Updated pangolin v4.2 pangolin-data 1.18 scorpio v0.3.17 constellations v0.1.10

Author: fredericlemoine

pangolin/v4.2-v1.18-v0.3.17-v0.1.10/Dockerfile

@@ -0,0 +1,34 @@
+# Largely inspired from
+#  https://github.com/cov-lineages/pangolin/blob/master/Dockerfile
+
+FROM continuumio/miniconda3:4.9.2-alpine
+LABEL version="4.2" \
+      description="Docker image for Pangolin"
+
+ENV VERSION "v4.2"
+ENV DATAVERSION "v1.18"
+ENV SCORPIOVERSION "v0.3.17"
+ENV CONSTELLATIONVERSION "v0.1.10"
+
+# Install git for pangolin
+RUN apk update && \
+    apk add git bash
+
+RUN cd / \
+    && git clone https://github.com/cov-lineages/pangolin.git \
+    && cd pangolin \
+    && git checkout $VERSION \
+    && cd .. \
+    && sed -i 's/name: pangolin/name: base/' /pangolin/environment.yml \
+    && sed -i s=git+https://github.com/cov-lineages/pangolin-data.git=git+https://github.com/cov-lineages/pangolin-data.git@$DATAVERSION= /pangolin/environment.yml \
+    && sed -i s=git+https://github.com/cov-lineages/scorpio.git=git+https://github.com/cov-lineages/scorpio.git@$SCORPIOVERSION= /pangolin/environment.yml \
+    && sed -i s=git+https://github.com/cov-lineages/constellations.git=git+https://github.com/cov-lineages/constellations.git@$CONSTELLATIONVERSION= /pangolin/environment.yml \
+    && conda install mamba  -c conda-forge \
+    && mamba env update  --quiet -f /pangolin/environment.yml && conda clean -a \
+    && cd /pangolin \
+    && pip install . && rm -rf /root/.cache/pip \
+    && pangolin --version &> /pangolin-version.txt
+    
+WORKDIR /tmp/
+
+ENTRYPOINT ["pangolin"]