nchenche
commented
2 months ago Hi @brspurri,
You will find below the Dockerfile instructions. It's been a long time since I have not seen it, so it certainly is optimizable.
Also, before running the Dockerfile,you will need to create a softwares directory where you must add APBS-3.4.1 (from https://github.com/Electrostatics/apbs/releases/tag/v3.4.1).
├── CHANGELOG.md
├── doc
├── Dockerfile
├── LICENSE
├── MANIFEST.in
├── README.md
├── setup.py
├── softwares
└── APBS-3.4.1.Linux
├── surfmap
Dockerfile
# 1st build stage: base image for ubuntu
#################
FROM ubuntu:22.04 as base_os_ubuntu
# to not the user being asked validations upon install process
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update && apt-get install -y \
software-properties-common \
&& add-apt-repository ppa:deadsnakes/ppa
RUN apt-get update && apt-get install -y \
build-essential \
fort77 \
gcc-11 \
less \
vim-tiny
# 2nd build stage: add R
#################
FROM base_os_ubuntu as base_os_with_r
RUN apt-get update && apt-get install -y \
r-base
# 3rd build stage: add python3.10
#################
FROM base_os_with_r as base_os_with_python
RUN apt-get update && apt-get install -y \
python3.10 \
python3-pip
# 4th build stage: add R library dependencies
#################
FROM base_os_with_python as base_os_with_r_lib
RUN R -e "install.packages(c('optparse', 'data.table', 'mapproj'))"
# 5th build stage: add APBS-3.4.1 (from https://github.com/Electrostatics/apbs/releases/tag/v3.4.1) - requires to be placed in a directory called 'softwares' at the same level of Dockerfile
#################
FROM base_os_with_r_lib as base_os_with_apbs
# go to home surfmap
WORKDIR /surfmap
# copy APBS in /surfmap
COPY softwares/APBS-3.4.1.Linux APBS/
# set env vars for APBS
ENV APBS=/surfmap/APBS
ENV LD_LIBRARY_PATH=$APBS/lib
ENV PATH=$APBS/bin:$PATH
# 6th build stage: add surfmap package
#################
FROM base_os_with_apbs as surfmap_package
WORKDIR /surfmap
# install virtualenv, create one and add its bin directory into PATH
RUN pip install virtualenv && \
virtualenv -p python3.10 .env
ENV PATH=/surfmap/.env/bin:$PATH
# add surfmap packages and setup.py
COPY ./ ./
# # install ORFmine python libraries & dependencies
RUN pip install -e .
# create surfmap group and user (from https://github.com/dnaprawa/dockerfile-best-practices#run-as-a-non-root-user)
RUN adduser surfmap
# go to home surfmap
WORKDIR /home/surfmap
# run container as surfmap user and add input & output dirs
USER surfmap
RUN mkdir input output
Bests
Feature Title
Dockerfile
Feature Summary
Can the Dockerfile used to create the referenced docker image be added to the repo? It would be very useful as I need to recreate the image with a minor modification.
Motivation and Context
Currently, the docker image cannot be recreated.
Technical Details and Implementation
No response
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