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Docker file for anvi'o versions
FROM ubuntu:xenial
ENV ANVIO_VERSION 5.1
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update
RUN apt-get install locales
RUN locale-gen en_US.UTF-8
ENV LANG='en_US.UTF-8' LANGUAGE='en_US:en' LC_ALL='en_US.UTF-8'
RUN apt-get install -y --no-install-recommends \
build-essential \
gsl-bin \
hmmer \
libgsl-dbg \
libgsl-dev \
libgsl2 \
python3 \
python3-pip \
python3-dev \
python3-numpy \
python3-scipy \
sqlite3 \
wget \
automake \
libboost-all-dev \
bsdmainutils \
libblas-dev \
liblapack-dev \
libatlas-base-dev \
gfortran \
libzeep-dev \
zlib1g-dev \
libhdf5-serial-dev \
libhdf5-dev \
mcl \
ncbi-blast+ \
muscle \
&& mkdir -p /tmp/build \
&& wget https://github.com/bbuchfink/diamond/releases/download/v0.8.38/diamond-linux64.tar.gz -O /tmp/build/diamond-linux64.tar.gz \
&& tar -zxvf /tmp/build/diamond-linux64.tar.gz -C /tmp/build/ \
&& cp /tmp/build/diamond /usr/bin/ \
&& wget https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz -O /tmp/build/v2.6.3.tar.gz \
&& tar -zxvf //tmp/build/v2.6.3.tar.gz -C /tmp/build/ \
&& make -C /tmp/build/Prodigal-2.6.3/ \
&& cp /tmp/build/Prodigal-2.6.3/prodigal /usr/bin/ \
&& wget https://github.com/cmbi/xssp/archive/3.0.1.tar.gz -O /tmp/build/3.0.1.tar.gz \
&& tar -zxvf /tmp/build/3.0.1.tar.gz -C /tmp/build/ \
&& cd /tmp/build/xssp-3.0.1/ \
&& ./autogen.sh && ./configure && make && make install && cd - \
&& wget https://github.com/refresh-bio/FAMSA/releases/download/v1.2.1/famsa-1.2.1-linux -O /usr/bin/famsa \
&& chmod +x /usr/bin/famsa \
&& wget http://www.microbesonline.org/fasttree/FastTree -O /usr/local/bin/FastTree \
&& chmod +x /usr/local/bin/FastTree \
&& pip3 install setuptools==35.0.1 \
&& pip3 install \
cython==0.25.2 \
bottle==0.12.13 \
pysam==0.14.1 \
ete3==3.1.1 \
scikit-learn==0.19.1 \
django==2.0.2 \
"h5py>=2.8.0rc1" \
cherrypy==8.9.1 \
requests==2.10.0 \
psutil==5.0.1 \
mistune==0.7.4 \
six==1.11.0 \
pandas==0.20.1 \
"matplotlib>=2.2.0" \
pyani==0.2.7 \
statsmodels==0.9.0 \
snakemake==4.7.0 \
&& pip3 install --upgrade numpy==1.13.0 \
&& pip3 install --no-deps anvio==$ANVIO_VERSION \
&& apt-get remove -y \
binutils \
build-essential \
g++ \
g++-4.8 \
gcc \
gcc-4.8 \
make \
patch \
&& apt-get -y autoremove \
&& apt-get -y autoclean \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/*
RUN echo "export PS1=\"\[\e[0m\e[47m\e[1;30m\] :: anvi'o :: \[\e[0m\e[0m \[\e[1;34m\]\]\w\[\e[m\] \[\e[1;32m\]>>>\[\e[m\] \[\e[0m\]\"" >> /root/.bashrc
CMD /bin/bash -l
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