Dockerfile

FROM ubuntu:latest
MAINTAINER Nuno Agostinho <nunodanielagostinho@gmail.com>

RUN apt-get update

# samtools
# Usage: samtools [OPTIONS]
RUN apt-get install -y gcc
RUN apt-get install -y libncurses5-dev
RUN apt-get install -y libbz2-dev
RUN apt-get install -y liblzma-dev
RUN apt-get install -y libcurl4-openssl-dev
RUN apt-get install -y libssl-dev
RUN apt-get install -y zlib1g-dev
RUN apt-get install -y make

ENV SW=/root/software
WORKDIR ${SW}

ENV samtools=samtools-1.5
ADD ${samtools}.tar.bz2 .
WORKDIR ${samtools}

RUN ./configure
RUN make
RUN make install
WORKDIR ${SW}

# STAR
# Usage: STAR [options]
ENV star=STAR-2.5.3a
ADD ${star}.tar.bz2 .
ENV PATH="${PATH}:${SW}/${star}/bin"

# Python 2.7
ADD get-pip.py .
RUN apt-get install -y python
RUN python get-pip.py
RUN rm get-pip.py

RUN pip install --upgrade pip
RUN pip install numpy
RUN pip install scipy
RUN pip install pysam

RUN apt-get install -y python-dev
RUN apt-get install -y build-essential
RUN pip install matplotlib

RUN apt-get install -y bedtools

# rMATS
# Usage: python ${rmats}/RNASeq-MATS.py [options]
ENV rmats=rMATS.3.2.5
ADD ${rmats}.tar.bz2 .
WORKDIR ${rmats}

ENV file=RNASeq-MATS.py
RUN echo '#!/usr/bin/env python2.7' | \
	cat - ${file} > tmp && mv tmp ${file}
RUN chmod 777 ${file}

ENV file=bin/trimFastq.py
RUN echo '#!/usr/bin/env python2.7' | \
	cat - ${file} > tmp && mv tmp ${file}
RUN chmod 777 ${file}

ENV PATH="${PATH}:${SW}/${rmats}:${SW}/${rmats}/bin"