Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

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Installation notes for alpha-CENTAURI version 0.2 commit 6a8659c on Oct 7, 2015

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Prerequisites

Installation

  1. $ sudo mkdir /usr/share/alpha-CENTAURI
  2. $ sudo chmod 777 /usr/share/alpha-CENTAURI
  3. $ export CENT_HOME=/usr/share/alpha-CENTAURI
  4. $ virtualenv -p /usr/bin/python2.7 $CENT_HOME 
    Running virtualenv with interpreter /usr/bin/python2.7
New python executable in /usr/share/alpha-CENTAURI/bin/python2.7
Also creating executable in /usr/share/alpha-CENTAURI/bin/python
Installing setuptools, pkg_resources, pip, wheel...done.
  5. $ cd $CENT_HOME
  6. $ . bin/activate
  7. $ pip install numpy
  8. $ pip install networkx
  9. $ pip install git+https://github.com/PacificBiosciences/FALCON.git@96230ec9d6027e465deaccdb6fe3c045e5b820a3#falcon 
    Collecting git+https://github.com/PacificBiosciences/FALCON.git@96230ec9d6027e465deaccdb6fe3c045e5b820a3#falcon
  Cloning https://github.com/PacificBiosciences/FALCON.git (to 96230ec9d6027e465deaccdb6fe3c045e5b820a3) to /tmp/pip-qCNNS_-build
  Could not find a tag or branch '96230ec9d6027e465deaccdb6fe3c045e5b820a3', assuming commit.
Requirement already satisfied: networkx>=1.7 in ./lib/python2.7/site-packages (from falcon-kit==0.2.1)
Requirement already satisfied: decorator>=4.1.0 in ./lib/python2.7/site-packages (from networkx>=1.7->falcon-kit==0.2.1)
Installing collected packages: falcon-kit
  Running setup.py install for falcon-kit ... done
Successfully installed falcon-kit-0.2.1
  10. 64-bit hmmer is already installed
  11. $ git clone https://github.com/volkansevim/alpha-CENTAURI.git
  12. $ chmod +x bin/activate
  13. $ chmod +x alpha-CENTAURI/src/*.py

To run alpha-CENTAURI

  1. $ export CENT_HOME=/usr/share/alpha-CENTAURI
  2. $ . $CENT_HOME/bin/activate
  3. The two scripts from alpha-CENTAURI can then be run with:
    $ $CENT_HOME/alpha-CENTAURI/src/chop_to_monomers.py
    $ $CENT_HOME/alpha-CENTAURI/src/monomer_graph_analysis.py