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Bam_QC

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This repository wraps BamQC as tool and pipeline. BamQC gives a summary statistic report of different aspects of a bam file. It generates an html file with the reports on the passed bam file, both summarized, and graphs.

Requirements

  • pyenv and pyenv-virtualenv
  • Python 2.7.12
  • Python Modules:
    • pylint
    • pytest
    • mg-tool-api

Installation

Directly from GitHub:

cd ${HOME}/code

git clone https://github.com/rehamFatima/Bam_QC.git

cd Bam_QC

Install Ant

wget http://www.mirrorservice.org/sites/ftp.apache.org//ant/binaries/apache-ant-1.10.5-bin.zip
unzip apache-ant-1.10.5-bin.zip

Install Bamqc

git clone https://github.com/s-andrews/BamQC.git
cd BamQC
chmod +x bamqc

Setup symlinks

cd ${HOME}/bin

ln -s ${HOME}/lib/apache-ant-1.10.5/bin/ant ant 
ln -s ${HOME}/lib/BamQC/bamqc bamqc

Create the Python environment

pyenv-virtualenv 2.7.12 mg-bamqc
pyenv activate mg-bamqc
pip install -e .
pip install -r requirements.txt