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  • 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.

  • #2
    I would use Ubuntu. I hate Red Hat.

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    • #3
      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

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      • #4
        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???

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        • #5
          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.

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          • #6
            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)

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            • #7
              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

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              • #8
                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.

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                • #9
                  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.

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                  • #10
                    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.

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                    • #11
                      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. :-)

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                      • #12
                        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.

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                        • #13
                          What about CentOS? What is its advantage over Ubuntu???

                          Comment


                          • #14
                            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).

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                            • #15
                              No doubt that the best option is ubuntu linux.

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