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Last pushed: a year ago
Short Description
version v1.0
Full Description

#----------------------------------------------------------------------------------
Vardict Dockerfile
Remember to put the dockerfile in the same directory of Vardict
Versions: Vardict:v1.0

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

FROM java:7

WORKDIR /home

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

ADD . /home

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

#Let's build Vardict!

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

WORKDIR /home/VarDictJava

RUN chmod 755 gradlew

RUN /home/VarDictJava/gradlew clean installApp

RUN ln -s /home/VarDictJava/build/install/VarDict/bin/VarDict /usr/local/bin
RUN ln -s /home/VarDictJava/VarDict/testsomatic.R /usr/local/bin
RUN ln -s /home/VarDictJava/VarDict/var2vcf_somatic.pl /usr/local/bin
RUN ln -s /home/vardict.sh /usr/local/bin

WORKDIR /home

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

ENV HELP='usage: VarDict [-n name_reg] [-b bam] [-c chr] [-S start] [-E end] [-s seg_starts] [-e seg_ends] [-x #_nu] [-g gene] [-f freq] [-r #_reads] [-B #_reads] region_info'

CMD echo $HELP

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bmslab