5plugin>=3.10.0
+
+  # system tools:
+  - procps-ng
+  - gcc
+  - gxx_impl_linux-64
+  - gxx_linux-64
+  - binutils_impl_linux-64
+  - binutils