This page was last updated on Thursday, 31-Dec-2015 10:38:41 CST

Installation notes for SpliceGrapher version 0.2.5

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Prerequisites

• numpy
  Already installed
• matplotlib
  1. $ sudo
     yumapt-get
     install python-matplotlib
• PyML
  1. $ wget -N http://downloads.sourceforge.net/project/pyml/PyML-0.7.11.tar.gz
  2. $ tar -zxvf PyML-0.7.11.tar.gz
  3. $ cd PyML-0.7.11
  4. $ python setup.py build
  5. $ sudo python setup.py install
• For error AttributeError: 'csamtools.AlignedRead' object has no attribute 'next_reference_id'
  in program sam_filter.py, I needed to update pysam
  1. $ sudo apt-get install python-setuptools
  2. $ wget -N https://pypi.python.org/packages/source/p/pysam/pysam-0.8.4.tar.gz
  3. $ tar -xf pysam-0.8.4.tar.gz
  4. $ cd pysam-0.8.4
  5. $ sudo python setup.py install
  6. $ cd .. && sudo rm pysam-0.8.4 -rf

Installation

1. $ ver="0.2.5"
2. $ cd /programinstallers/
3. $ wget -N http://downloads.sourceforge.net/project/splicegrapher/SpliceGrapher-$ver.tgz
4. $ tar -zxvf SpliceGrapher-$ver.tgz
5. $ cd SpliceGrapher-$ver
6. $ python setup.py build
7. $ sudo python setup.py install
8. Cleanup
   $ cd -
9. $ rm SpliceGrapher-$ver -rf