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Installing Galaxy-P on Linux Server

In the Genomics world, Galaxy has been well known. Originally PennState researchers created as an interface to access, manage and manipulate genomic data (e.g. DNA sequences).  Recently, Galaxy-P was developed by University of Minnesota as a multi-omics analysis platform. There are public Galaxy-P sites where you and I can send mass spec data, then search databases and analyze the results. You can also locally install the platform, and then you can develop a new tool and manage the server for future expansion and development. Here I will be installing Galaxy-P on my linux server (running Ubuntu) and test it out its functionality.

First you need to install Mercurial by following command

>sudo apt-get install mercurial

This will take  a few MB of disk space.  Then you need to get Galaxy-P source code distribution.

>hg clone https://bitbucket.org/galaxyp/galaxyp-central

If everything is downloaded correctly, you see the messages like this.
install_galaxy-p

To start running a Galaxy-P server, type

>sh run.sh –reload

To test if all installation and running server are correctly done, open web browser (firefox or something), and type localhost:8080 in the address box.

Galaxy-P_start_up

You should see the GUI of Galaxy-P in the browser.

Now, let’s make this accessible from anywhere on the internet. Right now you have an access to Galaxy-P on local computer only.

First we need to modify configuration file called universe_wsgi.ini

Change the current directory to galaxyp-central and open universe_wsgi.ini file using text editor. For example,

>vim universe_wsgi.ini

Then change the line which defines port and host, then save.

For port we will use 8080 and host is changed to 0.0.0.0
Screen Shot 2013-08-06 at 8.00.25 PM

Then you need to open the port 8080. To do it, you need to change port forwarding if you are using router.

Screen Shot 2013-08-06 at 7.58.24 PM

Now the port is open, we are ready to run the server.

>sh run.sh –reload

If all successful, try accessing it outside the network by opening the browser and type the server’s IP address:8080 in the URL.
Either  XXX.XXX.XXX.XXX:8080 or domain_name:8080 is ok.

Screen Shot 2013-08-06 at 8.21.07 PM

The browser should start loading Galaxy-P and it will identical to localhost screen above.

The more detailed installation can be seen here and here.
This post is just to show you how to install Galaxy-P on your local machine or server. If it is installed on the server, you can use it remotely. I will likely discuss about their functionality in the future post.

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