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# Base container with tools needed for the IMP pipeline
#
# VERSION 0.1
FROM ubuntu:trusty
MAINTAINER yohan.jarosz@uni.lu
################
# dependencies #
################
RUN echo "deb http://ftp.halifax.rwth-aachen.de/ubuntu trusty main restricted universe multiverse" > /etc/apt/sources.list
RUN echo "deb http://ftp.halifax.rwth-aachen.de/ubuntu trusty-security main restricted universe" >> /etc/apt/sources.list
RUN echo "deb http://ftp.halifax.rwth-aachen.de/ubuntu trusty-updates main restricted universe multiverse">> /etc/apt/sources.list
RUN apt-get update \
&& apt-get install -yq python-software-properties software-properties-common \
&& add-apt-repository "deb http://cran.stat.ucla.edu/bin/linux/ubuntu trusty/" \
&& gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 \
&& gpg -a --export E084DAB9 | apt-key add - \
&& apt-get update \
&& apt-get -yq upgrade \
&& apt-get install -yq make cmake wget build-essential unzip openjdk-7-jdk ant git tig vim \
&& apt-get install -yq libboost-filesystem1.54-dev libboost-program-options1.54-dev libboost-regex1.54-dev libboost-system1.54-dev libboost-thread1.54-dev libboost-system1.54-dev \
&& apt-get install -yq bioperl=1.6.923-1 tabix=0.2.6-2 zlib1g zlib1g-dev samtools gnuplot python3 \
&& apt-get install -yq libncurses5 libncurses5-dev sudo libatlas-base-dev python2.7 gfortran python-dev \
&& update-alternatives --set java /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java
## Python dependencies and bioservices. Using version 1.3.5 because script doesn't work with latest version
RUN mkdir -p /home/imp/tmp /home/imp/lib \
&& cd /home/imp/tmp \
&& wget https://bootstrap.pypa.io/get-pip.py \
&& python3 get-pip.py \
&& python2.7 get-pip.py \
&& pip3 install snakemake docopt \
&& pip2.7 install numpy \
&& pip2.7 install scipy scikit-learn docopt \
&& pip install -Iv https://pypi.python.org/packages/source/b/bioservices/bioservices-1.3.5.tar.gz \
&& rm get-pip.py
# R with checkpoint libraries
ADD dependencies.R /home/imp/lib/
RUN mkdir /root/.checkpoint \
&& echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile \
&& Rscript -e "install.packages('checkpoint')" \
&& Rscript -e "library(checkpoint);checkpoint('2015-04-27', project='/home/imp/lib')" \
&& Rscript -e "source('http://bioconductor.org/biocLite.R');biocLite('genomeIntervals')"
######################################
# Tools installations #
######################################
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/FastUniq-1.1.tar.gz \
&& tar -xzf FastUniq-1.1.tar.gz \
&& cd FastUniq/source \
&& make \
&& mv fastuniq /usr/bin/. \
&& cd ../.. && rm -rf FastUniq* \
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/Trimmomatic-Src-0.32.zip \
&& unzip Trimmomatic-Src-0.32.zip \
&& cd trimmomatic-0.32 \
&& ant \
&& cp dist/jar/trimmomatic-0.32.jar /home/imp/lib/. \
#&& mkdir -p /usr/db/trimmomatic \
#&& cp adapters/* /usr/db/trimmomatic/. \
&& cd .. && rm -rf *rimmomatic*
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/idba-1.1.1.tar.gz \
&& tar -xzf idba-1.1.1.tar.gz \
&& cd idba-1.1.1 \
&& sed -i -e 's/static const uint32_t kMaxShortSequence = 128/static const uint32_t kMaxShortSequence = 2048/' src/sequence/short_sequence.h \
&& ./configure \
&& make \
&& make install \
&& mv bin/idba_ud /usr/bin \
&& mv bin/fq2fa /usr/bin \
&& cd .. && rm -rf idba* \
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/cap3.linux.x86_64.tar \
&& tar -xf cap3.linux.x86_64.tar \
&& cp CAP3/cap3 /usr/bin \
&& rm -rf cap3* CAP3 \
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/bwa-0.7.9a.tar.bz2 \
&& tar -xjf bwa-0.7.9a.tar.bz2 \
&& cd bwa-0.7.9a \
&& make \
&& mv bwa /usr/bin \
&& cd .. && rm -rf bwa*
## htsjdk - dependency of picard tools and FastQC (below)
RUN cd /home/imp/lib \
&& mkdir fastqc \
&& cd fastqc \
&& git clone https://github.com/samtools/htsjdk.git \
&& cd htsjdk/ \
&& ant htsjdk-jar \
## Picard tools - dependency of fastqc (below)
&& cd /home/imp/lib/fastqc \
&& git clone https://github.com/broadinstitute/picard.git \
&& mv /home/imp/lib/fastqc/htsjdk /home/imp/lib/fastqc/picard/ \
&& cd picard/ \
&& ant -lib lib/ant package-commands \
&& cd /home/imp/lib/fastqc \
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/fastqc_v0.11.3.zip \
&& unzip fastqc_v0.11.3.zip \
&& cd FastQC \
&& chmod 775 fastqc
RUN cd /home/imp/tmp \
&& git clone --recursive https://git-r3lab.uni.lu/R3/freebayes.git \
&& make \
&& make install \
&& cd .. && rm -rf freebayes \
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/vcftools_0.1.12b.tar.gz \
&& tar -xzf vcftools_0.1.12b.tar.gz \
&& cd vcftools_0.1.12b \
&& make \
&& make install \
&& cp -r bin/* /usr/bin \
&& cp -r perl/* /etc/perl/. \
&& cd .. && rm -rf vcftools*
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/prokka-1.11.tar.gz \
&& tar -xzf prokka-1.11.tar.gz \
&& cd prokka-1.11 \
&& cp bin/prokka* /usr/bin \
&& cp binaries/linux/* /usr/bin \
&& cd .. && rm -rf prokka* \
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/parallel-20140422.tar.bz2 \
&& tar -xjf parallel-20140422.tar.bz2 \
&& cd parallel-20140422 \
&& ./configure \
&& make \
&& make install \
&& cd .. && rm -rf parallel* \
## sortmerna
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/sortmerna.2.0.tgz \
&& tar -xzf sortmerna.2.0.tgz \
&& cd sortmerna-2.0 \
&& sh build.sh \
&& mv sortmerna indexdb_rna /usr/bin/. \
&& mv scripts/*.sh /home/imp/lib/. \
&& cd .. && rm -rf sortmerna* \
## bedtools2
&& git clone https://git-r3lab.uni.lu/R3/bedtools2.git \
Shaman Narayanasamy
committed
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/KronaTools-2.5.tar \
&& tar -xvf KronaTools-2.5.tar \
&& cd KronaTools-2.5 \
&& perl install.pl
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/htslib-1.2.1.tar.bz2 \
&& tar -jxvf htslib-1.2.1.tar.bz2 \
&& cd htslib-1.2.1 \
&& ./configure && make && make install \
&& cd .. && rm -rf htslib-1.2.1
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/Platypus-latest.tgz \
&& tar -xvzf Platypus-latest.tgz \
&& cd Platypus_0.8.1 \
&& bash buildPlatypus.sh
&& git clone https://git-r3lab.uni.lu/R3/megahit.git \
&& mv megahit* /usr/bin/. \
&& mv sdbg_builder_cpu /usr/bin/.
&& wget --no-check-certificate https://webdav-r3lab.uni.lu/public/R3lab/IMP/VizBin-dist.jar -O VizBin-dist.jar
## Quast/metaQuast
RUN cd /home/imp/lib \
&& git clone https://github.com/ablab/quast.git \
&& cd quast \
&& git checkout release_3.1 \
&& ./metaquast.py --test-no-ref \
&& ln -s $PWD/metaquast.py /usr/bin/metaquast \
&& apt-get update \
&& apt-get install python-matplotlib -y
######################
# ship pipeline code #
######################
# (commented for now)
#RUN cd /home/imp \
# && git clone https://git-r3lab.uni.lu/shaman.narayanasamy/IMP.git
######################
# set up environment #
######################
## add snakemake completion
RUN echo "`snakemake --bash-completion`" >> ~/.bashrc \
## add LD_LIBRARY_PATH
&& echo "export LD_LIBRARY_PATH=/usr/local/lib" >> ~/.bashrc
######################
# runtime parameters #
######################
ENV PATH /home/imp/lib/trinityrnaseq_r20140717:/home/imp/lib/Platypus_0.8.1:/home/imp/lib/megahit:/home/imp/lib/fastqc/FastQC:$PATH
ENV LD_LIBRARY_PATH /usr/local/lib/:/home/imp/lib/Platypus_0.8.1
VOLUME ["/data", "/output", "/databases", "/code"]
WORKDIR /code