Last active
May 1, 2019 20:24
-
-
Save meren/65b1f1bfea1b53e87e10f025d1e4c29a to your computer and use it in GitHub Desktop.
Docker file for anvi'o versions
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
FROM ubuntu:xenial | |
ENV ANVIO_VERSION 5.5 | |
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 \ | |
nano \ | |
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 wheel==0.33.1 \ | |
&& pip3 install \ | |
cython==0.28.5 \ | |
bottle==0.12.13 \ | |
pysam==0.15.2 \ | |
ete3==3.1.1 \ | |
scikit-learn==0.19.2 \ | |
django==2.0.10 \ | |
h5py==2.8.0 \ | |
cherrypy==8.9.1 \ | |
requests==2.20.0 \ | |
psutil==5.4.3 \ | |
mistune==0.8.1 \ | |
six==1.11.0 \ | |
pandas==0.23.1 \ | |
matplotlib==2.2.3 \ | |
pyani==0.2.7 \ | |
statsmodels==0.9.0 \ | |
snakemake==5.2.4 \ | |
colored==1.3.93 \ | |
illumina-utils==2.6 \ | |
&& pip3 install --upgrade numpy==1.15.1 \ | |
&& 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 rm /usr/bin/python && ln -s /usr/bin/python3 /usr/bin/python | |
RUN echo "export PS1=\"\[\e[0m\e[47m\e[1;30m\] :: anvi'o v$ANVIO_VERSION :: \[\e[0m\e[0m \[\e[1;34m\]\]\w\[\e[m\] \[\e[1;32m\]>>>\[\e[m\] \[\e[0m\]\"" >> /root/.bashrc | |
CMD /bin/bash -l |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment