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Quality control tools for NGS alignment file

Project Description
.. image:: https://raw.githubusercontent.com/mhammell-laboratory/bamqc/master/doc/bamqc-icon.png
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:alt: generated at codeology.braintreepayments.com/mhammell-laboratory/bamqc
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: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/>`_.
Release History

Release History

This version
History Node

0.6.5

History Node

0.6.4

History Node

0.5.6

History Node

0.5.5

Download Files

Download Files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
BAMQC-0.6.5.tar.gz (988.3 kB) Copy SHA256 Checksum SHA256 Source Feb 21, 2016

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