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INSTALL.rst

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Author:Gina Turco (gturco), Brent Pedersen (brentp)
Email:gturco88@gmail.com
License:MIT

The easiest way to install the pipeline is to:

  1. Install git and clone this package
  • Install git here (click the link and follow instructions for your system ):

    git clone git://github.com/gturco/find_cns.git
    cd find_cns
    

2a) SEE REQUIREMENTS SECTION or run on iplant's atmosphere image find_cns_pipeline (emi-8EF728EB)

OR

2b) run on iplant's atmosphere using image: find_cns_pipeline (emi-8EF728EB)

  1. run bootstrap Installation

    ARCHFLAGS='-arch i386 -arch x86_64' python bootstrap.py
    
  • If step 3 fails try installing the failed package (instructions in Manual Installation section) then re-run bootstrap
  1. run test case read how to run here:

    source ../cns_pipeline/bin/activate
    cd pipeline
    sh run.sh
    

Install the following (if not already installed) Instructions are provided below troubleshooting help available here

  • Python 2.7
  • gfortran
  • Blas
  • LAPACK
  • easy_install and pip
  • glpk and scip
  • virtualenv

Instructions below

Special Requirements for Mac

  • Install homebrew:

    ruby <(curl -fsSkL raw.github.com/mxcl/homebrew/go)
    
  • Add homebrew to your .bash_profile:

    touch ~/.bash_profile (if this is a new file check ~/.profile or ~/.bashrc)
    
Once one of the profiles are open add PATH="usr/local/bin/:${PATH}" and then export PATH to a new line Then open a new terminal window and type brew to make sure it was properly installed

Requirements for Mac and Unix

  • Python version >= 2.7 (you can use pythonbrew to install python):

    on mac:
      brew install python --framework --universal
      (edit .bash_profile)
      export PATH=/usr/local/share/python:$PATH
    on ubuntu/debian:
      sudo apt-get update; sudo apt-get install python2.7 python2.7-dev python-setuptools
    on centos/redhat:
      http://toomuchdata.com/2012/06/25/how-to-install-python-2-7-3-on-centos-6-2/
    
  • gfortran:

    on mac:
        brew install libblas gfortran
    on ubuntu/debian:
        sudo apt-get install build-essential liblas-dev liblapack-dev gfortran
    on centos/redhat:
    
  • BLAS:

    on mac:
      http://pheiter.wordpress.com/2012/09/04/howto-installing-lapack-and-blas-on-mac-os/
    on ubuntu/debian:
      sudo apt-get install libblas-dev
    on centos/redhat:
      sudo yum install blas-devel
    
  • LAPACK <http://www.netlib.org/lapack/>_:

    on mac:
      http://pheiter.wordpress.com/2012/09/04/howto-installing-lapack-and-blas-on-mac-os/
    on ubuntu/debian:
      sudo apt-get install liblapack-dev
    on centos/redhat:
      sudo yum install lapack-devel
    
  • GEOS:

    on mac:
       brew install geos
    on ubuntu/debian:
      sudo apt-get install libgeos-dev
    on centos/redhat:
      sudo yum install geos
    
    • PIP

      sudo easy_install pip
      
  • virtualenv:

    sudo pip install virtualenv
    virtualenv --distribute cns_pipeline --python=python2.7
    
  • scip Download here choose operating system and accept user agreement on next page:

    #may need to scp from your computer to server
    unzip scip-x.x.x
    mv scip-x.x.x cns_pipeline/bin/scip
    
    if on ubuntu/debian need unzip:
      sudo apt-get install unzip (add if not installed)
    
  • gpkl:

    wget glpk-newest_version.tar.gz
    tar -xvzf <somepath>/glpk-newest_version.tar.gz
    cd glpk-newest_version
    ./configure
    make
    sudo make install
    

bootstrap.py runs the commands below. If you are having trouble installing one of these packages, use the links provided. troubleshooting numpy and scipy

Python packages

  • First activate your virtualenv so everything downloads to your cns_pipeline/bin:

    virtualenv --distribute cns_pipeline --python=python2.7
    (creates folder if not already created)
    

    Then activate:

    source cns_pipeline/bin/activate
    (to deactivate just type: deactivate)
    
  • numpy:

    pip install numpy
    
  • processing:

    pip install processing
    
  • shapely:

    pip install shapely
    
  • pyfasta:

    pip install pyfasta
    
  • scipy:

    pip install scipy
    
  • Cython:

    pip install Cython
    
  • pandas:

    pip install pandas
    
  • flatfeature:

    pip install git+https://github.com/brentp/flatfeature.git
    
  • quota-align:

    git clone https://github.com/tanghaibao/quota-alignment.git
    mv quota-alignment  cns_pipeline/bin/
    

    (change path in quota.sh if not moved to cns_pipeline/bin)

  • gffparser:

    git clone https://github.com/chapmanb/bcbb.git
    cd gff
    python setup.py install
    
  • bpbio:

    cd pipeline/coann/brents_bpbio/biostuff/
    python setup.py install
    cd pipeline/coann/brents_bpbio/blasttools/blast_misc/
    python setup.py install
    cd pipeline/coann/brents_bpbio/biostuff/co-anno/
    python setup.py install
    

C packages

-if on mac:

brew install wget
  • (NON-blast+) blast

    download latest blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/:

    wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.5/blast-2.2.5-ia32-linux.tar.gz
    tar -xvzf <somepath>/blast-X.X.X-XXXX.tar.gz
    mv <somepath>/blast-XX.X.X/ cns_pipeline/bin/ #(change path in run.sh file if diff)
    
  • lastz

    (install instructions ) and adjust path in quota.sh):

    wget http://www.bx.psu.edu/~rsharris/lastz/newer/lastz-1.03.02.tar.gz
    tar -xvzf <somepath>/lastz-distribute-X.XX.XX.tar.gz
    cd <somepath>/lastz-distrib-X.XX.XX/src
    make
    LASTZ_INSTALL=/usr/local/bin/ make install