bmslab/vardict_g repository overview

#---------------------------------------------------------------------------------- Vardict Dockerfile for GERMLINE CALLING 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

#-- WORKDIR /home/VarDictJava/VarDict

RUN chmod 777 teststrandbias.R RUN chmod 777 var2vcf_valid.pl

WORKDIR /home/VarDictJava

#--

RUN ln -s /home/VarDictJava/build/install/VarDict/bin/VarDict /usr/local/bin RUN ln -s /home/VarDictJava/VarDict/teststrandbias.R /usr/local/bin RUN ln -s /home/VarDictJava/VarDict/var2vcf_valid.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