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----------
MicrobeGPS
----------
(Version 1.0.0)
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 [not yet available].
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, lindnerm@rki.de
- Other/general questions: Bernhard Renard, renardb@rki.de
|
