Metadata-Version: 1.1
Name: BAMQC
Version: 0.6.5
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: 
        
        .. image:: https://raw.githubusercontent.com/mhammell-laboratory/bamqc/master/doc/bamqc-icon.png
           :width: 200 px
           :alt: generated at codeology.braintreepayments.com/mhammell-laboratory/bamqc
           :align: right
           :target: http://codeology.braintreepayments.com/mhammell-laboratory/bamqc
        
        BAMQC
        =====
        
        Version 0.6.5
        
        `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/0.6.4.tar.gz>`_
        
        `Pypi <https://pypi.python.org/pypi?:action=display&name=BAMQC&version=0.6.5>`_
        
        *Prerequisites:*
           * `python2.7 <https://www.python.org/download/releases/2.7/>`_
           * `R <https://www.r-project.org/>`_
           * `corrplot <https://cran.r-project.org/web/packages/corrplot/>`_
           * `GCC 4.8.1 or greater <https://gcc.gnu.org/gcc-4.8/>`_
        
        While there are multiple methods of installing the prerequistes it may
        help to look at (if using a yum based linux distro):
        
           * `Devtoolset-3 <https://access.redhat.com/documentation/en-US/Red_Hat_Developer_Toolset/3/html/User_Guide/sect-Red_Hat_Developer_Toolset-Install.html>`_ for GCC compilers
           * `IUS <https://ius.io/>`_ for Python2.7
           * `Software Collections <https://www.softwarecollections.org/>`_ for collections of software (like devtoolset 3 or python)
           * `rpmfinder <https://www.rpmfind.net/>`_ for searching rpms across mutliple systems
        
        *Setup*
        
        make sure that the GCC comiler is in your PATH
        
        .. code:: bash
         export PATH=/path/to/gcc:$PATH
        
        
        make sure that python2.7 is is in your PYTHONPATH, for permance add it to your .bashrc
        
        .. code:: bash
         export PYTHONPATH=/path/to/python2.7/site-packages:$PYTHONPATH
        
        There are three methods of installation of BAMqc, from source, setup.py, and from pypi, once prequistes are setup. 
        
        *From Source*
        
        download source 
        
        .. code:: bash
         wget https://github.com/mhammell-laboratory/bamqc/archive/0.6.4.tar.gz
         tar xvfz bamqc-0.6.4.tar.gz
         cd bamqc-0.6.4
        
        run make on htslib
        
        note: make sure to have -fPIC in your cflags ie: ``export CFLAGS="$CFLAGS -fPIC"``
        
        .. code:: bash
         
         cd src/htslib
         make 
        
        run make 
        
        .. code:: bash
        
         cd ../..
         make
        
        *From Setup.py*
        
        .. code:: bash
        
         python2.7 setup.py install 
        
        *From Pypi*
        
        .. code:: bash
        
         pip2.7 install BAMqc
        
        Contacts
        --------
        
        Ying Jin: yjin@cshl.edu
        
        Acknowledgements goes to
        ------------------------
        
        #) Samtools and pysam contributors
        #) Molly Hammell and members of her laboratory at Cold Spring Harbor Laboratory
        #) 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
Classifier: Development Status :: 4 - Beta
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 :: Unix
