GASiC - Genome Abundance Similarity Correction


Downloading
-----------

GASiC is hosted on sourceforge.net

  http://sourceforge.net/projects/gasic/

Further information can be found on the group homepage:

  http://www.rki-ng4.de/


System Requirements
-------------------

GASiC was built and tested on Linux operating systems.

For Windows or Mac OS users, we provide a virtual machine (VM) with a 
pre-installed and tested version of GASiC. Download links and further
information can be found at:

  http://sourceforge.net/projects/gasic/

and

  http://www.rki-ng4.de/

The VirtualBox software is reqired to run the virtual machine. It can
can be obtained at:

  https://www.virtualbox.org/


Documentation
-------------

Documentation can be found in the folder 'doc/'. The sourceforge wiki
pages also contain useful information.

GASiC is self-documenting. Calling a script with the '--help' option
displays help on the script functionality. 

The GASiC source code is thoroughly commented. Developers might find
answers there.


Installation
------------

GASiC is a Python script library and does not need installation. If all 
dependencies are installed correctly, GASiC scripts can be run directly
from the main folder.

We recommend to add the GASiC main directory to your PYTHONPATH environment
variable. On the console type:
  export PYTHONPATH=$PYTHONPATH:/path/to/GASiC

To use GASiC from any directory, you may also adjust your PATH environment
variable:
  export PATH=$PATH:/path/to/GASiC


Dependencies
------------

GASiC was tested with the software listed below. Older versions might still
work, but are not tested.

  * Python 2.7, http://www.python.org/

  * NumPy 1.6.1, http://numpy.scipy.org/
  * SciPy 0.10.0, http://www.scipy.org/
  * BioPython 1.58, http://biopython.org/wiki/Biopython
  * pysam 0.6, http://code.google.com/p/pysam/

GASiC calls alignment tools and read simulators from the command line. These
tools must be installed and added to the PATH before GASiC can be used.
We tested GASiC with the following tools:

  * bowtie, http://bowtie-bio.sourceforge.net/index.shtml
  * bowtie2, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
  * bwa, http://bio-bwa.sourceforge.net/bwa.shtml

  * Mason, http://www.seqan.de/projects/mason/
  * dwgsim, http://dnaa.sourceforge.net/


Bug Reporting
-------------

You can send GASiC bug reports to <LindnerM@rki.de>.

Please provide a minimal example of the code producing the error and the
error message(s). Also check which libraries (see Dependencies) you use.




-------------------------------------------------------------------------------
Copyright (c) 2012, Martin S. Lindner, LindnerM@rki.de, 
Robert Koch-Institut, Germany,
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
    * Redistributions of source code must retain the above copyright
      notice, this list of conditions and the following disclaimer.
    * Redistributions in binary form must reproduce the above copyright
      notice, this list of conditions and the following disclaimer in the
      documentation and/or other materials provided with the distribution.
    * The name of the author may not be used to endorse or promote products
      derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL MARTIN S. LINDNER BE LIABLE FOR ANY
DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
