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

[Bishwa Kiran]

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.
And, I also realize that several bio informatics tools are little old and
do not update automatically.
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.

Also, the portabale installation of biolinux cannot wake up after putting
to sleep. Any suggestions?

Thanks, in advance !

On Thu, Jan 21, 2016 at 6:06 AM, Tony Travis <tony.travis at abdn.ac.uk> wrote:

> On 21/01/16 09:44, Tim Booth wrote:
> > ...continued from post to bio-linux-list
> >
> > Regarding the upgrade script, yes please contribute fixes!
> >
> > There's no need to go ferreting around to find the code, as it's all on
> > GitHub.  Fork it, patch it, test it, submit bugs, send pull requests,
> > etc.  It's all good!
> >
> >
> https://github.com/environmentalomics/build-bio-linux/tree/master/upgrade_to_8
>
> Hi, Tim.
>
> OK - I've raised an issue on GitHub and submitted this patch:
>
> --- upgrade_to_8.sh.old 2016-01-21 10:58:26.679395436 +0000
> +++ upgrade_to_8.sh     2016-01-21 11:00:12.383392313 +0000
> @@ -239,8 +239,8 @@
>
>  # If this was run on a Vanilla Ubuntu 14.04 box then
> Universe/Multiverse sources
>  # will not be active.  Tell the user about it.
> -if grep -q '^deb .*/ [a-z ]\+ universe$'   /etc/apt/sources.list && \
> -   grep -q '^deb .*/ [a-z ]\+ multiverse$' /etc/apt/sources.list ; then
> +if grep -qw universe   /etc/apt/sources.list && \
> +   grep -qw multiverse /etc/apt/sources.list ; then
>      true
>  else
>      echo "**** Warning:"
>
> > Note that I don't any longer have access to the nebc.nerc.ac.uk server
> > that hosts some of the Bio-Linux static files like this script, but I
> > can edit content on environmentalomis.org and I have full control of the
> > Luanchpad and GitHub accounts.
>
> Is someone at NERC/EOS taking over responsibility for Bio-Linux?
>
> Bye,
>
>   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.
> Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir.
> SC013683.
> _______________________________________________
> Bio-Linux-devel mailing list
> Bio-Linux-devel at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel
>



-- 
- Bish
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20160125/b73d54bf/attachment.html>