Extend nextstrain/base with mamba

Author: victorlin

Dockerfile

@@ -1,21 +1,13 @@
-# Stage 1: Create conda environment
-FROM mambaorg/micromamba:2.0.8 AS conda-builder
-
-COPY --chown=$MAMBA_USER:$MAMBA_USER env.yaml /tmp/env.yaml
-RUN micromamba create -y -n env -f /tmp/env.yaml && \
-    micromamba clean --all --yes
-
-# Stage 2: Build final image extending nextstrain/base
 FROM nextstrain/base:latest
 
-# Copy the conda environment from the previous stage
-COPY --from=conda-builder /opt/conda/envs/env /opt/conda/envs/env
-
-# Add environment bin to PATH
-# Notes:
-# 1. This makes the conda-installed tools available but isn't equivalent to
-#    activating the environment since micromamba itself is not part of the final
-#    image.
-# 2. nextstrain/base puts programs in /usr/local/bin, and those should take
-#    precedence.
-ENV PATH="/usr/local/bin:/opt/conda/envs/env/bin:$PATH"
+# Install micromamba and set up root
+# FIXME: check permissions
+RUN curl -L micro.mamba.pm/install.sh | bash && \
+    ln -s micromamba /nextstrain/.local/bin/mamba && \
+    mkdir -p /nextstrain/micromamba && \
+    chmod -R 777 /nextstrain/micromamba
+ENV MAMBA_EXE=/nextstrain/.local/bin/micromamba
+ENV MAMBA_ROOT_PREFIX=/nextstrain/micromamba
+
+# Make mamba/micromamba available in PATH
+ENV PATH="/nextstrain/.local/bin:$MAMBA_ROOT_PREFIX/bin:$PATH"