Windows 8 / Linux Mint Dual-Boot Partition Sizes For Bioinformatics

Question

[Louis]

I'm setting up a new laptop and want to work on RNA-seq and other genomic datasets in R, Python, Perl and R. I've got a 1 TB SSD and have a few days before it arrives to decide how best to partition it, and was wondering what advice anyone has on proper partition sizes should be including a recovery partition.

The preinstalled OS is Windows 8 and I'll be adding Linux Mint — there doesn't seem to be any overwhelming warnings against this distro for bioinformatics.

This isn't asking for any guidance on how to partition, just the recommended sizes for a bioinformatics machine.

Sorry if this is a basic question but I can only find advice for "video editing" and things, which I'm not sure is really compatible, and "gaming" is more graphics-oriented so I don't quite know what I'd compare "bioinformatics tools" to.

[User 59]

As with anything it depends what you're doing. I couldn't do my RNA-Seq work on anything other than a server with a few TB of disk space. There's a big difference between doing mammalian sized genomes with dozens of samples and doing it on prokaryotes with a few samples. So what exactly are you hoping to achieve with your laptop setup. "RNA-Seq" is not descriptive enough.

[Louis]

I'm an undergrad just at the half-way point in my degree so it's kind of an open question based on how my work develops, so sorry I can't be more specific. It's for getting to know bioinformatics and I know RNA-seq will be a component soon for a couple of projects that haven't been spelled out in full yet. I'll probably have access to servers if greater horsepower is necessary but ideally I want to have a good setup myself. Thanks for the feedback though, v helpful in weighing things up

[Alex Reynolds]

These folks know everything and more. You should follow their advice.

[Michael]

Use an operating system, remove Windows (this laptop is for working, not for gaming right?) ;)

Answer 1

[Michael]

Is there a (relevant) bioinformatics application that runs only on windows, especially for NGS? I don't think so. You need all the space you can get, 1T is possibly barely enough, and you probably don't need Windows, and you possibly cannot waste space for an OS that is not needed. Remove the windows partition, and use ext4 filesystem plus swap on the whole disk. If you need you can run Windows inside of a Virtual Machine under Linux.

[Giovanni M Dall'Olio]

I completely agree - just swipe our Windows and you won't miss it. I usually install / and /home into two separate partitions, reserving about 20GB for /, and the rest for /home (or just use LVM). If you are going to share the computer with other persons, you may consider storing data files into another partition - e.g .something like a /scratch or /data partition. I can't recommend any specific file system, but ext4 worked fine for me in the last few years.

[Louis]

I discussed this with the seller who said that removing Windows would be “wasting what is essentially a £70 license” but I appreciate hearing the option is there/recommended. I'll definitely consider it (and avoids problems I've been wondering about re: moving my old software licenses across from Win7 machine...)

[Michael]

Well, the retailer definitely has point, but that's his fault because often they don't offer the machine without OS or Linux preinstalled, some retailers do though, then it might be a little cheaper even. It's our decision what you do with your stuff, my recommendations were based on the following assumptions:

• dedicated work machine (no gaming, really the only reason to keep a windows partition)
• you want to use that professionally for NGS analysis (there might be servers in your lab for that)
• you can never attach an external drive (this is ofc bogus)
• all the hardware works (there is sometimes some hardware that's not working optimally under Linux, maybe the camera, sleep mode, etc.) If you need those, then it's just annoying if they don't. So try everything out with a LiveCD.