ILRI Research Computing

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

==== v1.0.0 ====
  * Version: 1.0.0
  * Added: January, 2015
  * Link: http://picrust.github.io/picrust/

=== Usage ===
  * Show all available versions of picrust<code>module avail picrust</code>
  * Load picrust module: <code>module load picrust/1.0.0</code>


=== Installation ===
  * picrust has a bunch of python modules dependencies, so we'll just install them in python/2.7.8<code>- 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
</code>
  * picrust module file<code>
#%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
}
</code>

  * deploy the new module using ansible<code>ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=module</code>