bioinfo tools and ubuntu 14.04

[carolW]

Hi,
Do you know if the bioinfo tools like blast or mappers such as bowtie could be run without problem on ubuntu 14.04 LTS?

Look forward to your reply,

Carol

[biocomputer]

Are you having problems getting things to run on Ubuntu 14.04? That's what I'm using and I haven't had any problems with Bowtie and a bunch of other tools.

[GenoMax]

If the "problems" refer to missing libraries/dependencies then those can certainly be fixed with a recent release of linux such as 14.04.

If you would rather not deal with those fixes then you could download a pre-configured distro such as "bio-linux" that has many of the popular packages included.

[Bukowski]

Some will only work for certain applications on 64bit architectures so it's not just a matter of the distribution/release.

I've never had a problem with a 64bit Ubuntu installation for bioinformatics work.

[bt27uk]

If you don't want to install a new distro, for example, Bio-Linux 8.0, then you can choose to get just the Bio-Linux packages. Information on that can be found at:

http://nebc.nerc.ac.uk/tools/bio-linux-7/other-bl-docs/package-repository

I have not tested this for Bio-Linux 8, but would be surprised if that doesn't work.

Alternatively, Bio-Linux is also distributed as an OVA file, as described around 3/4 of the way down this page:

http://environmentalomics.org/bio-linux-installation/

So if you are running (or you start running) VirtualBox, it is a snap to get Bio-Linux running on your existing system. This assumes that the machine you are working on has enough umph to run a virtual machine on it, of course.

[Baseless]

Dear Carol,
I can confirm BWA, samtools, picard and GATK running smoothly. BCL2fastq is a bit painful, but there is an entry somewhere around this forum which has a solution using perlbrew, which works - so in general, Ubuntu 14.04 shoud be fine as long as you watch out for installing dependencies when necessary.