From fe7e037c6d0d934d8b44b93397b3920df03009c1 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 4 Jul 2024 22:06:11 +0200
Subject: [PATCH] update Dockerfile
---
docker/Dockerfile | 43 ++++++++++++-------------------------------
1 file changed, 12 insertions(+), 31 deletions(-)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index b7bbf68ab..8168e9022 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -5,9 +5,7 @@ FROM ubuntu:22.04
ARG OPENSTRUCTURE_VERSION="2.8.0"
ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=2
-ARG OPENMM_VERSION="7.7.0"
-ARG OPENMM_INCLUDE_PATH="/usr/local/openmm/include/"
-ARG OPENMM_LIB_PATH="/usr/local/openmm/lib/"
+
ARG DEBIAN_FRONTEND=noninteractive
# INSTALL SYSTEM DEPS
@@ -29,29 +27,15 @@ RUN apt-get update -y && apt-get install -y cmake \
python3-scipy \
python3-pandas \
python3-networkx \
- doxygen \
- swig \
clustalw \
- cython3 \
voronota \
+ libopenmm-dev \
+ libopenmm-plugins \
+ libparasail-dev \
locales && \
# CLEANUP
rm -rf /var/lib/apt/lists/*
-
-# INSTALL OPENMM
-################
-RUN cd ${SRC_FOLDER} && \
- wget -O openmm-${OPENMM_VERSION}.tar.gz -nc https://github.com/pandegroup/openmm/archive/${OPENMM_VERSION}.tar.gz && \
- mkdir ${SRC_FOLDER}/openmm-${OPENMM_VERSION} && \
- tar xf openmm-${OPENMM_VERSION}.tar.gz -C ${SRC_FOLDER}/openmm-${OPENMM_VERSION} --strip-components=1 && \
- mkdir -p ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && \
- cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build && \
- cmake .. && make -j $CPUS_FOR_MAKE && make install && \
- cd ${SRC_FOLDER}/openmm-${OPENMM_VERSION}/build/python && \
- python3 setup.py build && python3 setup.py install && \
- rm ${SRC_FOLDER}/openmm-${OPENMM_VERSION}.tar.gz && \
- rm -rf ${SRC_FOLDER}/openmm-${OPENMM_VERSION}
-
+
# INSTALL OST
#############
RUN cd ${SRC_FOLDER} && \
@@ -61,17 +45,14 @@ RUN cd ${SRC_FOLDER} && \
tar xf openstructure-${OPENSTRUCTURE_VERSION}.tar.gz -C ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION} --strip-components=1 && \
mkdir -p ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && \
cd ${SRC_FOLDER}/openstructure-${OPENSTRUCTURE_VERSION}/build && \
- cmake .. -DOPTIMIZE=ON \
- -DENABLE_MM=ON \
+ cmake .. -DOPTIMIZE=1 \
+ -DENABLE_MM=1 \
+ -DOPEN_MM_PLUGIN_DIR=/lib/x86_64-linux-gnu/openmm/plugins \
+ -DENABLE_PARASAIL=1 \
-DCOMPILE_TMTOOLS=1 \
- -DOPEN_MM_LIBRARY=$OPENMM_LIB_PATH/libOpenMM.so \
- -DOPEN_MM_INCLUDE_DIR=$OPENMM_INCLUDE_PATH \
- -DOPEN_MM_PLUGIN_DIR=$OPENMM_LIB_PATH/plugins \
- -DENABLE_GFX=ON \
- -DENABLE_GUI=OFF \
- -DENABLE_INFO=OFF \
- -DCMAKE_C_FLAGS="-isystem /usr/include/boost/ -isystem ${OPENMM_INCLUDE_PATH}/include" \
- -DCMAKE_CXX_FLAGS="-isystem /usr/include/boost/ -isystem ${OPENMM_INCLUDE_PATH}/include" && \
+ -DENABLE_GFX=1 \
+ -DENABLE_GUI=0 \
+ -DENABLE_INFO=0 && \
make -j ${CPUS_FOR_MAKE} && \
wget ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz && \
stage/bin/chemdict_tool create components.cif.gz compounds.chemlib pdb && stage/bin/chemdict_tool update ../modules/conop/data/charmm.cif compounds.chemlib charmm && \
--
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