Yesterday I mentioned rPath linux. I am again in love with this application. rPath linux and their free rBuilder application stack is something that the bioinformatics community should consider jumping at. Regardless as to whether you are a grad-student interested in high-performance bioinformatics computing, a postDoc with a big problem or a technologist in a core facility, there is something that you could do with rPath.
I have decided to put together a tutorial series on rPath and my own (very-much-in-progress) version of bioinformatics-oriented linux. In this tutorial we are going to start out with a linux running inside a virtual machine. This will be configured with up-to-date and interesting packages that are of relavance to tasks within genomics, transcriptomics and metabolomics. The virtual machine will be re-iteratively improved and we will prepare our own version of “bioram-linux”. This will be made available as a standalone linux distribution and will be integrated in an environment to deploy across a computer cluster dedicated to bioinformatics. We will use some of my ideas, some of Aschwin’s ideas and hopefully, you, the wider community will start to comment and update us with your feelings, opinion and ideas.
The final version will be made available at rPath rBuilder. The packages and modules can be copied, modified and altered to suit your needs within your own projects – this is just a push to hopefully increase the amount of content and knowledge within the bioinformatics community in relation to rPath.
As a first note (self-important mumbling to self even), please acknowledge that I am no expert in linux administration (I am a comfortable super user) and will undoubtedly introduce faux-pas within the pipeline and workflow. Please let me know when I am going wrong and hopefully together we can do something rather clever? The project is called “bioram-linux”. BioRAM was the name of a company that I planned to start during 2002 / 2003; the domain was registered and ideas and business plans collected. This idea was on the back-burner and seemed like a good idea when I registered for rPath a couple of years ago. Please accept the name, I like it 
In today’s tutorial we are going to head over to rPath, find the bioram-linux / Mnemosyne BioSciences LabManager development image and will download it. We will then install the appropriate linux within a VMWare based virtual machine running on our host computer. For the time being all images are x86, and will stay that way until much later tutorials when we will start to cross-compile packages for the x86_64 platforms.
Let’s get cracking
- Head over to the rBuilder pages at rPath. In the search box at the top of the page, click on “product”, and search for the term “bioram”. Press “search” and the Mnemosyne BioSciences product for bioram-linux should be returned as one of the top matches, click on this link. The pages for bioram can also be found directly by using the URL http://www.rpath.org/project/bioram-linux/
- On the bioram pages, use the right-hand panel to select for the option to “View Releases”. A page similar to the one shown below should be shown. This provides a link to the BioRAM linux download page. If, of course, you are looking at this page more than a few days after the first posting of this blog article then things may have changed! Select the link for the “Mnemosyne Biosciences – BioRAM linux for bioinformatics”, and proceed to download the VMWare image. Please note both the size of the file (it is not a very small file ..) and ideally the md5sum checksum. You can then validate that what you download is the same as what was present on the server.
- When the file has downloaded, ensure that the file checksums match and extract the .tar.gz archive. If you don’t already have the VMware player, VMware Fusion or some other VMware environment you should arrange this now. I can recommend the VMware player for linux, this is great. I use Fusion on my MacBook Pro and this is even better. Load the downloaded VMware image into your VM software of choice and start the VM up for the first time …
- Provide the path to the downloaded BioRAM installation page
- View and review system settings and make any changes that you feel would benefit your system!
- Everything should now be set! Click the various boxes and boot your newly defined Virtual Machine for the first time. Good luck! There will be a minute or so of linux loading and the standard process messages will be written to the screen – there should be no need for panic!
- Once the BioRAM linux has loaded, it will complain about an improperly configured X. Let the system know that you are in control, make the error message go away by clicking “YES” I know what I am doing and have used linux before boxes. X will start and you will be prompted to configure X to your specifications. I would recommend something along the lines of what is shown below. Make sure that the VMware graphics adapter is configured and everything should be fine.
- You are now able to log on with the “root” account – there is no password, so the very first things that you should do are to ensure that at least networking works and that you have a secure root password implemented!
You have done really well getting to the end of this first BioRAM linux tutorial. I am aware that I am not the best tutorial writer, but the only way to learn in by doing it, and receiving comments and criticisms from the readers. I hope that you have gotten this far, in the coming few weeks we are going to do a whole lot more with this.
In the next session (Thursday) we will configure our new virtual machine for package building, maintenance and compiling. We will define a new version of the “R” package and will create version 2.8.1 of R for our virtual machine. This will be installed and we will have a little think about how we can get “Bioconductor” installed and in use.
