bmslab/gatk repository overview

#---------------------------------------------------------------------------------- GATK Dockerfile Remember to put the dockerfile in the same directory of GenomeAnalysisTK-2.3-9-ge5ebf34 Versions: GATK:v2.3.9 (ge5ebf34) #----------------------------------------------------------------------------------

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 GATK! #----------------------------------------------------------------------------------

WORKDIR /home/GenomeAnalysisTK-2.3-9-ge5ebf34

RUN ln -s /home/GenomeAnalysisTK-2.3-9-ge5ebf34/resources /usr/local/bin RUN ln -s /home/GenomeAnalysisTK-2.3-9-ge5ebf34/gatk2.3.9.jar /usr/local/bin

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

ENV HELP='usage for single sample: java -jar GenomeAnalysisTK.jar -R file.fasta -T HaplotypeCaller -I sample.bam -o output.vcf'

CMD echo $HELP