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Last pushed: a year ago
Short Description
version 0.5.3
Full Description

#----------------------------------------------------------------------------------
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 <COMMAND> [OPTIONS]\n\tscalpel-export <COMMAND> [OPTIONS]'

CMD echo $HELP

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bmslab

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