Best ubuntu version for bioinformatics?
3
0
Entering edit mode
11 months ago
avelarbio46 ▴ 10

Hello everyone!

We bought a new server to analyze our data, but our infrastructure is small. I was wondering, what version of ubuntu is the best for bioinformatics?

I had a lot of problems with 18.04 because many packages were broken, and when I search for ubuntu 20.04, I see that people are not asking about it so I supposed that people are not using it.

I'm worried about compatibility issues, so which would be the best option in your opinion?

ubuntu • 847 views
ADD COMMENT
2
Entering edit mode

Are other users actively using this machine or are you the sole user? That makes a big difference in "administration" of a system and choices you make in practice.

ADD REPLY
1
Entering edit mode

We also had issues with Ubuntu 18.04. Ubuntu 16.04 is great but it reaches end of life in April. I've upgraded one machine from 18.04 to 20.04 and it seems to work fine. However, I use Ubuntu for desktops and laptops. For servers, I use CentOS although now that CentOS is not going to be the stable OS it used to be, I'll be looking for something else. Given that I already use Debian-based distros, I am thinking of moving my servers to Debian.

ADD REPLY
6
Entering edit mode
11 months ago
Mensur Dlakic ★ 15k

This is the first I have ever heard of a particular version of Ubuntu being best (or not best) for bioinformatics. My opinion is that all of them are the same, though more recent versions are preferred for security reasons. I can say this with some authority because I have computers that run Ubuntu 12.04, 16.04, 18.04 and 20.04. If you are installing the system from scratch, the only difference is that certain aptitude packages will not be available for the latest version (20.04) because of the normal lag. I don't rely on aptitude to install any bioinformatics packages, so this particular problem never comes up for me. It should make no difference what system version is there for installing python and R modules, though some older packages may only work with earlier python and R versions, and some may need the latest. In most cases that has nothing to do with the system version.

I do caution about upgrading the system to a newer version, as in my hands that almost always creates more work than it is worth. I don't update systems as a general rule, and the reason I have so many different versions is because these computers were put in production at different times - I always install the most up-to-date system available. About two months ago I deviated from this rule and upgraded a 18.04 system to 20.04. The upgrade went without any hitch and the computer is fully functional in general terms. As I ran various programs over the past few weeks, I have discovered that some python modules need to be reinstalled, or that some programs need to be re-compiled because the old libraries were removed. The same was true when about a year ago I was forced to upgrade two computers from 12.04 to 18.04 (security reasons), and had to do various tweeks to get everything to work as before. I know this may not be a popular opinion as many people upgrade as soon as the new version is available.

ADD COMMENT
3
Entering edit mode

I agree with not upgrading servers, at least until the version runs out of support. The only issue with this is that sometimes new software requires newer versions of libraries.

ADD REPLY
2
Entering edit mode

I agree on waiting to update, especially out of an LTS version. I'd much rather have 100% working slightly older OS than 90% functional bleeding edge new OS.

ADD REPLY
2
Entering edit mode

Just an N=1 here, but on my (personal) system I've never had an issue with installing every newest Ubuntu update.

ADD REPLY
0
Entering edit mode

That's certainly possible, as for me most packages continue to work after upgrades. Depending on how many packages you have and how they were installed, some may never cause problems. I have a bunch of old programs that were statically compiled in Free Pascal back in 2005, and all of them still work through all the processor and kernel changes.

ADD REPLY
2
Entering edit mode

I would add that it is a good idea to keep a LOG of every program you installed, and how you installed it. For me, I just keep a running list of install commands and download links in a .log file.

ADD REPLY
0
Entering edit mode

Second this. I also do this and I also include eventual configuration settings/changes (e.g. for Apache servers) and where the configuration files are.

ADD REPLY
1
Entering edit mode

Well, I'm a newbie, so take this with a grain of salt:

I tried using a program named RNAeditor in Ubuntu 18.04. This is an ~old~ program, and the GUI was created using PYqt4 web kit.

This function was deprecated in python3, so I manually installed SIP and PYQT4 packages with web kit in a virtual env in python 2. But I couldn't get it to work with ubuntu 18.04, only 16. Of course most popular packages are very easy to install in 20.04, but I'm still testing them! So I thought, why not ask people with experience? Thanks for your answer!

Also, we updated from 16.04 to 18.04 LTS, and it screwed our installation very badly on our Dell workstation with dual-boot (windows 10 and linux). I had to do a fresh install of linux after that upgrade!

ADD REPLY
0
Entering edit mode

Also, we updated from 16.04 to 18.04 LTS, and it screwed our installation very badly on our Dell workstation with dual-boot (windows 10 and linux). I had to do a fresh install of linux after that upgrade!

Your experience seems to be consistent with most of us here. I don't think anything was wrong in particular with the 18.04 version - I fully expect that some older packages will stop working each time I upgrade.

I have all the data and manually installed programs in a non-system partition. That way everything stays in place even if you have to do a fresh install. In fact, that's what I did when upgrading from 12.04 to 18.04, because I suspected that such a huge jump in system versions would cause too many incompatibility issues.

ADD REPLY
3
Entering edit mode
11 months ago

The choice of the distribution isn't that important. Choose any more or less current one. To install and manage your bioinformatics tools use conda with the bioconda channel activated. The first part of my tutorial might be helpful.

fin swimmer

ADD COMMENT
3
Entering edit mode
11 months ago
GenoMax 110k

You should consider using LTS variant since they are guaranteed longer term support. If you are not a card carrying system administrator then staying with a newer release and keeping up with updates (program and security) would be a prudent choice.

Using conda to manage your software installations would again be advisable if you are not comfortable futzing with compiling things and finding libraries etc. This should in theory avoid problems with getting the programs to run as well.

Ultimately you need to conform to local IT security landscape. Check with your IT organization to stay compliant with any local policy (security or otherwise).

ADD COMMENT

Login before adding your answer.

Traffic: 2958 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6