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Updates to support Amber22 #1

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Updates to support Amber22 #1

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210d2eb
update description for v23
samburger Jun 22, 2023
e66045e
update Ubuntu LTS version for newer gcc etc
samburger Jun 22, 2023
b0d2af6
update to required cmake, gcc packages
samburger Jun 22, 2023
420151b
update dir names for v23
samburger Jun 22, 2023
aec74a8
update cmake to required 3.10
samburger Jun 27, 2023
0a88bf0
update tigervnc download link
samburger Jun 27, 2023
558005c
Add platform tag to fix rosetta build errors on M1
samburger Jun 27, 2023
9bf602f
Set tigerVNC download link to v1.8
samburger Jun 27, 2023
fb3483a
add tigervnc binaries to path
samburger Jun 27, 2023
c47a51e
re-enable cmake configs
samburger Jun 27, 2023
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49 changes: 29 additions & 20 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,43 +1,49 @@
FROM ubuntu:16.04
FROM --platform=linux/amd64 ubuntu:18.04

LABEL Description="Amber and Amber Tool 18"
LABEL Description="Amber and Amber Tool 23"

# Mount Point
RUN mkdir -p /data
VOLUME /data

# Instalol c++ Chain
RUN apt-get update && apt-get install -y cmake wget csh flex patch gfortran g++ make xorg-dev libbz2-dev zlib1g-dev libboost-dev libboost-thread-dev libboost-system-dev bash xorg lightdm
# Install c++ Chain
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install tzdata
RUN apt-get install -y cmake wget csh libfl-dev libbison-dev patch gfortran gcc-6 make xorg-dev libbz2-dev zlib1g-dev libboost-dev libboost-thread-dev libboost-system-dev bash xorg lightdm
# Update cmake to minimum required for building Amber22/23
RUN apt remove cmake -y && \
wget -q https://cmake.org/files/v3.10/cmake-3.10.3-Linux-x86_64.sh && \
chmod +x cmake-3.10.3-Linux-x86_64.sh && \
bash cmake-3.10.3-Linux-x86_64.sh --skip-license

# Install OpenMPI
#RUN apt-get install -y openmpi-bin libopenmpi-dev


# Amber source code
RUN mkdir /amber_source && mkdir /amber
COPY Amber18.tar.bz2 /amber_source/
COPY AmberTools18.tar.bz2 /amber_source/
RUN mkdir /amber22_src && mkdir /amber
COPY Amber22.tar.bz2 /amber22_src/
COPY AmberTools23.tar.bz2 /amber22_src/


WORKDIR /amber_source

RUN tar -jxvf AmberTools18.tar.bz2 && \
tar -jxvf Amber18.tar.bz2 && \
rm -rf AmberTools18.tar.bz2 && \
rm -rf Amber18.tar.bz2
WORKDIR /amber22_src

RUN tar -jxf AmberTools23.tar.bz2 && \
tar -jxf Amber22.tar.bz2 && \
rm -rf AmberTools23.tar.bz2 && \
rm -rf Amber22.tar.bz2

# CMake
RUN cd amber18 && \
mkdir build && \
cd build && \
cmake .. -DAPPLY_UPDATES=TRUE -DCMAKE_INSTALL_PREFIX=/amber -DBUILD_GUI=TRUE -DBUILD_PERL=TRUE -DCOMPILER=GNU -DCUDA=FALSE -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE && \
make && \
make install
RUN cd amber22_src && \
cd build && \
cmake .. -DAPPLY_UPDATES=TRUE -DCMAKE_INSTALL_PREFIX=/amber -DBUILD_GUI=TRUE -DBUILD_PERL=TRUE -DCOMPILER=GNU -DCUDA=FALSE -DDOWNLOAD_MINICONDA=TRUE -DMINICONDA_USE_PY3=TRUE && \
make && \
make install

ENV AMBERHOME=/amber
ENV PATH=/amber/bin:$PATH
ENV LD_LIBRARY_PATH=/amber/lib:$LD_LIBRARY_PATH
RUN rm -rf /amber_source
RUN rm -rf /amber22_src
RUN echo "source /amber/amber.sh" >> /root/.bashrc

###### VNC #######

Expand Down Expand Up @@ -74,6 +80,8 @@ ENV LANG='en_US.UTF-8' LANGUAGE='en_US:en' LC_ALL='en_US.UTF-8'
### Install xvnc-server & noVNC - HTML5 based VNC viewer
RUN $INST_SCRIPTS/tigervnc.sh
RUN $INST_SCRIPTS/no_vnc.sh
# tigervnc script installs vncserver binary to /usr/libexec
ENV PATH=/usr/libexec:$PATH

### Install firefox
RUN $INST_SCRIPTS/firefox.sh
Expand Down Expand Up @@ -101,6 +109,7 @@ RUN cd vmd-1.9.3 && \
cd src && \
make install
RUN cd / && rm -rf /othertools
WORKDIR /

USER 1000

Expand Down
2 changes: 1 addition & 1 deletion src/ubuntu/install/tigervnc.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -2,4 +2,4 @@
set -e

echo "Install TigerVNC server"
wget -qO- https://dl.bintray.com/tigervnc/stable/tigervnc-1.8.0.x86_64.tar.gz | tar xz --strip 1 -C /
wget -qO- https://sourceforge.net/projects/tigervnc/files/stable/1.8.0/tigervnc-1.8.0.x86_64.tar.gz/download | tar xz --strip 1 -C /