Metadata-Version: 1.1
Name: BAMQC
Version: 0.5.6
Summary: Quality control tools for NGS alignment file
Home-page: http://hammelllab.labsites.cshl.edu/software#BAMqc
Author: Ying Jin
Author-email: yjin@cshl.edu
License: GPLv3
Description: BAMQC
        =====
        
        *Version 0.5.6*
        
        `Github Page <https://github.com/mhammell-laboratory/bamqc>`_
        
        `Pypi Page <https://pypi.python.org/pypi/BAMQC>`_
        
        `MHammell Lab <http://hammelllab.labsites.cshl.edu/software>`_
        
        Installation guide for BAMQC for from source installs
        -----------------------------------------------------
        
        `Source Code <https://github.com/mhammell-laboratory/bamqc/archive/0.5.5.tar.gz>`_
        
        `With Prebuilt Binary <https://github.com/mhammell-laboratory/bamqc/releases/download/0.5.5/BAMQC-0.5.5.tar.gz>`_
        
        `Pypi <https://pypi.python.org/pypi?:action=display&name=BAMQC&version=0.5.5>`_
        
        *Prerequisites:*
           * python2.7
           * R (corrplot package)
           * GCC 4.8.1 or greater (Linux), Xcode 4.2 or greater (MacOSX) 
             if compiling from source
        
        Below is an example of installing BAMQC on Linux system using BASH. You need to change '--prefix' directory, PYTHONPATH and PATH accordingly
        
        ::
        
            tar -zxf BAMQC-VERSION.tar.gz
            cd BAMQC-VERSION
        
        To install BAMQC at the system level (which will require root privileges):
        
        ::
        
            python setup.py install
        
        To install BAMQC in a custom location (e.g. /home/user/BAMQC):
        
        ::
        
            export PYTHONPATH=/home/user/BAMQC/lib/python2.7/site-packages:$PYTHONPATH.
            # This sets up PYTHONPATH so that BAMQC knows where to install, later import, BAMQC modules.
            export PATH=/home/user/BAMQC/bin:$PATH
            # This sets up PATH, so that system knows where to find the executable file.
            python setup.py install --prefix=/home/user/BAMQC
            # This will install BAMQC at the user specified location (/home/user/BAMQC)
        
        
        *NOTE:*
        
        * To produce graphical outputs, R (and the corrplot R package) must be installed.
        * If the installation failed with error like: /usr/bin/ld: cannot find -lz, you may need to install a shared zlib library on your system.
        
        Contacts
        --------
        
        Ying Jin: yjin@cshl.edu
        
        Acknowledgements goes to
        ------------------------
        
        1. Samtools and pysam contributors
        2. Molly Hammell and members of her laboratory at Cold Spring Harbor Laboratory
        3. Users' valuable feedback
        
        Copying & distribution
        ----------------------
        
        BAMQC is free software: you can redistribute it and/or modify
        it under the terms of the GNU General Public License as published by
        the Free Software Foundation, either version 3 of the License, or
        (at your option) any later version.
        
        This program is distributed in the hope that it will be useful,
        but *WITHOUT ANY WARRANTY*; without even the implied warranty of
        *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE*.  See the
        GNU General Public License for more details.
        
        You should have received a copy of the GNU General Public License
        along with BAMQC.  If not, see `this website <http://www.gnu.org/licenses/>`_.
        
        
Keywords: Quality control BAM file
Platform: Linux
Platform: MacOS
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: C++
Classifier: Operating System :: MacOS
Classifier: Operating System :: Unix
