SuperPhy Step by Step Setup

#####This tutorial is using linuxmint-17.3-cinnamon-64bit.iso

These steps are contained in the program setup.py.

"mod_wsgi"

The main purpose of mod_wsgi was to revise the code and file structure in the project. The mod_wsgi package implements a simple to use Apache module which can host any Python web application which supports the Python WSGI specification.

Assume you have a new system.

Make sure you have Java downloaded or updated. The following command will take a few minutes to complete.

 $ sudo apt-get install openjdk-7-jre 

Also important is to install the wrapper for supporting Java applications on your web browser, the Iced-Tea Java Plugin.

$ sudo apt-get install icedtea-plugin 

To make sure you have the most updated version of Java, run the following command:

$ sudo update-alternatives --config java 

This updates and upgrades your current system.

$ sudo apt-get update && sudo apt-get upgrade -y

Adds the git repository to your files. This is version controll for our project.

$ sudo apt-get install git -y

Install the other sudo packages we need to run SuperPhy on the machine

These libraries need to be installed. Use the following command.

$ sudo apt-get install apache2 curl git libapache2-mod-wsgi libyajl2 MUMmer muscle python-dev python-virtualenv wget xvfb -y

Download the master branch from our project. Currently it is located at the URI mentioned below.

$ git clone https://github.com/superphy/semantic.git ~/superphy

Then:

$ cd ~/superphy
$ python setup.py install --sys
$ python setup.py run --pyserver

Navigate to localhost:5000, and verify the page loads, go back to the terminal and hit ctrl-c, then navigate to localhost, and verify the apache-mod_wsgi server is running.

Optional:

# To enable mod_wsgi, run the following command:

$ sudo a2enmod wsgi

Configure and Enable your virtual host: (deploying to apache)

• copy 000-default.conf to /etc/apache2/sites-available

$ sudo cp ~/superphy/development_virtualhost.conf /etc/apache2/sites-available/000-default.conf
$ sudo service apache2 reload

Sublime Text

If you want to use sublime-text as your word processor, now is the time to Download it.

$ sudo apt-get install sublime-text-installer -y

If you get an error after running the previous command, try running the following commands in order.

$ sudo apt-get install software-properties-common python-software-properties 
$ sudo add-apt-repository ppa:webupd8team/sublime-text-3
$ sudo apt-get update
$ sudo apt-get install sublime-text-installer
$ sudo apt-get install sublime-text

If any errors persist, consult Google!

---

####Assume you have set up the system,

$ cd ~/superphy

$ ln -s ~/superphy ~/Desktop/superphy

start and download the blazegraph java file.

$ bash superphy/database/scripts/start.sh

$ apache='/var/www/SuperPhy'

$ project=$(pwd)/var_www_SuperPhy

$ sudo rm -f $apache

$ sudo ln -s $project $apache

virtualenv --no-site-packages venv

$ source venv/bin/activate

$ pip install --upgrade pip && pip install -r venv/requirements.txt

$ nodeenv -p --prebuilt --requirements=venv/npm-requirements.txt

How to deactivate

This may become deprecated soon. These are bower js components for mithril.

if ! find var_www_SuperPhy/SuperPhy/static/js/bower_components/mithril-components | read v; then git clone --depth=1 https://github.com/eddyystop/mithril-components.git var_www_SuperPhy/SuperPhy/static/js/bower_components/mithril-components; fi

• This is a very large download. If you aren't going to be uploading data, don't bother downloading it.

$ mkdir blast &> /dev/null 
$ cd blast
if ! find ncbi*/ | read v; then
    wget -rc -nd -A "*x64-linux.tar.gz" "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/"
    tar zxvpf *x64-linux.tar.gz
fi && cd ..

How to Recompile

bash var_www_SuperPhy/SuperPhy/static/compile.sh sudo /etc/init.d/apache2 reload