-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDockerfile
54 lines (42 loc) · 2.03 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
52
53
54
FROM ubuntu:18.04 AS builder
LABEL version="1.0"
LABEL maintainer="[email protected]"
# build dependencies
RUN apt-get -y update && apt-get -y upgrade && apt-get -y install \
git wget make gcc g++ zlib1g-dev unzip autoconf file cpio \
cmake \
libboost-program-options-dev libboost-iostreams-dev \
libboost-graph-dev libboost-system-dev libboost-filesystem-dev libboost-serialization-dev
# runtime dependencies
#
# libxml2: magicblast
# libperl5.26: Sys::Hostname for bowtie2
# python: bowtie2
# metaphlan2: python, python-numpy
# metabat: boost
# checkm: python-numpy python-pysam python-dendropy python-matplotlib
RUN apt-get -y install libgomp1 libxml2 libperl5.26 openjdk-8-jre-headless python python-numpy \
libboost-program-options1.65.1 libboost-iostreams1.65.1 \
libboost-graph1.65.1 libboost-system1.65.1 libboost-filesystem1.65.1 libboost-serialization1.65.1
RUN groupadd mgxserv && useradd -m -g mgxserv mgxserv && chown -R mgxserv /home/mgxserv
COPY . /tmp/tools
RUN cd /tmp/tools && for f in `cat build_order`; do \
bash -x ${f}.build || exit 1; \
done
#RUN apt-get -y purge git wget make gcc g++ zlib1g-dev unzip autoconf file cpio \
# cmake \
# libboost-program-options-dev libboost-iostreams-dev \
# libboost-graph-dev libboost-system-dev libboost-filesystem-dev libboost-serialization-dev
#
#RUN apt-get -y autoremove && apt-get -y clean && rm -rf /tmp/tools && \
# rm -rf /var/lib/apt/lists/* /var/lib/dpkg/info/* /var/log/dpkg.log /root/.wget-hsts
FROM ubuntu:18.04
# runtime dependencies
RUN apt-get -y update && apt-get -y install libgomp1 libxml2 libperl5.26 openjdk-8-jre-headless python python-numpy \
libboost-program-options1.65.1 libboost-iostreams1.65.1 \
libboost-graph1.65.1 libboost-system1.65.1 libboost-filesystem1.65.1 libboost-serialization1.65.1 \
python-numpy python-pysam python-dendropy python-matplotlib
COPY --from=builder /vol/mgx-sw/ /vol/mgx-sw
COPY --from=builder /etc/profile.d/mgx-sw.sh /etc/profile.d/
ENV PATH="/vol/mgx-sw/bin:${PATH}"
#USER mgxserv