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########################################################
# Dockerfile for automated build of latest SONAR code #
# #
# Please see https://github.com/scharch/SONAR for more #
# information. #
########################################################
FROM ubuntu:bionic
MAINTAINER Chaim Schramm [email protected]
ENV DEBIAN_FRONTEND=noninteractive
WORKDIR /
#install Python
RUN apt-get update
RUN apt-get install -y \
build-essential \
zlib1g-dev \
libncurses5-dev \
libgdbm-dev \
libnss3-dev \
libssl-dev \
libreadline-dev \
libffi-dev \
wget \
python3 \
python3-pip
#get biopython
RUN pip3 install "biopython==1.73"
#add docopt
RUN pip3 install docopt
#add fuzzywuzzy for master script
RUN pip3 install fuzzywuzzy
#install libraries for bioperl
RUN apt-get install -y \
gcc-multilib \
perl \
cpanminus \
liblwp-protocol-https-perl \
libnet-https-any-perl \
libdb-dev \
graphviz \
make \
libexpat1-dev \
libatlas-base-dev \
gfortran
#install perl modules that are prerequisites
RUN cpanm \
CPAN::Meta \
YAML \
Digest::SHA \
Module::Build \
Test::Most \
Test::Weaken \
Test::Memory::Cycle \
Clone \
HTML::TableExtract \
Algorithm::Munkres \
Algorithm::Combinatorics \
Statistics::Basic \
List::Util \
PDL::LinearAlgebra::Trans \
Array::Compare \
Convert::Binary::C \
Error \
GraphViz \
Inline::C \
PostScript::TextBlock \
Set::Scalar \
Sort::Naturally \
Math::Random \
Spreadsheet::ParseExcel \
IO::String \
JSON \
Data::Stag \
CGI \
Bio::Phylo \
Switch
#now actually install BioPerl
RUN cpanm -v \
https://github.com/bioperl/bioperl-live/archive/release-1-7-2.tar.gz
#install PyQt and ete3
RUN apt-get install -y \
python3-pyqt4 python3-pyqt4.qtopengl python-lxml python-six
RUN pip3 install --upgrade ete3
#install AIRR reference library
RUN pip3 install airr
#install networkx for single cell clonality
RUN pip3 install networkx
#install Levensthein
RUN pip3 install python-Levenshtein
#install R
RUN echo "deb http://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" >> /etc/apt/sources.list
RUN gpg --keyserver keyserver.ubuntu.com --recv-key 51716619E084DAB9
RUN gpg -a --export 51716619E084DAB9 | apt-key add -
RUN apt-get update && apt-get install -y r-base r-base-dev
#install R packages
RUN R --vanilla -e 'install.packages(c("docopt","MASS","ggplot2","ptinpoly"), repos="http://cran.r-project.org/")'
#install Xvfb for 4.4
RUN apt-get install -y xvfb
#get fastq-dump for vignette
RUN apt-get install -y curl
RUN curl -O https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.6-1/sratoolkit.2.9.6-1-ubuntu64.tar.gz
RUN tar -xzf sratoolkit.2.9.6-1-ubuntu64.tar.gz
RUN ln -s /sratoolkit.2.9.6-1-ubuntu64/bin/fastq-dump /usr/bin/fastq-dump
#pull latest SONAR source code and set it up
RUN apt-get install -y git libidn11
RUN git clone https://github.com/scharch/SONAR.git
WORKDIR SONAR
RUN echo | ./setup.py
RUN cp sonar /usr/bin
WORKDIR /