####This tutorial is using linuxmint-17.3-cinnamon-64bit.iso
Make sure you have Java dowloaded 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
Optional (for development): This adds the respository for sublime text 3. If you are using a different Text editor, then you don't need this repo. Likewize, you don't need to
$ sudo add-apt-repository ppa:webupd8team/sublime-text-3
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
Download the master branch from our prject. Currently it is located at the URI mentioned below.
$ git clone -b mod_wsgi https://github.com/superphy/semantic.git ~/superphy
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
- Install the other sudo packages we need to run SuperPhy on the machine
####note: sort these!
$ sudo apt-get install apache2 curl git libapache2-mod-wsgi libyajl2 MUMmer muscle python-dev python-virtualenv wget xvfb -y
- 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
####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
------What's happening here?--------
$ apache='/var/www/SuperPhy'
$ project=$(pwd)/app
$ 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
if ! find app/SuperPhy/static/js/bower_components/mithril-components | read v; then git clone --depth=1 https://github.com/eddyystop/mithril-components.git app/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 ..
bash app/SuperPhy/static/compile.sh sudo /etc/init.d/apache2 reload