<div dir="ltr">Thanks Tony !!!<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Jan 25, 2016 at 11:21 AM, Tony Travis <span dir="ltr"><<a href="mailto:tony.travis@abdn.ac.uk" target="_blank">tony.travis@abdn.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">On 25/01/16 16:06, Bishwa Kiran wrote:<br>
> I was using vcftools in biolinux and found that the pre-installed<br>
> version was a very old one. I found it out because the vcftools was not<br>
> working out a particular task I wanted. I managed to download the latest<br>
> vcftools but could not get rid of the older one. The new version is<br>
> installed at another bin directory.<br>
<br>
</span>Hi, Bishwa.<br>
<br>
The version of "vcftools" pre-installed in Bio-Linux is not "very" old:<br>
<br>
root@beluga:~# apt-cache policy vcftools<br>
vcftools:<br>
Installed: 0.1.11+dfsg-1<br>
Candidate: 0.1.11+dfsg-1<br>
Version table:<br>
*** 0.1.11+dfsg-1 0<br>
500 <a href="http://gb.archive.ubuntu.com/ubuntu/" rel="noreferrer" target="_blank">http://gb.archive.ubuntu.com/ubuntu/</a> trusty/universe amd64<br>
Packages<br>
100 /var/lib/dpkg/status<br>
<br>
[The current version on GitHub is v0.1.14]<br>
<br>
To get rid of the old version of "vcftools", just run:<br>
<br>
sudo apt purge vcftools<br>
<span class=""><br>
> And, I also realize that several bio informatics tools are little old<br>
> and do not update automatically.<br>
<br>
</span>You can do 'unattended' upgrades, but you can check your system is<br>
up-to-date manually at any time. By default, security upgrades are<br>
installed automatically. However, it's not always convenient to upgrade<br>
all parts of the system if, for example, you are in the middle of a long<br>
analysis and want to do it all using the same version of a program.<br>
<span class=""><br>
> How is it possible to update all the (if not most) bio-informatics tools<br>
> to latest version with minimal efforts of downloading, making and<br>
> installing. I mean is there any terminal command which can search for<br>
> updates of these tools and replace the older version.<br>
<br>
</span> sudo apt update<br>
sudo apt full-upgrade<br>
<span class=""><br>
> Also, the portabale installation of biolinux cannot wake up after<br>
> putting to sleep. Any suggestions?<br>
<br>
</span>Don't use a screen saver...<br>
<br>
HTH,<br>
<div class="HOEnZb"><div class="h5"><br>
Tony.<br>
<br>
--<br>
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and<br>
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen<br>
AB24 3UU, Scotland, UK. tel <a href="tel:%2B44%280%291224%20272700" value="+441224272700">+44(0)1224 272700</a>, fax <a href="tel:%2B44%20%280%291224%20272%20396" value="+441224272396">+44 (0)1224 272 396</a><br>
<a href="http://www.abdn.ac.uk" rel="noreferrer" target="_blank">http://www.abdn.ac.uk</a>, mailto:<a href="mailto:tony.travis@abdn.ac.uk">tony.travis@abdn.ac.uk</a>, skype:ajtravis<br>
<br>
<br>
The University of Aberdeen is a charity registered in Scotland, No SC013683.<br>
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div><font face="'comic sans ms', sans-serif">- Bish </font></div><div><font face="Comic Sans MS"></font> </div><div><img src="http://cndesigns.files.wordpress.com/2012/01/favim-com-1237.jpg" width="149" height="200"></div><div> </div></div>
</div>