[Bio-linux-devel] [Bio-linux-list] Future of Bio-Linux (BL 9 & Ubuntu 16.04) ?

[Bishwa Kiran]

Thanks Tony !!!

On Mon, Jan 25, 2016 at 11:21 AM, Tony Travis <tony.travis at abdn.ac.uk>
wrote:

> On 25/01/16 16:06, Bishwa Kiran wrote:
> > I was using vcftools in biolinux and found that the pre-installed
> > version was a very old one. I found it out because the vcftools was not
> > working out a particular task I wanted. I managed to download the latest
> > vcftools but could not get rid of the older one. The new version is
> > installed at another bin directory.
>
> Hi, Bishwa.
>
> The version of "vcftools" pre-installed in Bio-Linux is not "very" old:
>
> root at beluga:~# apt-cache policy vcftools
> vcftools:
>   Installed: 0.1.11+dfsg-1
>   Candidate: 0.1.11+dfsg-1
>   Version table:
>  *** 0.1.11+dfsg-1 0
>         500 http://gb.archive.ubuntu.com/ubuntu/ trusty/universe amd64
> Packages
>         100 /var/lib/dpkg/status
>
> [The current version on GitHub is v0.1.14]
>
> To get rid of the old version of "vcftools", just run:
>
>   sudo apt purge vcftools
>
> > And, I also realize that several bio informatics tools are little old
> > and do not update automatically.
>
> You can do 'unattended' upgrades, but you can check your system is
> up-to-date manually at any time. By default, security upgrades are
> installed automatically. However, it's not always convenient to upgrade
> all parts of the system if, for example, you are in the middle of a long
> analysis and want to do it all using the same version of a program.
>
> > How is it possible to update all the (if not most) bio-informatics tools
> > to latest version with minimal efforts of downloading, making and
> > installing. I mean is there any terminal command which can search for
> > updates of these tools and replace the older version.
>
>   sudo apt update
>   sudo apt full-upgrade
>
> > Also, the portabale installation of biolinux cannot wake up after
> > putting to sleep. Any suggestions?
>
> Don't use a screen saver...
>
> HTH,
>
>   Tony.
>
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>
>
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
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-- 
- Bish
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