forked from sanger-pathogens/seroba
-
Notifications
You must be signed in to change notification settings - Fork 1
/
Dockerfile
49 lines (39 loc) · 1.13 KB
/
Dockerfile
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
# This container will install SeroBA from master
# base image
FROM ubuntu:bionic as app
# set workdir to default for building; set to /data at the end
WORKDIR /
# Install ubuntu dependencies
RUN apt-get update && apt-get -y upgrade && apt-get -y install git \
wget \
unzip \
zlib1g-dev \
libbz2-dev \
libjpeg-dev \
liblzma-dev \
python3 \
python3-pip \
libpython3-dev \
python3-setuptools \
python-minimal && \
apt-get clean && apt-get autoclean && rm -rf /var/lib/apt/lists/*
# Copy repository into the image and install dependencies
COPY . /seroba/
RUN cd seroba && \
/seroba/install_dependencies.sh
# set path
ENV PATH="/seroba:/seroba/build:/seroba/build/bin:/seroba/build/MUMmer3.23:/seroba/build/bowtie2-2.3.1-legacy:/seroba/build/cdhit-4.6.8:${PATH}"
# install seroba and create database (/seroba/database/)
RUN cd /seroba && \
python3 setup.py install && \
seroba createDBs database/ 71
RUN mkdir /data
WORKDIR /data
# new base for testing
FROM app as test
# print out various help options and version
RUN seroba version && \
seroba --help
# run built-in test
RUN cd /seroba && \
python3 setup.py test