diff --git a/compile_waterz b/compile_waterz deleted file mode 100755 index 7a7d0517f..000000000 --- a/compile_waterz +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env python3 -import waterz - -if __name__ == "__main__": - waterz.agglomerate() diff --git a/docker/Dockerfile.all b/docker/Dockerfile.all index da122f364..c5f1a91eb 100644 --- a/docker/Dockerfile.all +++ b/docker/Dockerfile.all @@ -19,7 +19,12 @@ RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \ && ./install_zutils.py --dockerfile --mode modules \ && rm -rf /root/.cache/bazel/ \ && apt-mark auto '.*' > /dev/null \ - && apt-mark manual $savedAptMark zstd parallel coreutils libtbb2 libjemalloc2 \ + && apt-mark manual \ + $savedAptMark \ + # abiss + zstd parallel coreutils libjemalloc2 \ + # waterz + libboost-dev g++ \ && find /usr/local/lib /opt/conda -type f -executable -exec ldd '{}' ';' \ | awk '/=>/ { print $(NF-1) }' \ | sort -u \ diff --git a/docker/Dockerfile.all_pcg b/docker/Dockerfile.all_pcg index 21fd1c966..f1d3fc8d6 100644 --- a/docker/Dockerfile.all_pcg +++ b/docker/Dockerfile.all_pcg @@ -19,7 +19,12 @@ RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \ && ./install_zutils.py --dockerfile --mode modules --pcg \ && rm -rf /root/.cache/bazel/ \ && apt-mark auto '.*' > /dev/null \ - && apt-mark manual $savedAptMark zstd parallel coreutils libtbb2 libjemalloc2 \ + && apt-mark manual \ + $savedAptMark \ + # abiss + zstd parallel coreutils libjemalloc2 \ + # waterz + libboost-dev g++ \ && find /usr/local/lib /opt/conda -type f -executable -exec ldd '{}' ';' \ | awk '/=>/ { print $(NF-1) }' \ | sort -u \ diff --git a/install_zutils.py b/install_zutils.py index b8b3b33e0..13a392492 100755 --- a/install_zutils.py +++ b/install_zutils.py @@ -628,21 +628,22 @@ def main(): "git", "build-essential", "wget", - "ffmpeg", - "libsm6", - "libxext6", - "curl", - "cmake", - "ninja-build", - "pkg-config", - "zstd", - "parallel", - "coreutils", - "libboost-system-dev", - "libboost-iostreams-dev", - "libjemalloc-dev", - "libtbb-dev", - "unixodbc-dev", + "ffmpeg", # opencv + "libsm6", # opencv + "libxext6", # opencv + "curl", # abiss + "cmake", # abiss + "ninja-build", # abiss + "pkg-config", # abiss + "zstd", # abiss + "parallel", # abiss + "coreutils", # abiss + "libboost-system-dev", # abiss + "libboost-iostreams-dev", # abiss + "libjemalloc-dev", # abiss + "libtbb-dev", # abiss + "libboost-dev", # waterz + "unixodbc-dev", # ??? ] run_command(f"{sudo_prefix}apt-get update", "Updating package lists") apt_install_flags = '-y --no-install-recommends -o Dpkg::Options::="--force-confdef" -o Dpkg::Options::="--force-confold"' @@ -669,7 +670,6 @@ def main(): run_command( f"pip install --upgrade .[{install_mode}]", "Installing `zetta_utils` python package" ) - run_command("python3 ./compile_waterz", "Compiling waterz") if args.pcg: run_command( "pip install --no-deps git+https://github.com/CAVEconnectome/PyChunkedGraph.git@v2.18.3",