Dockerfile1

### Try to dockerize the Tophat version 2.0.11.
## 1.import the samtools from the images registry.

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# I tried to compile the boost_1_55_0 for the tophat, but it seems that there some trivial errors when compiling it, also the time for compiling is too long for a laptop.
# Therefore, I use the already exited the dockerized Tophat which with samtools installe # to be my base image.
####

From octavianus90/samtools-0.1.19

# Mark the maintainer 
MAINTAINER David Weng weng@email.arizona.edu
RUN echo "deb http://archive.ubuntu.com/ubuntu precise main universe" > /etc/apt/sources.list
RUN apt-get update

## 2.Install Boost which is needed by the tophat.
RUN wget https://www.dropbox.com/s/fl2wc8ndndmico6/boost_1_55_0.tar.gz
RUN tar zxvf boost_1_55_0.tar.gz
WORKDIR boost_1_55_0
RUN ./bootstrap.sh
RUN apt-get install -y g++

#!!! Problem here the follwing command took almost 15 minutes to compile, and at the end, it does not report useful error code.
RUN ./bjam --prefix=/home/vagrant/boost_1_55_0 link=static stage install

## 3.Install Tophat
RUN wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.11.tar.gz
RUN tar zxvf tophat-2.0.11.tar.gz
WORKDIR tophat-2.0.11
RUN ./configure