-
Notifications
You must be signed in to change notification settings - Fork 7
/
Dockerfile
106 lines (88 loc) · 3.1 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
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
99
100
101
102
103
104
105
106
# Base Image
FROM biocontainers/biocontainers:latest
# Metadata
LABEL base.image="biocontainers:latest"
LABEL version="3"
LABEL software="deSRA"
LABEL software.version="0.0.1"
LABEL description="An automated protocol to extract variation or expression from public NGS datasets"
LABEL website="https://github.com/NCBI-Hackathons/deSRA"
LABEL documentation="https://github.com/NCBI-Hackathons/deSRA"
LABEL license="https://github.com/NCBI-Hackathons/deSRA/blob/master/LICENSE"
LABEL tags="SRA,RNA-seq"
# Maintainer
MAINTAINER Roberto Vera Alvarez <[email protected]>
USER root
RUN apt-get update && \
apt-get install -y \
libncurses5-dev \
libncursesw5-dev \
libbz2-dev \
lzma lzma-dev liblzma-dev \
libcurl4-gnutls-dev \
python3 python3-pip \
nodejs npm \
liblwp-protocol-https-perl \
r-base r-base-dev && \
apt-get clean && \
apt-get purge && \
pip3 install numpy pysam scipy && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN R -e "install.packages('shiny', repos = 'http://cran.us.r-project.org')" && \
R -e "install.packages('shinyjs', repos = 'http://cran.us.r-project.org')" && \
R -e "install.packages('DT', repos = 'http://cran.us.r-project.org')" && \
R -e "install.packages('rglwidget', repos = 'http://cran.us.r-project.org')" && \
R -e "install.packages('plotly', repos = 'http://cran.us.r-project.org')" && \
R -e "install.packages('dplyr', repos = 'http://cran.us.r-project.org')" && \
R -e "install.packages('reshape2', repos = 'http://cran.us.r-project.org')" && \
R -e "source('http://bioconductor.org/biocLite.R');biocLite('Biobase')"
USER biodocker
ENV ZIP=samtools-1.6.tar.bz2
ENV URL=https://github.com/samtools/samtools/releases/download/1.6/
ENV FOLDER=samtools-1.6
ENV DST=/tmp
RUN wget $URL/$ZIP -O $DST/$ZIP && \
tar xvf $DST/$ZIP -C $DST && \
rm $DST/$ZIP && \
cd $DST/$FOLDER && \
./configure --prefix=/home/biodocker && \
make && \
make install && \
cd / && \
rm -rf $DST/$FOLDER
ENV ZIP=ncbi-magicblast-1.3.0-x64-linux.tar.gz
ENV URL=ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/
ENV FOLDER=ncbi-magicblast-1.3.0
ENV INSTALL_FOLDER=/home/biodocker/
ENV DST=/tmp
RUN cd $DST && \
wget $URL/$ZIP -O $DST/$ZIP && \
tar xzfv $DST/$ZIP -C $DST && \
mv $DST/$FOLDER/LICENSE $DST/$FOLDER/README /home/biodocker/bin/ && \
mv $DST/$FOLDER/bin/* /home/biodocker/bin/ && \
rm -rf $DST/$FOLDER
ENV ZIP=edirect-7.50.20171103.tar.gz
ENV URL=ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/7.50.20171103/
ENV FOLDER=edirect
ENV INSTALL_FOLDER=/home/biodocker/
ENV DST=/tmp
RUN cd $DST && \
wget $URL/$ZIP -O $DST/$ZIP && \
tar xzfv $DST/$ZIP -C $DST && \
mv $DST/$FOLDER/* /home/biodocker/bin/ && \
rm -rf $DST/$FOLDER
RUN mkdir /home/biodocker/.ncbi && \
mkdir /home/biodocker/web/
COPY bin/* /home/biodocker/bin/
COPY web/* /home/biodocker/web/
COPY config/user-settings.mkfg /home/biodocker/.ncbi/
RUN cd /home/biodocker/web/ && \
npm install
USER biodocker
ENV DB=/data/db.sqlite3
ENV BIN=/home/biodocker/bin
ENV DATA=/data
ENV JOBS=/data/jobs
ENV WORKDIR=/data
WORKDIR /data/
EXPOSE 8000