ACTio-ReACTio/Dockerfile at master · nebblu/ACTio-ReACTio · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
FROM ubuntu:20.04

MAINTAINER Maria Tsedrik <mtsedrik@ed.ac.uk>

## Make sure building of image doesn't get stuck at any selection stages

ENV DEBIAN_FRONTEND=noninteractive


## Update apt get

RUN apt-get update && apt-get -y install

    #######################################

## Install pip install and gfortran

RUN apt-get -y install python3-pip
RUN apt-get update -y && \
    apt-get install -y gfortran

    #######################################


## GCC, G++ and GSL

RUN apt-get -y install gcc && \
    apt-get -y install g++ && \
    apt-get -y install libgsl-dev

    #######################################


## Python

RUN apt-get -y install python3 && \
    apt-get -y install python3-setuptools


    #######################################

## Jupyter

RUN pip3 install jupyter


    #######################################

## git and vim

RUN apt-get -y install git && \
    apt-get -y install vim


    #######################################

## Install main packages

RUN pip install scipy numpy matplotlib camb==1.3.5
    #######################################

## Sundials

RUN apt-get -y install cmake && \
    mkdir sundials && cd sundials && \
   ## git clone -b release-4.1.0 https://github.com/LLNL/sundials.git && \
    git clone -b v4.1.0 https://github.com/LLNL/sundials.git && \
    mkdir instdir && \
    mkdir builddir && \
    cd builddir && \
    cmake -DCMAKE_INSTALL_PREFIX=/sundials/instdir \
     -DEXAMPLES_INSTALL_PATH=sundials/instdir/examples \
     ../sundials && \
     make && \
     make install && \
     cd

     #######################################

## pyHMcode

RUN pip install pyhmcode

     #######################################

## React

RUN  git clone https://github.com/nebblu/ACTio-ReACTio.git

RUN  cd ACTio-ReACTio && \
     sed -i "s/CPPFLAGS +=/CPPFLAGS += -I\/sundials\/instdir\/include/g" pyreact/Makefile && \
     sed -i "s/LDFLAGS +=/LDFLAGS += -L\/sundials\/instdir\/lib/g" pyreact/Makefile &&\
     python3 setup.py develop

## set correct library paths in the container environment

ENV LD_LIBRARY_PATH /sundials/instdir/lib:/ACTio-ReACTio/reactions/lib