From d2bd79d9e543d12da07ecf179dc63765d53213ff Mon Sep 17 00:00:00 2001
From: Fortune Iriaye <firiaye@uab.edu>
Date: Thu, 21 Nov 2024 07:42:01 -0600
Subject: [PATCH] Update Dockerfile
---
docker/Dockerfile | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index ec52f98..1fbb04d 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -11,12 +11,14 @@
FROM nvidia/cuda:12.6.0-base-ubuntu22.04
# Some RUN statements are combined together to make Docker build run faster.
-# Get latest package listing, install software-properties-common, git and wget.
+# Get latest package listing, install software-properties-common, git, wget,
+# compilers and libraries.
# git is required for pyproject.toml toolchain's use of CMakeLists.txt.
+# gcc, g++, make are required for compiling hmmer and AlphaFold 3 libaries.
+# zlib is a required dependency of AlphaFold 3.
RUN apt update --quiet \
&& apt install --yes --quiet software-properties-common \
- && apt install --yes --quiet git wget \
- && apt install --yes --quiet g++ make build-essential cmake
+ && apt install --yes --quiet git wget gcc g++ make zlib1g-dev zstd
# Get apt repository of specific Python versions. Then install Python. Tell APT
# this isn't an interactive TTY to avoid timezone prompt when installing.
@@ -46,7 +48,6 @@ COPY . /app/alphafold
WORKDIR /app/alphafold
# Install the Python dependencies AlphaFold 3 needs.
-RUN pip3 install setuptools wheel build
RUN pip3 install -r dev-requirements.txt
RUN pip3 install --no-deps .
# Build chemical components database (this binary was installed by pip).
@@ -60,4 +61,4 @@ ENV XLA_FLAGS="--xla_gpu_enable_triton_gemm=false"
ENV XLA_PYTHON_CLIENT_PREALLOCATE=true
ENV XLA_CLIENT_MEM_FRACTION=0.95
-CMD ["python3", "run_alphafold.py"]
+CMD ["python3", "run_alphafold.py"]
\ No newline at end of file
--
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