3. Installation

proBAMconvert exists as a 'one-click', stand-alone executable, providing a GUI and CLI version of proBAMconvert without requiring any preinstalled software. Simply opening the executable will open a graphical user interface which allows to use proBAMconvert in an intuitive manner. The executable can also be run trough a command line interface. However, there are some minor differences between executables from different operating systems, which are explained below.

proBAMconvert is written in python and the python scripts are available on github. If prefered proBAMconvert can be executed as a python script, however this requires the installation of some packages which proBAMconvert uses, more information can be found below. The stand alone executables are only for the GUI implementation (Except for UNIX, where a CLI executable is provided for server use),

While proBAMconvert should work on most systems, in case of trouble please report the experienced issues on https://github.com/Biobix/proBAMconvert/issues.

stand alone executable

To install the proBAMconvert GUI stand-alone application simply download and unzip the executable for your system. To run the GUI application, simply double click the proBAMcovert_GUI executable. Important!: When executing proBAMconvert on UNIX, you might need to provide the executable with permissions to execute, this can be provided in the following manner:


chmod +x [proBAMconvert_UNIX_location]



Using the CLI differs slightly for each executable, an overview is given below

WINDOWS


proBAMconvert_WIN_location.exe [options]

OSX


./proBAMcovert_OSX_location.app/Contents/MacOS/proBAMconvert_OSX [options]

UNIX


./proBAMconvert_UNIX_location [options]

The input options can be found in section 4: "options", you can also run the "-h" or "--help" option to get an overview of all options and how to use the CLI. WARNING: Due to the absence of open source "sam to bam converters" for windows, the windows application is unable to create BAM files and a SAM file will be created instead.


operating system download
OSX (mac) download
UNIX download
WINDOWS download

python

proBAMconvert is developed in python, however several dependencies are required for proBAMconvert to work properly. We recommend installation through pip, the default python binairy installer (installation instructions : https://pip.pypa.io/en/stable/installing/).

the following dependencies are required: lxml numpy matplotlib pyteomics cogent bioservices mysql-python pysam sqlalchemy

installation through pip:



  pip install lxml numpy matplotlib pyteomics cogent bioservices mysql-python sqlalchemy


NOTE: pysam is only available for unix based system and OSX, no open source tools exists for sam to bam conversion on windows.



  pip install pysam


Dowload the proBAMconvert python implementation from our github repository. To run the GUI execute the proBAMconvert_GUI.py script with python.



  python proBAM.py



To run the command line proBAMconvert application execute the proBAM.py script with python. The command line option are described in the next section (section 4: "options").



  python proBAM.py [options]


Continue to the next chapter "options" where the different proBAMconvert options are discussed.


Next Chapter: options