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

[Tony Travis]

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


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