#!/bin/bash
#
# Copyright (c) 2014 Science Automation, Inc. http://www.scivm.com.  All rights reserved.
# 
# email: contact@scivm.com
# support:  http://support.scivm.com
#
# The MIT License (MIT)
# 
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.  The motd file shall remain
# included to the Dockerfile and unmodified.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
#
export LD_LIBRARY_PATH=/usr/local/lib/intel

# build numpy from source to use mkl blas and lapack
cd /tmp
gunzip numpy-1.8.0.tar.gz
tar xvf numpy-1.8.0.tar
cd numpy-1.8.0
cp /tmp/site.cfg .
python setup.py config install
cd /tmp
rm -r -f /tmp/numpy-1.8.0 numpy-1.8.0.tar.gz

# build scipy from source to use mkl blas and lapack
cd /tmp
gunzip scipy-0.13.2.tar.gz
tar xvf scipy-0.13.2.tar
cd scipy-0.13.2
python setup.py config install
cd /tmp
rm -r -f /tmp/scipy-0.13.2 scipy-0.13.2


# install rest of scipy
pip install distribute==0.6.49
pip install pyzmq==14.0.0
pip install ipython==1.1.0
pip install matplotlib==1.3.1
pip install pandas==0.12.0
pip install sympy==0.7.3
pip install nose==1.3.0

# other packages
pip install argparse==1.2.1
pip install beautifulsoup==3.2.0
pip install biopython==1.62
pip install boto==2.15.0
pip install cython==0.19.2
pip install faulthandler==2.2
pip install h5py==2.2.0
pip install html5lib==0.99
pip install httplib2==0.8
pip install lxml==3.2.3
pip install mdp==3.3
pip install mysql-python==1.2.4
pip install nltk==2.0.4
pip install numexpr==2.2.2
pip install oursql==0.9.3.1
pip install paramiko==1.8.0
pip install PIL==1.1.7
pip install ply==3.4
pip install psutil==1.1.3
pip install psycopg2==2.5.1
pip install pycrypto==2.6.1
pip install pyface==4.3.0
pip install pyfits==3.1.2
pip install pyflakes==0.7.3
pip install pyglet==1.1.4
pip install pymc==2.3
pip install pyparsing==2.0.1
pip install Pyrex==0.9.9
pip install python-dateutil==2.1
pip install pytz==2013.7
pip install PyYAML==3.10
pip install scikits-image==0.7.1
pip install scikit-learn==0.14.1
pip install patsy==0.2.1
pip install statsmodels==0.5.0
pip install simplejson==3.3.1
pip install six==1.4.1
pip install SQLAlchemy==0.8.3
pip install storm==0.20
pip install tables==3.0.0
pip install tornado==3.1.1
pip install traits==4.3.0
pip install traitsui==4.3.0
pip install Twisted==13.1.0
pip install wsgiref==0.1.2
pip install zope.interface==4.0.5