github.com/apptainer/singularity@v3.1.1+incompatible/examples/legacy/2.2/contrib/ubuntu-bio.def (about) 1 # Copyright (c) 2016, Ontropos, Inc. All rights reserved. 2 # 3 # Copyright (c) 2015-2017, Gregory M. Kurtzer. All rights reserved. 4 # 5 # "Singularity" Copyright (c) 2016, The Regents of the University of California, 6 # through Lawrence Berkeley National Laboratory (subject to receipt of any 7 # required approvals from the U.S. Dept. of Energy). All rights reserved. 8 9 BootStrap: debootstrap 10 OSVersion: trusty 11 MirrorURL: http://archive.ubuntu.com/ubuntu/ 12 Include: bash 13 14 15 %post 16 # Prep work 17 mkdir -p /tmp/work 18 cd /tmp/work 19 sed -i 's/main/main restricted universe/g' /etc/apt/sources.list 20 apt-get update 21 apt-get -y install wget bzip2 build-essential zlib1g-dev software-properties-common libncurses5-dev 22 apt-get clean 23 24 25 # Install BWA 26 wget "http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.15.tar.bz2?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fbio-bwa%2Ffiles%2F&ts=1473712599&use_mirror=heanet" -O bwa-0.7.15.tar.bz2 27 tar -xvjf bwa-0.7.15.tar.bz2 28 cd bwa-0.7.15/ 29 make 30 cp bwa /usr/bin/bwa 31 cd /tmp/work 32 33 34 # Install SAM Tools 35 wget "http://downloads.sourceforge.net/project/samtools/samtools/1.3.1/samtools-1.3.1.tar.bz2?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fsamtools%2Ffiles%2Fsamtools%2F1.3.1%2F&ts=1473713899&use_mirror=pilotfiber" -O samtools-1.3.1.tar.bz2 36 tar -xvjf samtools-1.3.1.tar.bz2 37 cd samtools-1.3.1 38 ./configure 39 make 40 cp samtools /usr/bin/samtools 41 42 43 # Install java prereq 44 apt-add-repository -y ppa:webupd8team/java 45 apt-get update 46 echo 'oracle-java8-installer shared/accepted-oracle-license-v1-1 select true' | debconf-set-selections 47 apt-get -y install oracle-java8-installer 48 apt-get clean 49 50 51 # This is now ready to have GATK (Genomic Analysis Took Kit) installed 52 # from: https://software.broadinstitute.org/gatk/download/ 53