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example 2014-03-28 11 weekly downloads
MicrobeGPS_1_0_0_linux.tar.gz 2014-03-20 81.2 MB 11 weekly downloads
README 2014-03-20 3.6 kB 11 weekly downloads
MicrobeGPS-1.0.0.tar.gz 2014-03-20 22.3 MB 33 weekly downloads
MicrobeGPS_1_0_0_win.zip 2014-03-20 89.6 MB 11 weekly downloads
LICENSE 2014-03-19 1.5 kB 11 weekly downloads
---------- 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
Source: README, updated 2014-03-20