mheiges/singularity-craig:latest

$ singularity pull shub://mheiges/singularity-craig:latest

Singularity Recipe

BootStrap: docker
From: centos:7

%runscript
    exec echo "The runscript is the containers default runtime command!"

%environment
  SAMTOOLS_VER=1.7
  export PREFIX_INSTALLATION=/opt/craig
  export CRAIG_HOME="${PREFIX_INSTALLATION}"
  export SAMTOOLS_HOME=/opt/samtools
  export REGTOOLS_HOME=/opt/regtools
  export PATH="${CRAIG_HOME}/bin:${CRAIG_HOME}/perl/bin:${CRAIG_HOME}/python/bin:${REGTOOLS_HOME}/build:${SAMTOOLS_HOME}/bin:${PATH}"
  export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${CRAIG_HOME}/lib"

%labels
   AUTHOR mheiges@uga.edu

%post
  source /.singularity.d/env/90-environment.sh

  WORKDIR=/tmp
  
  yum install -y --disableplugin=fastestmirror epel-release && \
  yum clean all
  yum update -y --disableplugin=fastestmirror

  # build tools that will be uninstalled after compile to reduce image
  # size
  yum install -y --disableplugin=fastestmirror \
    autoconf \
    automake \
    boost-regex \
    bzip2 \
    bzip2-devel \
    cmake \
    gcc \
    gcc-c++ \
    git \
    libtool \
    make \
    ncurses-devel \
    python2-pip \
    xz-devel \
    zlib-devel
  yum_txn_id=$(yum history list  |  sed -n '/^---/{n;p}' | awk '{print $1}')

  cd "${WORKDIR}"
  if [[ -e sparsehash ]]; then
    pushd sparsehash
    git reset -- .
    git clean -f -x -d -- .
    git pull
    popd
  else
    git clone https://github.com/sparsehash/sparsehash.git
  fi

  cd sparsehash && \
    ./configure && \
    make install

  # regtools
  # https://regtools.readthedocs.io/en/latest/
  if [[ -e "${REGTOOLS_HOME}" ]]; then
    pushd "${REGTOOLS_HOME}"
    git reset -- .
    git clean -f -x -d -- .
    git pull
    popd
  else
    git clone https://github.com/griffithlab/regtools "${REGTOOLS_HOME}"
  fi
  cd "${REGTOOLS_HOME}"
  mkdir build
  cd build/
  cmake ..
  make

  # uncomment '#1' when working with dev CraiG fork
  cd "${WORKDIR}"
  if [[ -e CraiG ]]; then
    pushd CraiG
    git reset -- .
    git clean -f -x -d -- .
    #1 git fetch
    #1 git checkout ebrc_working
    git pull
    popd
  else
    git clone https://github.com/axl-bernal/CraiG
    #1 git clone https://github.com/mheiges/CraiG.git
    #1 pushd CraiG
    #1 git checkout ebrc_working
    #1 popd
  fi

  cd CraiG  && \
    ./autogen.sh  && \
    ./configure --prefix="${PREFIX_INSTALLATION}" CXXFLAGS="$CXXFLAGS -std=c++11" --enable-opt=yes --enable-mpi=no && \
    make && make install && make installcheck && \
      # chmod models is temporary until better design is available
    chmod 1777 "${PREFIX_INSTALLATION}/models" && \
    if [[ -f python/requirements.txt ]]; then pip install -r python/requirements.txt; fi

  cd "${WORKDIR}"
  curl -L "https://sourceforge.net/projects/samtools/files/samtools/${SAMTOOLS_VER}/samtools-${SAMTOOLS_VER}.tar.bz2/download" -o samtools-${SAMTOOLS_VER}.tar.bz2
  rm -rf "samtools-${SAMTOOLS_VER}"
  tar xf "samtools-${SAMTOOLS_VER}.tar.bz2"
  pushd "samtools-${SAMTOOLS_VER}"
  ./configure --prefix=/opt/samtools
  make
  make install
  popd

  pip install numpy

  # uninstall build tools
  #yum history undo -y ${yum_txn_id}

  # packages that persist in final image
  yum install -y --disableplugin=fastestmirror \
    python \
    perl

  yum clean all && rm -rf /var/cache/yum
  
  if [[ "${WORKDIR}" != "/tmp" ]]; then
    rm -rf "${WORKDIR}"
  fi

Collection

• Name: mheiges/singularity-craig
• License: None

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