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