FROM ubuntu:16.04

MAINTAINER Diego Villamaina version: 0.2

## Update repo list and install required packages ####
RUN apt-get update -y && apt-get install -y \
    software-properties-common \
    git-core \
    apt-transport-https \
    wget \
    unzip \
    build-essential \
    time \
    libfindbin-libs-perl \
    libz-dev \
    libbz2-dev \
    liblzma-dev \
    zlib1g-dev \
    libncurses5-dev \
    libncursesw5-dev \
    libcurl4-openssl-dev \
    libxml2-dev \
    gfortran \
    g++ \
    libreadline6-dev \
    libx11-dev \
    libxt-dev \
    tk-dev \
    libpng12-dev \
    libjpeg-dev \
    libcairo2-dev \
    libarmadillo-dev \
    libarmadillo6 \
    libffi-dev \
    libssl-dev \
    docker.io \
    python-dev \
    python3-pip \  
    python2.7-dev \ 
    python-pip \
    python-numpy \
    python-matplotlib \
    python-pysam \
    sortmerna \  
    trimmomatic \ 
    bedtools 

## Install snakemake (Require python >= 3.5)
RUN pip3 install snakemake

## Grna app 
COPY Snakefile grna.py /grna/

## Cannot run pip install <package> gives: ImportError: cannot import name main  
RUN pip install --upgrade pip && \
    python -m pip install htseq && \
    python -m pip install multiqc && \
    python -m pip install virtualenv 
    
### Install gc3pie ###

#RUN wget https://raw.githubusercontent.com/uzh/gc3pie/master/install.py && \
COPY install.py /root/ 
RUN  python /root/install.py --develop -y

## Install packages within gc3pie virtualenv
RUN . /root/gc3pie/bin/activate && \
    pip install os-client-config \ 
    python-novaclient \
    python-neutronclient \
    python-openstackclient

# Add gc3pie.conf file (my own conf for demo)
COPY gc3pie.conf /root/.gc3/

# Add SC auth file
COPY enhancer.ch-openrc.sh run_grna.sh /

## Install FASTQC ###
WORKDIR /opt
RUN wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip && \
    unzip fastqc_v0.11.8.zip && \
    chmod 755 /opt/FastQC/fastqc && \
    rm /opt/fastqc_v0.11.8.zip 

###  Install R ###
#WORKDIR /opt
#ENV R_VERS=R-3.4.1

#RUN wget https://cran.r-project.org/src/base/R-3/$R_VERS.tar.gz && \
#    tar -xzf $R_VERS.tar.gz && \
#    cd /opt/$R_VERS && \
#    ./configure && make && make install && \ 
#    rm /opt/$R_VERS.tar.gz

## Install DESeq2 ###
#RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLite("DESeq2", dep = TRUE)'


############## STAR 2.6.0 ###############
WORKDIR /opt 
RUN wget https://github.com/alexdobin/STAR/archive/2.6.0a.tar.gz && \
    tar -xzf 2.6.0a.tar.gz && \ 
    cd /opt/STAR-2.6.0a/source && \
    make STAR && \
    rm /opt/2.6.0a.tar.gz

################ #Samtools 1.3.1# #########
WORKDIR /opt 
RUN wget https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2 && \
    tar --bzip2 -xf samtools-1.2.tar.bz2 && \
    cd samtools-1.2 && \
    make && \
    make install && \
    rm /opt/samtools-1.2.tar.bz2

###### Add tools PATHS to $PATH #########
ENV PATH="/opt/STAR-2.6.0a/source/:/opt/FastQC/:${PATH}"

######## sortmerna: Download the database and index it #####
WORKDIR /usr/bin  
RUN /usr/share/sortmerna/rRNA_databases/scripts/fetch_rrna_data.sh && \
    mkdir -p /usr/share/sortmerna/rRNA_databases/index && \
    ./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-arc-16s-id95 && \
    ./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-arc-23s-id98 && \
    ./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-bac-16s-id90 && \
    ./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-bac-23s-id98 && \
    ./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-euk-18s-id95 && \
    ./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/silva-euk-28s-id98 && \
    ./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/rfam-5.8s-database-id98 && \
    ./indexdb_rna --ref /usr/share/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta,/usr/share/sortmerna/rRNA_databases/index/rfam-5s-database-id98  

ENTRYPOINT ["/run_grna.sh"]