bmslab/scalpel repository overview

#---------------------------------------------------------------------------------- Scalpel Dockerfile Remember to put the dockerfile in the same directory of Scalpel Versions: Scalpel:v0.5.3 #----------------------------------------------------------------------------------

FROM ubuntu:16.04

WORKDIR /home

RUN apt-get update && apt-get install -y
build-essential
cmake
zlib1g-dev
libncurses-dev
git

#---------------------------------------------------------------------------------- #Let's build Scalpel! #----------------------------------------------------------------------------------

ADD . /home

WORKDIR /home

RUN tar -x -f scalpel-0.5.3.tar

WORKDIR /home/scalpel-0.5.3

RUN make

WORKDIR /usr/local/bin RUN mkdir ./bamtools-2.3.0/ WORKDIR /usr/local/bin/bamtools-2.3.0/ RUN mkdir ./bin/ WORKDIR /home/scalpel-0.5.3

RUN ln -s /home/scalpel-0.5.3/scalpel-discovery /usr/local/bin RUN ln -s /home/scalpel-0.5.3/scalpel-export /usr/local/bin RUN ln -s /home/scalpel-0.5.3/FindSomatic.pl /usr/local/bin RUN ln -s /home/scalpel-0.5.3/FindDenovos.pl /usr/local/bin RUN ln -s /home/scalpel-0.5.3/FindVariants.pl /usr/local/bin RUN ln -s /home/scalpel-0.5.3/HashesIO.pm /usr/local/bin RUN ln -s /home/scalpel-0.5.3/Usage.pm /usr/local/bin RUN ln -s /home/scalpel-0.5.3/Utils.pm /usr/local/bin RUN ln -s /home/scalpel-0.5.3/Microassembler/Microassembler /usr/local/bin RUN ln -s /home/scalpel-0.5.3/Microassembler/bamtools-2.3.0/bin/bamtools /usr/local/bin/bamtools-2.3.0/bin/ RUN ln -s /home/scalpel-0.5.3/Microassembler/bcftools-1.1/bcftools /usr/local/bin RUN ln -s /home/scalpel-0.5.3/Microassembler/samtools-1.1/samtools /usr/local/bin

#----------------------------------------------------------------------------------

ENV HELP='\nusage:\n\tscalpel-discovery [OPTIONS]\n\tscalpel-export [OPTIONS]'

CMD echo $HELP