jcuhpc/picard-tools repository overview

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. Contents of the Dockerfile:

FROM ubuntu:18.04 MAINTAINER [email protected]⁠

ENV PACKAGES picard-tools

ENV PICARD_VERSION 2.8.1

WORKDIR /home

RUN apt-get update &&
apt-get upgrade -y &&
useradd -ms /bin/bash luser &&
printf "#!/bin/bash\nexport DEBIAN_FRONTEND=noninteractive\napt-get install -y tzdata\nln -fs /usr/share/zoneinfo/Australia/Brisbane /etc/localtime\ndpkg-reconfigure --frontend noninteractive tzdata\n" >tzinst && chmod 700 tzinst && ./tzinst && rm -f tzinst &&
apt-get install -y ${PACKAGES} &&
apt-get clean

USER luser WORKDIR /home/luser ENV PICARD /usr/share/java/picard.jar