<div dir="ltr"><div><div><div><div>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.<br></div>And, I also realize that several bio informatics tools are little old and do not update automatically.<br></div>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.<br><br></div>Also, the portabale installation of biolinux cannot wake up after putting to sleep. Any suggestions?<br><br></div>Thanks, in advance !<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 21, 2016 at 6:06 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 21/01/16 09:44, Tim Booth wrote:<br>
> ...continued from post to bio-linux-list<br>
><br>
> Regarding the upgrade script, yes please contribute fixes!<br>
><br>
> There's no need to go ferreting around to find the code, as it's all on<br>
> GitHub. Fork it, patch it, test it, submit bugs, send pull requests,<br>
> etc. It's all good!<br>
><br>
> <a href="https://github.com/environmentalomics/build-bio-linux/tree/master/upgrade_to_8" rel="noreferrer" target="_blank">https://github.com/environmentalomics/build-bio-linux/tree/master/upgrade_to_8</a><br>
<br>
</span>Hi, Tim.<br>
<br>
OK - I've raised an issue on GitHub and submitted this patch:<br>
<br>
--- upgrade_to_8.sh.old 2016-01-21 10:58:26.679395436 +0000<br>
+++ upgrade_to_8.sh 2016-01-21 11:00:12.383392313 +0000<br>
@@ -239,8 +239,8 @@<br>
<span class=""><br>
# If this was run on a Vanilla Ubuntu 14.04 box then<br>
Universe/Multiverse sources<br>
# will not be active. Tell the user about it.<br>
</span>-if grep -q '^deb .*/ [a-z ]\+ universe$' /etc/apt/sources.list && \<br>
- grep -q '^deb .*/ [a-z ]\+ multiverse$' /etc/apt/sources.list ; then<br>
+if grep -qw universe /etc/apt/sources.list && \<br>
+ grep -qw multiverse /etc/apt/sources.list ; then<br>
true<br>
else<br>
echo "**** Warning:"<br>
<span class=""><br>
> Note that I don't any longer have access to the <a href="http://nebc.nerc.ac.uk" rel="noreferrer" target="_blank">nebc.nerc.ac.uk</a> server<br>
> that hosts some of the Bio-Linux static files like this script, but I<br>
> can edit content on <a href="http://environmentalomis.org" rel="noreferrer" target="_blank">environmentalomis.org</a> and I have full control of the<br>
> Luanchpad and GitHub accounts.<br>
<br>
</span>Is someone at NERC/EOS taking over responsibility for Bio-Linux?<br>
<br>
Bye,<br>
<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>
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