singularity.def

Bootstrap: library
From: ubuntu:16.04

%files
  .git /topmed_variant_calling/.git
  .gitmodules /topmed_variant_calling/.gitmodules
  apigenome /topmed_variant_calling/apigenome
  bamUtil /topmed_variant_calling/bamUtil
  bcftools /topmed_variant_calling/bcftools
  cramore /topmed_variant_calling/cramore
  htslib /topmed_variant_calling/htslib
  invNorm /topmed_variant_calling/invNorm
  king /topmed_variant_calling/king
  libStatGen /topmed_variant_calling/libStatGen
  libsvm /topmed_variant_calling/libsvm
  samtools /topmed_variant_calling/samtools
  scripts /topmed_variant_calling/scripts
  vt-topmed /topmed_variant_calling/vt-topmed

%environment
  export LC_ALL=C

%post
  set -eu

  apt-get update && apt-get install -y \
    apt-utils \
    automake \
    autoconf \
    build-essential \
    cmake \
    default-jre \
    default-jdk \
    gdb \
    git \
    ghostscript \
    gnuplot \
    groff \
    libcurl4-gnutls-dev \
    liblzma-dev \
    libncurses5-dev \
    libssl-dev \
    libzstd-dev \
    python3 \
    r-base \
    wget \
    zlib1g-dev

  cd /topmed_variant_calling

  git submodule init
  git submodule update

  git clone https://github.com/samtools/htslib htslib-1.13
  cd htslib-1.13
  git checkout 1.13
  git submodule update --init --recursive
  autoreconf -i
  ./configure --disable-libcurl
  make
  cd ..

  mkdir plink
  cd plink/
  wget http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20190617.zip
  unzip plink_linux_x86_64_20190617.zip
  rm plink_linux_x86_64_20190617.zip
  install -T plink /usr/local/bin/plink-1.9
  cd ..

  wget https://sourceforge.net/projects/snpeff/files/snpEff_v4_3t_core.zip/download
  unzip download
  rm download
  rm -r clinEff/

  cd libsvm/
  make clean
  make
  cd ..

  cd apigenome
  git clean -fdx
  autoreconf -vfi
  ./configure --prefix $PWD
  make
  make install
  cd ..
 
  cd libStatGen
  git clean -fdx
  make
  cd ..
 
  cd bamUtil
  git clean -fdx
  make
  cd ..
  
  cd invNorm
  git clean -fdx
  make
  cd ..

  cd htslib
  git clean -fdx
  autoheader
  autoconf
  ./configure --disable-libcurl
  make
  install bgzip /usr/local/bin
  install tabix /usr/local/bin
  cd ..

  cd vt-topmed
  git clean -fdx
  make
  cd ..
  
  cd cramore
  git clean -fdx
  mkdir build
  cd build
  cmake -DCMAKE_BUILD_TYPE=Release -DHTS_INCLUDE_DIRS=/topmed_variant_calling/htslib-1.13  -DHTS_LIBRARIES=/topmed_variant_calling/htslib-1.13/libhts.a ..
  make
  cd ../..
  
  cd samtools
  git clean -fdx
  autoheader
  autoconf -Wno-syntax
  ./configure
  make
  make install
  cd ..
  
  cd bcftools
  git clean -fdx
  make
  make install
  cd ..

  cd king
  rm -f king *.o
  g++ -O3 -fopenmp -o king *.cpp -lm -lz
  cd ..