INSTALL

Before using oqtans, install the following 
standard linux software packages:

Ubuntu/Debian:
     make gcc g++ git libhdf5-lam-1.8.4 libfontconfig1 libgl1-mesa-glx 
     libglu1-mesa libreadline5 libgfortran3 gfortran libqrupdate1 
     python-dev pkg-config libncurses5-dev libreadline-dev libltdl-dev
     libpcre3-dev libhdf5-serial-dev gnuplot libidn11-dev cmake m4
     help2man texinfo texlive python2.6 (or python2.7)
     libcholmod1.7.1 libcurl4-openssl-dev libglu1-mesa-dev libfltk1.3-dev
     libfreetype6-dev libgraphicsmagick1-dev libgraphicsmagick++3 libgraphicsmagick++1-dev
     libfontconfig1-dev libfftw3-3 python-numpy python-matplotlib
     default-jre

Redhat/CentOS
     pkgconfig python-devel make gcc gcc-c++ cmake m4 texlive-latex texinfo texinfo-tex
     libtool-ltdl-devel pcre-devel libgfortran gcc-gfortran bison bison-runtime
     automake bison-devel readline-devel ncurses-devel zlib-devel help2man 
     numpy-f2py python2.6 (or python2.7) 

Mac OS X (macports packages with system python v2.7)
     py27-scipy py27-numpy help2man git-core gcc46 texlive
     m4 cmake texinfo R pkgconfig libpng 
     g95 qhull pcre gnuplot fltk-devel hdf5 readline-5
     qhull GraphicsMagick wget fftw-3-single hdf5-18

     also set the gcc compiler to gcc46:	
     sudo port select --set gcc mp-gcc46

Update the file
   oqtans/oqtans_conf.sh
to reflect the location of oqtans components and source it in galaxy's ~/.bashrc.

In addition we need the following software packages:
   octave version>=3.4, shogun version>=1.1, R version>=2, glpk, scipy version>=0.10, swig, samtools, numpy version>=1.6
These packages are available precompiled from 
   https://github.com/ratschlab/oqtans_dep
for multiple platforms.
The source code of these packages together with additional instructions are avialable from
   https://github.com/ratschlab/oqtans_src

Run
   cd oqtans ;
   ./oqtans_make.sh all
to compile all needed software components of oqtans tools.

Include the content of 
   tool_conf.xml.oqtans
into your galaxy's tool_conf.xml file.
   
Source oqtans/oqtans_conf.sh and restart galaxy.
Now you should be able to use oqtans without your galaxy instance.