File	Date	Author	Commit
microbegps	2015-03-23	Martin S. Lindner	[d42f17] Minor fixes and security checks
CHANGES	2014-05-07	Martin S. Lindner	[383374] Replaced NCBI catalog by gi -> taxid mapping file
LICENSE	2015-04-29	Martin S. Lindner	[0454a7] Removed old invalid email address. Contact Bern...
MANIFEST.in	2014-03-19	Martin S. Lindner	[ac47f7] adding MicrobeGPS source code
MicrobeGPS.spec	2014-03-19	Martin S. Lindner	[ac47f7] adding MicrobeGPS source code
README	2015-04-29	Martin S. Lindner	[0454a7] Removed old invalid email address. Contact Bern...
microbegps-cmd.py	unknown
run.py	2014-03-19	Martin S. Lindner	[ac47f7] adding MicrobeGPS source code
setup.py	2014-05-08	Martin S. Lindner	[8dba1e] Replaced NCBI catalog by gi -> taxid mapping file

Read Me

----------
MicrobeGPS
----------

(Version 1.0.1)


What is MicrobeGPS?
-------------------

MicrobeGPS is a bioinformatics tool for the analysis of metagenomic sequencing
data. The goal is to profile the composition of metagenomic communities as 
accurately as possible and present the results to the user in a convenient
manner. One main focus is reliability: the tool calculates quality metrics for
the estimated candidates and allows the user to identify false candidates
easily.

For more information about MicrobeGPS, including detailed description of the
underlying methodology, performance evaluation and use case examples, please
have a look at our publication in PLOS ONE:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117711


Availability
------------

MicrobeGPS is open source and freely available. The project is hosted on 
Sourceforge:
https://sourceforge.net/p/microbegps/

Binary distributions and source code can be downloaded there.


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

Detailed information about how to use MicrobeGPS is available from the project
wiki pages:
https://sourceforge.net/p/microbegps/wiki/


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

  * Windows
    We recommend to use the binary distribution which can be downloaded from
    the project page (see Availability). Download the .zip file with the 
    current version of MicrobeGPS and run the MicrobeGPS.exe executable file.

  * Linux
    We recommend to use the binary distribution which can be downloaded from
    the project page (see Availability). Download the .tar.gz file with the 
    current version of MicrobeGPS and run the MicrobeGPS executable file.

  * Source distribution
    Download the MicrobeGPS source file from the project home page. This method
    requires you to have Python (>= 2.7), PyQt4 and pip installed. To install 
    MicrobeGPS, run the following command from your command line:
    > pip install MicrobeGPS-X.X.tax.gz
    Now you can run the program by typing MicrobeGPS on the command line.

  * Development snapshot
    Check out a current development snapshot from the MicrobeGPS project page.
    Navigate to the MicrobeGPS directory. Now you can directly run MicrobeGPS  
    from the command line with:
    > python run.py
    Install MicrobeGPS using the provided setup.py script:
    > python setup.py install
    Now you can run the program by typing MicrobeGPS on the command line.


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

If you use one of the binary distributions, you do not need to install any
other software.

If you want to use the source distribution, please make sure that you meet the
following dependencies.

Software:
  * Python (2.7)
Python packages:
  * setuptools (1.3)
  * PyQt4 (4.9)

The following Python packages must be installed manually, if the tool is not
installed as a python egg or via the setup.py script:
  * numpy (1.8.0)
  * scipy (0.13.0)
  * matplotlib (1.3.1)
  * matplotlib_venn (0.9)

Note: we tested MicrobeGPS using the given version numbers. However, MicrobeGPS
should also work with older verions.


Licensing
---------

Please see the file called LICENSE.


Contact
-------

  * For questions about using MicrobeGPS, please consult the resources listed 
    in section Documentation. If this does not help, you may directly contact 
    the author (see below).

  * Bugs or technical problems can be reported on the project home page. If you
    are not sure if it's MicrobeGPSs fault or yours, you should contact the 
    author first.

  * Contact the author via email, if no documentation is available for your
    problem:

    - Technical questions: Martin Lindner, marzin@mail-lindner.de
    - Other/general questions: Bernhard Renard, renardb@rki.de