# Base container with tools needed for the IMP pipeline
#
# VERSION       0.1

#FROM debian:wheezy
FROM ubuntu:trusty
MAINTAINER yohan.jarosz@uni.lu


################
# dependencies #
################
RUN apt-get update && apt-get -yq upgrade
RUN apt-get install -yq libboost-dev
RUN apt-get install -yq make cmake wget build-essential unzip
RUN apt-get install -yq openjdk-7-jdk ant git tig vim
RUN 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
RUN apt-get install -yq bioperl=1.6.923-1 tabix=0.2.6-2 zlib1g zlib1g-dev
RUN apt-get install -yq samtools gnuplot python3
RUN apt-get install -yq r-base r-base-dev
RUN apt-get install -yq libncurses5 libncurses5-dev sudo libatlas-base-dev python2.7 gfortran python-dev \
&& rm -rf /var/lib/apt/lists/*
#
RUN update-alternatives --set java /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java


######################################
# Add user IMP and add it to sudoers #
#         Setup directories          #
#        Tools installations         #
######################################

## Add SNAKEMAKE and python3 dependencies
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 \
## Install bioservices. Using version 1.3.5 because script doesn't work with latest version
&& pip install -Iv https://pypi.python.org/packages/source/b/bioservices/bioservices-1.3.5.tar.gz \
&& rm get-pip.py \
## fastuniq
&& wget http://downloads.sourceforge.net/project/fastuniq/FastUniq-1.1.tar.gz \
&& tar -xzf FastUniq-1.1.tar.gz \
&& cd FastUniq/source \
&& make \
&& mv fastuniq /usr/bin/. \
&& cd ../.. && rm -rf FastUniq* \
## Trimmomatic
&& wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/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*
## idba ud
RUN wget http://hku-idba.googlecode.com/files/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* \
## cap3
&& wget http://seq.cs.iastate.edu/CAP3/cap3.linux.x86_64.tar \
&& tar -xf cap3.linux.x86_64.tar \
&& cp CAP3/cap3 /usr/bin \
&& rm -rf cap3* CAP3 \
## bwa
&& wget http://downloads.sourceforge.net/project/bio-bwa/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*
## htqc toolbox
RUN wget http://downloads.sourceforge.net/project/htqc/htqc-1.91.1-Source.tar.gz \
&& tar -xzf htqc-1.91.1-Source.tar.gz \
&& cd htqc-1.91.1-Source \
&& mkdir build \
&& cd build \
&& cmake .. \
&& make \
&& make install \
&& cd ../.. && rm -rf htqc* \
## freebayes
&& git clone --recursive git://github.com/ekg/freebayes.git \
&& cd freebayes \
&& git checkout -b v0.9.16 v0.9.16 \
&& make \
&& make install \
&& cd .. && rm -rf freebayes \
## vcftools
&& wget http://downloads.sourceforge.net/project/vcftools/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*

## prokka
RUN wget http://www.vicbioinformatics.com/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* \
## parallel
&& wget ftp://ftp.gnu.org/gnu/parallel/parallel-20140422.tar.bz2 \
&& tar -xjf parallel-20140422.tar.bz2 \
&& cd parallel-20140422 \
&& ./configure \
&& make \
&& make install \
&& cd .. && rm -rf parallel* \
# sortmerna
&& wget https://github.com/biocore/sortmerna/archive/2.0.tar.gz -O 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* \
&& cd /home/imp/lib
# Bedtools
RUN git clone https://github.com/arq5x/bedtools2.git
&& cd bedtools2/
&& git checkout v2.22.0
&& make
# bh_tsne
RUN cd /home/imp/tmp \
&& git clone https://github.com/claczny/VizBin.git \
&& cd VizBin/src/backend/bh_tsne \
&& g++ quadtree.cpp tsne.cpp -o bh_tsne -O3 -I./CBLAS/include -L./ -lcblas \
&& mv bh_tsne /usr/bin/ \
&& cd /home/imp/tmp \
&& rm -rf VizBin \
&& rm -rf /home/imp/tmp

## R
RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile \
&& Rscript -e "install.packages('ggplot2')" \
&& Rscript -e "install.packages('gtools')" \
&& Rscript -e "install.packages('data.table')" \
&& Rscript -e "install.packages('reshape')" \
&& Rscript -e "install.packages('stringr')" \
&& Rscript -e "install.packages('xtable')" \
&& Rscript -e "install.packages('psych')" \
&& Rscript -e "install.packages('beanplot')" \
&& Rscript -e "source('http://bioconductor.org/biocLite.R');biocLite('genomeIntervals')"


## Install KronaPlot
RUN cd /home/imp/lib \
&& wget "http://downloads.sourceforge.net/project/krona/KronaTools (Mac, Linux)/KronaTools-2.5.tar" \
&& tar -xvf KronaTools-2.5.tar \
&& cd KronaTools-2.5 \
&& perl install.pl


## htslib
RUN cd /tmp \
&& wget https://github.com/samtools/htslib/releases/download/1.2.1/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

## Platypus
RUN cd /home/imp/lib \
&& wget http://www.well.ox.ac.uk/bioinformatics/Software/Platypus-latest.tgz \
&& tar -xvzf Platypus-latest.tgz \
&& cd Platypus_0.8.1 \
&& bash buildPlatypus.sh

## Megahit
RUN cd /home/imp/lib \
&& git clone https://github.com/voutcn/megahit.git \
&& cd megahit \
&& make


######################
# ship pipeline code #
######################
#COPY Snakefile /home/imp/integrated-metaomic-pipeline/Snakefile
#COPY src/ /home/imp/integrated-metaomic-pipeline/src

#################
# add test data #
#################
#COPY test/ /home/imp/integrated-metaomic-pipeline/test

# add snakemake completion
RUN echo "`snakemake --bash-completion`" >> ~/.bashrc
# add LD_LIBRARY_PATH
RUN 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:$PATH

VOLUME ["/shared"]
WORKDIR /home/imp/integrated-metaomic-pipeline
CMD ["/bin/bash"]