-
Notifications
You must be signed in to change notification settings - Fork 1
/
Dockerfile
51 lines (40 loc) · 1.67 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
50
51
FROM ubuntu:jammy-20221130
# GHCR related label
LABEL org.opencontainers.image.source=https://github.com/id-bioinfo/TIPars
LABEL org.opencontainers.image.description="TIPars - Taxa Insertion by Parsimony on Ubuntu Jammy"
LABEL org.opencontainers.image.licenses=LGPL-2.1
# Copy all files to /tipars/
COPY ./ /tipars/
# Update apt and apt-get
RUN apt-get update
RUN apt update
RUN apt upgrade -y
# Install java JRE
RUN apt install default-jre -y
# Setting timezone for installing python without manual user input
ENV TZ=Asia/Hong_Kong
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
# Install deadsnakes for python installation
RUN apt install software-properties-common -y
RUN add-apt-repository ppa:deadsnakes/ppa -y
# Install python3.11
RUN apt install python3.11 -y
# Install pip3
RUN apt install python3-pip -y
# Update python3 command to use python3.11 instead of 3.10
RUN update-alternatives --install /usr/bin/python3 python /usr/bin/python3.11 10
# Install Perl and Perl libraries
RUN apt install perl -y
RUN apt-get install libtime-hires-perl -y
RUN apt install libdata-dump-perl -y
# Install ete3 w/ pip
RUN python3.11 -m pip install six numpy
RUN python3.11 -m pip install ete3
# Install pastml w/ pip
RUN python3.11 -m pip install pastml
# Install gcc and OpenMP
RUN apt install gcc -y
RUN apt-get install libomp-dev -y
WORKDIR /home
# Default CMD: Tipars toy test
CMD ["/tipars/tipars", "-t", "/tipars/Benchmark_datasets/NDV/NDV_tree.nwk", "-s", "/tipars/Benchmark_datasets/NDV/NDV_taxa.fas", "-a", "/tipars/Benchmark_datasets/NDV/NDV_anc.fas", "-q", "/tipars/Benchmark_datasets/NDV/NDV_query.fas", "-o", "/tipars/Benchmark_datasets/NDV/tipars.tree"]