BAMQC 0.5.6

Quality control tools for NGS alignment file

Version 0.5.6

Github Page

Pypi Page

MHammell Lab

Installation guide for BAMQC for from source installs

Source Code

With Prebuilt Binary

Pypi

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: [e-mail]

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.