/
Dockerfile
executable file
·93 lines (81 loc) · 2.84 KB
/
Dockerfile
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############################################################
# Dockerfile to build haystack_bio
# Based on Ubuntu 16.04
############################################################
# Set the base image to Ubuntu
FROM ubuntu:16.04
RUN apt-get update \
&& apt-get install -y \
python-dev \
gfortran \
libopenblas-dev \
liblapack-dev \
zlib1g-dev \
libexpat1-dev \
libhtml-template-perl \
libxml-simple-perl \
libsoap-lite-perl \
libxml2-dev \
libxslt1-dev \
default-jre \
subversion \
curl \
python-pip \
unzip \
bedtools \
ghostscript \
&& rm -rf /var/lib/apt/lists/* \
&& python -m pip install --user \
setuptools==37.0.0 \
numpy==1.13.3 \
scipy==1.0.0 \
matplotlib==2.1.0 \
pandas==0.21.0 \
&& pip install \
bx-python==0.7.3 \
Jinja2==2.9.6 \
tqdm==4.19.4 \
weblogo==3.5.0 \
&& cpan \
inc::latest \
common::sense \
CGI::Application \
Log::Log4perl \
HTML::PullParser \
HTML::Parse \
Math::CDF JSON \
Types::Serialiser \
XML::Compile::SOAP11 \
XML::Compile::WSDL11 \
XML::Compile::Transport::SOAPHTTP
RUN mkdir -p /haystack_bio/binaries \
&& curl -fL http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig \
-o /haystack_bio/binaries/bedGraphToBigWig \
&& chmod +x /haystack_bio/binaries/bedGraphToBigWig \
&& curl -fL http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigAverageOverBed \
-o /haystack_bio/binaries/bigWigAverageOverBed \
&& chmod +x /haystack_bio/binaries/bigWigAverageOverBed \
&& curl -fL https://github.com/lomereiter/sambamba/releases/download/v0.6.6/sambamba_v0.6.6_linux.tar.bz2 \
-o /haystack_bio/binaries/sambamba_v0.6.6_linux.tar.bz2 \
&& tar -xvjf /haystack_bio/binaries/sambamba_v0.6.6_linux.tar.bz2 -C /haystack_bio/binaries \
&& rm -f /haystack_bio/binaries/sambamba_v0.6.6_linux.tar.bz2 \
&& ln -s /haystack_bio/binaries/sambamba_v0.6.6 /haystack_bio/binaries/sambamba \
&& curl -fL http://meme-suite.org/meme-software/4.11.2/meme_4.11.2_2.tar.gz \
-o /haystack_bio/binaries/meme_4.11.2_2.tar.gz \
&& tar -xzf /haystack_bio/binaries/meme_4.11.2_2.tar.gz -C /haystack_bio/binaries \
&& rm -f /haystack_bio/binaries/meme_4.11.2_2.tar.gz
WORKDIR /haystack_bio/binaries/meme_4.11.2
RUN ./configure --prefix=/haystack_bio/binaries/meme \
&& make clean \
&& make AM_CFLAGS='-DNAN="(0.0/0.0)"' \
&& make install \
&& rm -rf /haystack_bio/binaries/meme_4.11.2
RUN apt-get remove -y python-pip curl && apt-get clean
# Set the working directory to /haystack_bio
WORKDIR /haystack_bio_setup
# Copy the current directory contents into the container at /haystack_bio
COPY . /haystack_bio_setup
ENV PATH /haystack_bio/binaries:/haystack_bio/binaries/meme/bin:$PATH
RUN python setup.py install
RUN ln -s /usr/local/lib/python2.7/dist-packages/haystack_bio-0.5.3-py2.7.egg/haystack/haystack_data/genomes/ /haystack_genomes
RUN rm -Rf /haystack_bio_setup