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FROM cfljam/pyrat_genetics
MAINTAINER John McCallum [email protected]
# Set noninterative mode
ENV DEBIAN_FRONTEND noninteractive
################## BEGIN INSTALLATION ######################
## ipython/ipython is 14.04 (trusty) and ncurses is for samtools and precise dependencies are unresolved
RUN echo "deb http://archive.ubuntu.com/ubuntu trusty main universe" > /etc/apt/sources.list
##Install Prerequisites and BioPython
RUN set -xe ;\
apt-get update;\
apt-get -y upgrade;\
apt-get -y dist-upgrade ;\
apt-get autoremove;\
apt-get autoclean;\
apt-get install -y \
build-essential \
python-setuptools \
python-biopython
### Install python packages
### Note explicit use of Py version to avoid pip version issues
ADD requirements.txt /tmp/
RUN set -xe ;\
python2 /usr/local/bin/pip --default-timeout=100 install -r /tmp/requirements.txt
ENV PERL5LIB /usr/local/lib/perl5
## Install VCF lib
RUN set -xe ;\
git clone --recursive https://github.com/ekg/vcflib.git ;\
cd vcflib ;\
make ;\
cp ./bin/* /usr/local/bin/
## Install HTS lib
RUN set -xe ;\
git clone --branch=develop https://github.com/samtools/htslib.git ;\
cd htslib ;\
make ;\
make test ;\
make install
## Install samtools
RUN set -xe ;\
git clone --branch=develop https://github.com/samtools/samtools.git ;\
cd samtools ;\
make HTSDIR=/tmp/htslib;\
make test ;\
make install
## Install bedtools plus Python interface
RUN set -xe ;\
apt-get install -y bedtools
### Install Exonerate
RUN set -xe ;\
git clone https://github.com/nathanweeks/exonerate.git ;\
cd exonerate ;\
git checkout v2.4.0;\
autoreconf -f -i ;\
./configure ;\
make ;\
make check ;\
make install
## Install BCF tools
RUN set -xe ;\
git clone --branch=develop https://github.com/samtools/bcftools.git ;\
cd bcftools ;\
make HTSDIR=/tmp/htslib;\
make test ;\
make install
## Install VCF tools
RUN set -xe ;\
git clone https://github.com/vcftools/vcftools;\
cd vcftools; \
./autogen.sh;\
./configure;\
make;\
make install
##########################################
### Launch ipynb as default
CMD ipython notebook --ip=0.0.0.0 --port=8888 --no-browser
##################### INSTALLATION END #####################
## TEST
ADD test-suite.sh /tmp/test-suite.sh
RUN ./test-suite.sh
## Clean up
RUN rm -rf /tmp/*