Replace alpine in MMseqs2 Dockerfile with debian:stable-slim

Dockerfile

@@ -1,58 +1,63 @@
 ARG NAMESPACE=
-FROM alpine:3.7 as qemu-downloader
+FROM debian:stable-slim as qemu-downloader
 ARG NAMESPACE
-RUN apk add --no-cache wget && \
-  if [[ "$NAMESPACE" == "arm64v8/" ]]; then \
-    wget -nv -O "/usr/bin/qemu-aarch64-static" https://github.com/multiarch/qemu-user-static/releases/download/v3.1.0-2/qemu-aarch64-static; \ 
-  else \
-    echo -e '#!/bin/sh\n"$@"\n' > "/usr/bin/qemu-aarch64-static"; \
-  fi; \
-  chmod +x /usr/bin/qemu-aarch64-static;
-
-FROM ${NAMESPACE}alpine:3.7 as mmseqs-builder
+RUN apt-get update && apt-get install -y wget && rm -rf /var/lib/apt/lists/*
+RUN if [ X"$NAMESPACE" = X"arm64v8/" ]; then \
+      wget -nv -O "/usr/bin/qemu-aarch64-static" https://github.com/multiarch/qemu-user-static/releases/download/v3.1.0-2/qemu-aarch64-static; \
+    else \
+      echo -e '#!/bin/sh\n"$@"\n' > "/usr/bin/qemu-aarch64-static"; \
+    fi; \
+    chmod +x /usr/bin/qemu-aarch64-static;
+
+FROM ${NAMESPACE}debian:stable-slim as mmseqs-builder
 ARG NAMESPACE
 COPY --from=qemu-downloader /usr/bin/qemu-aarch64-static /usr/bin/qemu-aarch64-static
-RUN apk add --no-cache gcc g++ cmake musl-dev vim git ninja zlib-dev bzip2-dev
+
+RUN apt-get update && apt-get install -y \
+    build-essential cmake xxd git zlib1g-dev libbz2-dev \
+ && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /opt/mmseqs
 ADD . .
 RUN mkdir -p build_sse/bin && mkdir -p build_avx/bin && mkdir -p build_neon/bin
 
 WORKDIR /opt/mmseqs/build_sse
-RUN if [[ "$NAMESPACE" == "" ]]; then \
-    cmake -G Ninja -DHAVE_SSE4_1=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
-    ninja && ninja install; \
-  fi
+RUN if [ X"$NAMESPACE" = X"" ]; then \
+      cmake -DHAVE_SSE4_1=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
+      make -j $(nproc --all) && make install; \
+    fi
 
 WORKDIR /opt/mmseqs/build_avx
-RUN if [[ "$NAMESPACE" == "" ]]; then \
-    cmake -G Ninja -DHAVE_AVX2=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
-    ninja && ninja install; \
-  fi
+RUN if [ X"$NAMESPACE" = X"" ]; then \
+      cmake -DHAVE_AVX2=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
+      make -j $(nproc --all) && make install; \
+    fi
 
 WORKDIR /opt/mmseqs/build_neon
-RUN if [[ "$NAMESPACE" == "arm64v8/" ]]; then \
-    cmake -G Ninja -DHAVE_NEON=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
-    ninja && ninja install; \
-    touch /opt/mmseqs/build_sse/bin/mmseqs; \
-    touch /opt/mmseqs/build_avx/bin/mmseqs; \
-  elif [[ "$NAMESPACE" == "" ]]; then \
-    touch /opt/mmseqs/build_neon/bin/mmseqs; \
-  fi
-
-FROM ${NAMESPACE}alpine:3.7
+RUN if [ X"$NAMESPACE" = X"arm64v8/" ]; then \
+      cmake  -DHAVE_NEON=1 -DHAVE_MPI=0 -DHAVE_TESTS=0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=. ..; \
+      make -j $(nproc --all) && make install; \
+      touch /opt/mmseqs/build_sse/bin/mmseqs; \
+      touch /opt/mmseqs/build_avx/bin/mmseqs; \
+    else \
+      touch /opt/mmseqs/build_neon/bin/mmseqs; \
+    fi
+
+FROM ${NAMESPACE}debian:stable-slim
 ARG NAMESPACE
 MAINTAINER Milot Mirdita <milot@mirdita.de>
 COPY --from=qemu-downloader /usr/bin/qemu-aarch64-static /usr/bin/qemu-aarch64-static
 
-RUN apk add --no-cache gawk bash grep libstdc++ libgomp zlib libbz2
+RUN apt-get update && apt-get install -y \
+      gawk bash grep libstdc++6 libgomp1 zlib1g libbz2-1.0 \
+    && rm -rf /var/lib/apt/lists/*
 
 COPY --from=mmseqs-builder /opt/mmseqs/build_sse/bin/mmseqs /usr/local/bin/mmseqs_sse42
 COPY --from=mmseqs-builder /opt/mmseqs/build_avx/bin/mmseqs /usr/local/bin/mmseqs_avx2
 COPY --from=mmseqs-builder /opt/mmseqs/build_neon/bin/mmseqs /usr/local/bin/mmseqs_neon
 ADD util/mmseqs_wrapper.sh /usr/local/bin/mmseqs
 
-RUN if [[ "$NAMESPACE" == "arm64v8/" ]]; then mv -f /usr/local/bin/mmseqs_neon /usr/local/bin/mmseqs; fi
+RUN if [ X"$NAMESPACE" = X"arm64v8/" ]; then mv -f /usr/local/bin/mmseqs_neon /usr/local/bin/mmseqs; fi
 
 CMD ["/usr/local/bin/mmseqs"]