bmslab/radia repository overview

FROM ubuntu:14.04

RUN apt-get update && apt-get install -y
build-essential
cmake
wget
git
zlib1g-dev
libncurses-dev
libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev

ADD . /home

WORKDIR /home

RUN wget http://python.org/ftp/python/2.7.5/Python-2.7.5.tgz⁠ RUN tar -xvf Python-2.7.5.tgz

WORKDIR /home/Python-2.7.5

RUN ./configure RUN make RUN make install

RUN python /home/get-pip.py

RUN pip install pysam

ADD . /home

WORKDIR /home/samtools-1.2 RUN make RUN make install

WORKDIR /home/Radia_v1.1.3/scripts

ENV HELP="USAGE: python radia.py patientId chromId -n normalDnaBamFilename.bam -t tumorDnaBamFilename.bam -f fasta.fa -o output -i nomedelfasta

CMD echo $HELP