/
Dockerfile_test
66 lines (53 loc) · 1.54 KB
/
Dockerfile_test
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
FROM ubuntu:14.04.3
MAINTAINER Tomaz Curk <tomazc@gmail.com>
# thanks to https://github.com/bschiffthaler/ngs/blob/master/base/Dockerfile
# and https://github.com/AveraSD/ngs-docker-star/blob/master/Dockerfile
RUN useradd -m -d /home/icuser icuser
# update system
RUN apt-get update && apt-get upgrade -y && \
apt-get install -y \
build-essential \
gfortran \
libatlas-base-dev \
wget \
g++ \
make \
python3 \
python3-pip \
python3-setuptools \
python-virtualenv \
python-pip \
git && \
apt-get build-dep -y python3-matplotlib && \
apt-get install -y \
python3-matplotlib
RUN apt-get autoclean -y && \
apt-get autoremove -y
#################
### samtools
RUN apt-get install -y \
zlib1g-dev \
liblzma-dev \
libbz2-dev \
samtools
#################
#### iCount
RUN chown -R icuser.icuser /home/icuser
USER icuser
WORKDIR /home/icuser
RUN virtualenv -p python3 /home/icuser/.icountenv
USER root
RUN echo "source /home/icuser/.icountenv/bin/activate" >> /etc/bash.bashrc
USER icuser
WORKDIR /home/icuser
#################
### prerequisites for iCount
RUN /home/icuser/.icountenv/bin/pip install numpy
RUN /home/icuser/.icountenv/bin/pip install pandas
RUN /home/icuser/.icountenv/bin/pip install cutadapt
RUN /home/icuser/.icountenv/bin/pip install pysam
RUN /home/icuser/.icountenv/bin/pip install pybedtools
RUN /home/icuser/.icountenv/bin/pip install numpydoc
RUN /home/icuser/.icountenv/bin/pip install sphinx
RUN /home/icuser/.icountenv/bin/pip install matplotlib
CMD ["/bin/bash"]