PICRUSt is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.

• Version: 1.0.0
• Added: January, 2015
• Link: http://picrust.github.io/picrust/

• Show all available versions of picrust

  module avail picrust

• Load picrust module:

  module load picrust/1.0.0

• picrust has a bunch of python modules dependencies, so we'll just install them in python/2.7.8

  - load python/2.7.8, change ownership of $PYTHONHOME to yourself - 'coz we'll be installing lots of modules there.
  module load python/2.7.8
  scl enable devtoolset-1.1 bash
  sudo chown -R joguya:joguya /export/apps/python/2.7.8
  
  - Download & build matplotlib
  wget https://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.4.2/matplotlib-1.4.2.tar.gz
  tar -xvf matplotlib-1.4.2.tar.gz
  cd matplotlib-1.4.2
  python setup.py build
  python setup.py install
  
  - Download & build numpy
  wget "http://downloads.sourceforge.net/project/numpy/NumPy/1.9.1/numpy-1.9.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fnumpy%2Ffiles%2FNumPy%2F&ts=1420630876&use_mirror=liquidtelecom" -O "numpy-1.9.1.tar.gz"
  tar -xvf numpy-1.9.1.tar.gz
  cd numpy-1.9.1
  python setup.py build
  python setup.py install
  
  - Download & build scipy
  wget "http://downloads.sourceforge.net/project/scipy/scipy/0.14.1/scipy-0.14.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fscipy%2Ffiles%2Fscipy%2F&ts=1420633642&use_mirror=liquidtelecom" -O"scipy-0.14.1.tar.gz"
  tar xvf scipy-0.14.1.tar.gz
  cd scipy-0.14.1
  python setup.py build
  python setup.py install
  
  - Download & build pycogent
  wget "http://downloads.sourceforge.net/project/pycogent/PyCogent/1.5.3/PyCogent-1.5.3.tgz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fpycogent%2F&ts=1420724582&use_mirror=liquidtelecom" -O "PyCogent-1.5.3.tgz"
  tar xvf PyCogent-1.5.3.tgz
  python setup.py build
  python setup.py install
  
  - Download & build mysql-python
  wget "http://downloads.sourceforge.net/project/mysql-python/mysql-python-test/1.2.4b4/MySQL-python-1.2.4b4.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fmysql-python%2F&ts=1420724977&use_mirror=liquidtelecom" -O MySQL-python-1.2.4b4.tar.gz
  tar xvf MySQL-python-1.2.4b4.tar.gz
  cd MySQL-python-1.2.4b4
  python setup.py build
  python setup.py install
  
  - Download & build sqlalchemy
  wget "https://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.9.8.tar.gz" -O "SQLAlchemy-0.9.8.tar.gz"
  tar -xvf SQLAlchemy-0.9.8.tar.gz
  cd SQLAlchemy-0.9.8
  python setup.py build
  python setup.py install
  
  - Download & build mpi4py
  wget "https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-1.3.1.tar.gz" -O "mpi4py-1.3.1.tar.gz"
  tar -xvf mpi4py-1.3.1.tar.gz
  cd mpi4py-1.3.1
  module load openmpi/1.8.2
  python setup.py build
  python setup.py install
  
  - Download & build Sphinx
  wget "https://pypi.python.org/packages/source/S/Sphinx/Sphinx-1.3b2.tar.gz#md5=7ea36c45e795fd49185f8d4c075f6b62" -O "Sphinx-1.3b2.tar.gz"
  tar -xvf Sphinx-1.3b2.tar.gz
  cd Sphinx-1.3b2
  python setup.py build
  python setup.py install
  
  - Donwload & build pyqi
  wget "https://pypi.python.org/packages/source/p/pyqi/pyqi-0.3.2.tar.gz#md5=9507c06eeb22a816d963c860ad8e92ae" -O "pyqi-0.3.2.tar.gz"
  tar -xvf pyqi-0.3.2.tar.gz
  cd pyqi-0.3.2
  python setup.py build
  python setup.py install
  
  - Download & build cython
  wget http://cython.org/release/Cython-0.21.2.tar.gz -O Cython-0.21.2.tar.gz
  tar -xvf Cython-0.21.2.tar.gz
  cd Cython-0.21.2
  python setup.py build
  python setup.py install
  
  - Download hdf5 - already compiled, add lib dir to LD_LIBRARY_PATH. Create module for later use.
  wget "http://www.hdfgroup.org/ftp/HDF5/current/bin/linux-centos6-x86_64-gcc447/hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared.tar.gz" - O hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared.tar.gz
  cd hdf5-1.8.14-linux-centos6-x86_64-gcc447-shared
  module load openmpi/1.8.2
  sudo mkdir -p /export/apps/hdf5/1.8.14/
  sudo chown -R joguya:joguya /export/apps/hdf5/1.8.14/
  cp -r * /export/apps/hdf5/1.8.14/
  sudo chown -R root:root /export/apps/hdf5/1.8.14/
  
  - Download & build h5py
  wget "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz#md5=80c9a94ae31f84885cc2ebe1323d6758" -O h5py-2.4.0.tar.gz
  tar -xvf h5py-2.4.0.tar.gz
  cd h5py-2.4.0
  python setup.py build
  python setup.py install
  
  - Download & build biom-format - pycrust doesn't support biom-2.0 & above. use 1.3.1 instead
  wget https://pypi.python.org/packages/source/b/biom-format/biom-format-1.3.1.tar.gz -O "biom-format-1.3.1.tar.gz"
  tar -xvf biom-format-1.3.1.tar.gz
  cd biom-format-1.3.1
  python setup.py build
  python setup.py install
  
  - Download picrust
  wget "https://github.com/picrust/picrust/releases/download/1.0.0/picrust-1.0.0.tar.gz" -O "picrust-1.0.0.tar.gz"
  tar -xvf picrust-1.0.0.tar.gz
  cd picrust-1.0.0
  python setup.py build
  sudo mkdir -p /export/apps/picrust/1.0.0/bin/
  sudo chown -R joguya:joguya /export/apps/picrust/1.0.0/bin/
  python setup.py install --install-scripts=/export/apps/picrust/1.0.0/bin/
  sudo chown -R root:root /export/apps/picrust/1.0.0/bin/
  
  - revert permissions of $PYTHONHOME to root
  sudo chown -R root:root /export/apps/python/2.7.8

• picrust module file

  #%Module1.0
  #####################################################################
  ##
  ## PICRUSt Modulefile
  ## by James Oguya, <j.oguya@cgiar.org>
  ## January, 2015
  ##
  
  set appname         picrust
  set version         1.0.0
  set prefix          /export/apps/${appname}/${version}
  set exec_prefix     ${prefix}/bin
  set url             "http://picrust.github.io/picrust/"
  set msg             "PICRUSt (pronounced “pie crust”) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.\nOfficial Site: $url\n"
  
  module-whatis $msg
  
  proc ModulesHelp { } {
      puts stderr "$msg"
  }
  
  conflict            picrust
  
  prepend-path        PATH        ${exec_prefix}
  
  # load picrust dependencies
  if { ![is-loaded python/2.7.8] } {
      module load python/2.7.8
  }
  
  if { ![is-loaded hdf5/1.8.14] } {
      module load hdf5/1.8.14
  }

• deploy the new module using ansible

  ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=module