-
Notifications
You must be signed in to change notification settings - Fork 5
/
Dockerfile
60 lines (39 loc) · 2.3 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
FROM ubuntu:16.04
MAINTAINER Gemma Hoad <[email protected]>
# Install packages then remove cache package list information
RUN DEBIAN_FRONTEND=noninteractive apt-get update && apt-get -yq install openssh-client \
make \
curl \
wget \
apt-utils \
build-essential \
net-tools \
librpc-xml-perl \
bioperl \
ncbi-blast+-legacy \
nano \
libf2c2 \
libxmlrpc-lite-perl \
libextutils-makemaker-cpanfile-perl \
gcc
RUN DEBIAN_FRONTEND=noninteractive apt-get update && apt-get clean && rm -rf /var/lib/apt/lists/*
RUN mkdir -p /tmp/results && chmod 777 /tmp/results
WORKDIR /usr/local/bin
RUN mkdir pftools && cd pftools && wget ftp://ftp.lausanne.isb-sib.ch/pub/software/unix/pftools/pft2.3/executables/linux_x86_elf/static/pft2.3_static.tar.gz && tar xvf pft2.3_static.tar.gz && chmod 755 * && ln -s /usr/local/bin/pftools/pfscan /usr/local/bin/pfscan
WORKDIR /usr/local/src
RUN echo '/usr/local/lib64' >>/etc/ld.so.conf
RUN wget ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz && tar xvf ncbi-blast-2.6.0+-x64-linux.tar.gz && export PATH=$PATH:/usr/local/bin/ncbi-blast-2.6.0+/bin
RUN wget http://www.psort.org/download/libpsortb-1.0.tar.gz && tar zxvf libpsortb-1.0.tar.gz && cd libpsortb-1.0 && ./configure && make && make install && ldconfig
RUN mkdir -p /usr/local/src/blastdb
WORKDIR /usr/local/src
RUN wget http://www.psort.org/download/bio-tools-psort-all.3.0.6.tar.gz && tar zxvf bio-tools-psort-all.3.0.6.tar.gz
WORKDIR /usr/local/src/bio-tools-psort-all
RUN wget http://www.psort.org/download/docker/psortb_standalone_for_docker.tar.gz && tar xvf psortb_standalone_for_docker.tar.gz && mv psortb_standalone_for_docker/Makefile.PL ./
RUN wget http://www.psort.org/download/docker/psortb.defaults && perl Makefile.PL && make && make install
RUN mv /usr/local/psortb/bin /usr/local/psortb/bin_orig && mv psortb_standalone_for_docker/bin /usr/local/psortb/ && chmod +x /usr/local/psortb/bin
#cleanup
WORKDIR /usr/local/src
RUN rm libpsortb-1.0.tar.gz bio-tools-psort-all.3.0.6.tar.gz ncbi-blast-2.6.0+-x64-linux.tar.gz /usr/local/bin/pftools/pft2.3_static.tar.gz bio-tools-psort-all/psortb_standalone_for_docker.tar.gz
RUN rm -r /usr/local/src/bio-tools-psort-all/psortb_standalone_for_docker
ENTRYPOINT ["/usr/local/psortb/bin/psort"]
CMD []