FROM ubuntu:vivid
MAINTAINER Tiago Antao <tra@popgen.net>

ENV DEBIAN_FRONTEND noninteractive
#We need this for phylip
RUN echo 'deb http://archive.ubuntu.com/ubuntu vivid multiverse' >> /etc/apt/sources.list

RUN apt-get update
RUN apt-get upgrade -y
RUN apt-get install -y git python3-numpy wget gcc g++ python3-dev unzip make
RUN apt-get install -y python3-matplotlib python3-reportlab python3-pip r-base
RUN apt-get install -y clustalw fasttree t-coffee python3-pil
RUN apt-get install -y bwa ncbi-blast+ emboss clustalo phylip mafft muscle
RUN apt-get install -y samtools phyml wise raxml language-pack-en
RUN apt-get install -y embassy-phylip paml probcons
#For BioSQL
RUN apt-get install -y mysql-server python-mysqldb postgresql python3-psycopg2
RUN apt-get install -y python3-mysql.connector
RUN apt-get clean
#for Phylo_CDAO
RUN pip3 install rdflib

#Database servers
RUN echo "host    all             all             ::1/128                 trust" > /etc/postgresql/9.4/main/pg_hba.conf
RUN echo "service postgresql start" > .bashrc
RUN echo "service mysql start" >> .bashrc
RUN echo "export DIALIGN2_DIR=/tmp" >> .bashrc
RUN echo "export LANG=en_GB.UTF-8" >> .bashrc
RUN echo "service postgresql start" > entrypoint.sh
RUN echo "service mysql start" >> entrypoint.sh
RUN echo "export DIALIGN2_DIR=/tmp" >> entrypoint.sh
RUN echo "export LANG=en_GB.UTF-8" >> entrypoint.sh

#Manual software


#reportlab fonts
RUN wget http://www.reportlab.com/ftp/fonts/pfbfer.zip
WORKDIR cd /usr/lib/python3.4/dist-packages/reportlab
RUN  mkdir fonts
WORKDIR cd /usr/lib/python3.4/dist-packages/reportlab/fonts
RUN unzip /pfbfer.zip
WORKDIR /
RUN rm pfbfer.zip

#genepop
RUN mkdir genepop
WORKDIR /genepop
RUN wget http://kimura.univ-montp2.fr/~rousset/sources.tar.gz
RUN tar zxf sources.tar.gz
RUN g++ -DNO_MODULES -o Genepop GenepopS.cpp -O3
RUN cp Genepop /usr/bin
WORKDIR /
RUN rm -rf genepop

#msaprobs
RUN wget "http://sourceforge.net/projects/msaprobs/files/latest/download?source=files" -O MSA.tar.gz
RUN tar zxf MSA.tar.gz
WORKDIR /MSAProbs-0.9.7/MSAProbs
RUN make
RUN cp msaprobs /usr/bin
WORKDIR /

#DSSP
RUN wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64
RUN mv dssp-2.0.4-linux-amd64 /usr/bin/dssp
RUN chmod a+x /usr/bin/dssp

#XXmotif
WORKDIR /usr/local/bin
RUN wget "http://xxmotif.genzentrum.lmu.de/index.php?id=download&version=64" -O xx.tar.gz
RUN tar zxf xx.tar.gz
RUN rm xx.tar.gz
WORKDIR /
ENV PYTHON_PATH /biopython

#Biopython
RUN git clone https://github.com/biopython/biopython.git
WORKDIR /biopython
RUN python3 setup.py install