Author: | Gina Turco (gturco), Brent Pedersen (brentp) |
---|---|
Email: | gturco88@gmail.com |
License: | MIT |
Contents
The easiest way to install the pipeline is to:
- 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_cns2a) SEE REQUIREMENTS SECTION or run on iplant's atmosphere image find_cns_pipeline (emi-8EF728EB)
OR2b) run on iplant's atmosphere using image: find_cns_pipeline (emi-8EF728EB)
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
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 addPATH="usr/local/bin/:${PATH}"
and thenexport PATH
to a new line Then open a new terminal window and typebrew
to make sure it was properly installed
- Install and download Xcode here
Requirements for Mac and Unix
Python version >= 2.7 (you can use pythonbrew to install python):
on mac: brew install python --framework --universal (edit .bash_profile) export PATH=/usr/local/share/python:$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-develLAPACK <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-develGEOS:
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 sudo pip install virtualenv virtualenv --distribute cns_pipeline --python=python2.7scip 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)
-
pip install numpy
-
pip install processing
-
pip install shapely
-
pip install pyfasta
-
pip install scipy
-
pip install Cython
-
pip install pandas
-
pip install git+https://github.com/brentp/flatfeature.git
-
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)
-
git clone https://github.com/chapmanb/bcbb.git cd gff python setup.py install
-
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