PrimerDesign IPython Notebook for Primer Design Make a folder for the virtual environment

mkdir -p ~/venv/base
wget --no-check-certificate https://raw.github.com/pypa/virtualenv/master/virtualenv.py

Create a new virtual environment

python virtualenv.py --no-site-packages --no-setuptools ~/venv/base

Download get-pip.py for installing pip and setuptools in the new environment

wget --no-check-certificate https://bootstrap.pypa.io/get-pip.py

Activate the environment. This should be added to the .bashrc or run manually every time.

source ~/venv/base/bin/activate

Install pip and setuptools

python get-pip.py

Now everything is ready for installing the remaining dependencies

pip install ipython[all] 
pip install regex 
pip install pandas
pip install biopython
pip install runipy
pip install selenium

To install rpy2 it is necessary to load R 3.1.0

module load R/3.1.0
pip install rpy2

Installing the primer3 package

wget https://pypi.python.org/packages/source/p/primer3-py/primer3-py-0.3.1.tar.gz
tar -xvzf primer3-py-0.3.1.tar.gz
cd primer3-py-0.3.1
pip install primer3-py
cd ..

Download the latest firefox to your computer and scp the tar.gz file to your HPCC account and unzip it I added the following lines to my ~/.bashrc file:

module load R/3.1.0
source ~/venv/base/bin/activate

Instal the R packages (after loading the appropriate version of R R Code (type within R)

install.packages("ggplot2")
install.packages("plyr")
install.packages("reshape2")

To run the notebook in interactive mode Use the flag -X to display the browser in your computer.

ssh -XC user@hosname

Run the ipython notebook without a browser:

ipython notebook --no-browser &

Run firefox in background:

./firefox/firefox &

In the address bar type: http://127.0.0.1:8888/tree This will open the IPython notebook I was able to run the notebook without any problem using this setup If you don’t want to have to do this workaround everytime, you can create an IPython profile and set the browser appropriately. Don’t use the firefox originally available at HPCC because it crashes very easily. Any questions, feel free to contact me at teo.decarvalho@gmail.com

To run the notebook using qsub Install runipy

pip install runipy

See the file job_example.qsub for an example of running the Nitrosopumilus example. You will have to comment out part of the notebook or use "if" statements to select the section of the notebook that you want to run.