SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
New to Linux and Bioinformatics johnadam33 Bioinformatics 12 09-08-2011 01:40 PM
eagleview installation on linux litali Bioinformatics 0 07-20-2010 12:51 AM
Linux Distribution on next-gen analysis DZhang Bioinformatics 2 07-03-2010 12:11 AM
GD installation on ia64 linux edge Bioinformatics 12 01-27-2010 01:59 AM
Bioinformatics-ready linux distros... ECO Bioinformatics 0 09-11-2009 07:45 AM

Reply
 
Thread Tools
Old 04-30-2010, 06:45 AM   #1
ymc
Senior Member
 
Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default Which Linux distribution is the best for Bioinformatics???

Is Scientific Linux any good for bioinformatics? If yes, why?

Do we need Enterprise level Linux???

What Linux distribution are you using???

Thanks in advance.
ymc is offline   Reply With Quote
Old 04-30-2010, 06:50 AM   #2
NextGenSeq
Senior Member
 
Location: USA

Join Date: Apr 2009
Posts: 482
Default

I would use Ubuntu. I hate Red Hat.
NextGenSeq is offline   Reply With Quote
Old 04-30-2010, 06:54 AM   #3
Simon Anders
Senior Member
 
Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 993
Default

It really doesn't matter. Just use a distribution you feel comfortable with. As bioinformatics tools won't be find in any package management system, you have to install them manually (which is no real problem) and this is done the same way on all Unix OSes with GNU tool chain (no matter whether it is any of the Linux distributions or Mac OS X or something more esoteric).

And, no, you don't need "Enterprise level" Linux. This is just a fancy marketing term from the RedHat people with no meaning.

Personally, I am quite happy with Ubuntu.

Simon
Simon Anders is offline   Reply With Quote
Old 04-30-2010, 07:21 AM   #4
ymc
Senior Member
 
Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default

I have been using Debian. I heard that Ubuntu is based on Debian but it is more popular now. What makes it better than Debian???
ymc is offline   Reply With Quote
Old 04-30-2010, 07:27 AM   #5
ffinkernagel
Senior Member
 
Location: Marburg, Germany

Join Date: Oct 2009
Posts: 110
Default

I also primarily use ubuntu.

Ubuntu is basically debian without the focus on ultra-reliability (read old versions of everything) and therefore has a broader spectrum of packeted software. It inherits debian's sane package managment, adds in an easy way for the community to publish packages (PPA) and a lot of development effort to make it 'just work.
ffinkernagel is offline   Reply With Quote
Old 04-30-2010, 11:37 AM   #6
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
Default

You'd be surprised what bioinformatics tools are in distributions. E.g., blast2 (NCBI) is available for ubuntu. I think bioperl is also (though it may not be latest version)
krobison is offline   Reply With Quote
Old 05-03-2010, 12:40 PM   #7
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 623
Default

Well, I have switched from Ubuntu to Fedora, mainly because Fedora (RedHat) is heading gcc development. Compiling staden under ubuntu always was a hassle, but works like a charm under fedora :-)

But, as usual, the "best" linux distribution to use if you are not experienced is the one used in your environment, by your colleagues or friends.

cheers,
Sven
sklages is offline   Reply With Quote
Old 05-03-2010, 07:37 PM   #8
NextGenSeq
Senior Member
 
Location: USA

Join Date: Apr 2009
Posts: 482
Default

Today I had to reformat all my thumb drives I was using to copy large data NGS sets.

Everytime I used Red Hat the USB drives repeatedly crashed. Reformatting the drives in Ubuntu I could copy the data even in Red Hat and now they can be read on Ubuntu, Red Hat and even Microsoft (FAT formatting).

Red Hat and Microsoft are only concerned with profits not progress, let alone user friendliness.
NextGenSeq is offline   Reply With Quote
Old 05-04-2010, 12:36 AM   #9
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 870
Default

As others have said, to a great extent it doesn't matter.

Our choice is Fedora, for a few reasons:
  • It's close enough to RedHat to keep the corporate types happy
  • It's got the latest version of every library, so compiling packages is never an issue
  • I can send people on the excellent RedHat training courses and have the knowledge be immediately applicable
  • The package list has a surprising amount of bioinformatics programs in it (BioPerl, EMBOSS, Samtools etc)

To answer your original question you don't need to have an enterprise Linux distribution for bioinformatics (we even run enterprise things such as the Illumina pipeline under Fedora) - but you need to be confident in supporting yourself. If you're running a big pipeline and aren't happy sorting out problems with the OS then it can be really useful to have a number you can call where they won't tell you to RTFM.
simonandrews is offline   Reply With Quote
Old 05-04-2010, 12:38 AM   #10
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

We use Cent OS 5 on our servers. For Desktops/Laptops, each person has their own preference (Ubuntu or Fedora). Also, for Laptops, consider Mac OS X laptop as it has Word (good for interacting with the PI) and Unix under the hood.
nilshomer is offline   Reply With Quote
Old 05-05-2010, 07:12 AM   #11
jmw86069
Member
 
Location: RTP, NC, USA

Join Date: Jun 2009
Posts: 28
Default

I recommend Ubuntu but agree with others' points about Fedora for IT support. If you get your IT support's buy-in early on for Ubuntu then you're all set. I run Ubuntu on my laptop and if you're adventurous enough to do something like that, hands down Ubuntu would be your choice. For me the reason is that if you Google for almost any Linux related problem, the discussion and solution is typically found on ubuntuforums.org. It has the most active and vocal community of people using it and mutually helping each other support all the bleeding edge stuff we really want to use.

RedHat is by far the most IT supported, but when we tried to use it in a controlled environment we couldn't install many core tools due to older versions of various libraries which couldn't easily be updated without impacting other tools. That may happen with any Linux flavor, that after a couple years some tools basically drag down the Linux advances due to their specific (old) needs.

MacOS is based upon Linux and has an Apple scientific group supporting some aspects of it. For R they compile with all the little flags that make it the fastest possible, twice as fast as default Linux builds without some tweaking. But clearly not every tool builds smoothly, evinced by the number of tools with separate Mac compile directions. The problem is that you probably don't really want to build Mac clusters or buy a bunch of Mac servers. They'd perform well but not notably better then Linux boxes, and they'd be darn pricey. But due respect, they're good boxes. :-)
jmw86069 is offline   Reply With Quote
Old 06-07-2010, 12:31 AM   #12
robertorun
Member
 
Location: wuhan,China

Join Date: Nov 2009
Posts: 22
Default

I use Fedora,but the Fedora is updated so fast and only surpport server about 1 half year, so wang to use RedHat AS or CentOS.
robertorun is offline   Reply With Quote
Old 06-07-2010, 07:27 AM   #13
ymc
Senior Member
 
Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default

What about CentOS? What is its advantage over Ubuntu???
ymc is offline   Reply With Quote
Old 06-07-2010, 08:02 AM   #14
mrawlins
Member
 
Location: Retirement - Not working with bioinformatics anymore.

Join Date: Apr 2010
Posts: 63
Default

I describe Linux distributions as pre-selected dish combinations at an all-you-can-eat buffet. The differences between distribution X and distribution Y are:

which packages, and which versions they come with as a standard
how they prioritize performance, stability/maintainability and functionality
what options are available for technical support (i.e. forums only, or call-in help desk)
which personal preferences/aesthetic considerations are enabled by default

Use what works. If your IT department has a preference, go with that. If your colleagues have a preference, go with that. If you have a preference, go with that. If you really don't know (and hence have to ask on this forum), go with Ubuntu. It's not my favorite distribution, but it emphasizes making it easy to pick up and learn.
In the end, there's so little difference between the distributions that if you don't *know* what you want, it doesn't much matter which one you choose. All distributions will allow you to install and use almost all bioinformatics software (some Windows-only programs could be challenging, but there are alternatives).
mrawlins is offline   Reply With Quote
Old 03-07-2011, 03:59 AM   #15
danny0085
Junior Member
 
Location: danny0085

Join Date: Feb 2011
Posts: 3
Default

No doubt that the best option is ubuntu linux.
danny0085 is offline   Reply With Quote
Old 03-07-2011, 04:02 AM   #16
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 870
Default

Quote:
Originally Posted by danny0085 View Post
No doubt that the best option is ubuntu linux.
Because....?
simonandrews is offline   Reply With Quote
Old 03-07-2011, 04:19 AM   #17
TonyBrooks
Senior Member
 
Location: London

Join Date: Jun 2009
Posts: 298
Default

There is no best option specifically for bioinformatics. As mentioned previously, software can be compiled on any Linux system. More important is to find one you are comfortable with for the other functions that you may find useful.
Ubuntu is probably the most user friendly Linux distro. Most things work out of the box regardless of hardware and pretty much all non bioinformatics software is included in the repositories for easy install (OpenOffice, Filezilla etc). I just think there's less of a learning curve with Ubuntu for those who are comfortable with Windows or OS X (which constitute almost all of our collaborators).
TonyBrooks is offline   Reply With Quote
Old 03-07-2011, 04:35 AM   #18
ulz_peter
Senior Member
 
Location: Graz, Austria

Join Date: Feb 2010
Posts: 219
Default

I personally prefer Ubuntu as well (just found out that bwa and samtools is available in Ubuntu repositories), just because it is easy and getting help is facilitated by the great amunt of people using it. However I had trouble installing the Roche software.
Does anyone use the Bioinformatic Ubuntu distribution biolinux?:
http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-6.0

For file sharing with PIs, I think OpenOffice is sufficient as it can handle all the Ms office data formats.
ulz_peter is offline   Reply With Quote
Old 03-07-2011, 04:53 AM   #19
TonyBrooks
Senior Member
 
Location: London

Join Date: Jun 2009
Posts: 298
Default

Yes, the 454software is a bit of a pain to get installed and Roche won't support anything other than Redhat, Fedora or CentOS. There are posts on SeqAnswers on how other people have managed to install on Ubuntu though.
TonyBrooks is offline   Reply With Quote
Old 03-07-2011, 05:10 AM   #20
ulz_peter
Senior Member
 
Location: Graz, Austria

Join Date: Feb 2010
Posts: 219
Default

Quote:
Originally Posted by TonyBrooks View Post
Yes, the 454software is a bit of a pain to get installed and Roche won't support anything other than Redhat, Fedora or CentOS. There are posts on SeqAnswers on how other people have managed to install on Ubuntu though.
I actually ended up changing one of my computer's operating system to Fedora, before the solution was published on Seqanswers. As it runs Gnome as well the changes are minor, mostly only affecting directory structure...and bwa and samtools are in the Fedora repositories as well
ulz_peter is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:32 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO