<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yui_3_16_0_ym19_1_1464581207010_61567" dir="ltr">Thanks a lot Tony!</div><div id="yui_3_16_0_ym19_1_1464581207010_61565" dir="ltr"><br></div><div id="yui_3_16_0_ym19_1_1464581207010_61566" dir="ltr">Robert<br></div><div id="yui_3_16_0_ym19_1_1464581207010_61564"><span></span></div> <div class="qtdSeparateBR"><br><br></div><div style="display: block;" class="yahoo_quoted"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font face="Arial" size="2"> On Monday, May 30, 2016 5:31 PM, Tony Travis <tony.travis@abdn.ac.uk> wrote:<br></font></div> <br><br> <div class="y_msg_container">On 31/05/16 01:06, Robert Evans wrote:<br clear="none">> Thanks Tony,<br clear="none">><br clear="none">> I don't necessarily want to uninstall everything that isn't vanilla<br clear="none">> Ubuntu (I've installed various programs over the years), I just want to<br clear="none">> get the system set up in such a way that it will upgrade the core OS and<br clear="none">> utilities along the standard Ubuntu upgrade paths instead of the<br clear="none">> Biolinux/LTS upgrade paths.<br clear="none"><br clear="none">Hi, Robert.<br clear="none"><br clear="none">My script won't install/deinstall any packages - It just reports what<br clear="none">you would have to install/deinstall to reconcile differences between an<br clear="none">installed Bio-Linux (or Ubuntu) system and a list of packages based on<br clear="none">the 'manifest' file present on a 'live' Ubuntu DVD or another host.<br clear="none"><br clear="none">> I don't know if your tool does that? I'm quite happy manually<br clear="none">> uninstalling individual packages after deciding not to use them.<br clear="none"><br clear="none">That's what my script is for: It will simply list the packages you have<br clear="none">installed that are not part of the 'vanilla' Ubuntu distribution. You<br clear="none">decide what to keep and what to uninstall - I wrote it to use with:<br clear="none"><br clear="none"> dpkg --set-selections<br clear="none"> apt-get dselect-upgrade<br clear="none"><br clear="none">However, now I use it to generate a list of packages for:<br clear="none"><br clear="none"> apt install ...<br clear="none"> apt remove ...<br clear="none"><br clear="none">> I've considered deselecting/deleting the Biolonux repositories in the<br clear="none">> Software Updater, and switching to upgrade to all new Ubuntu releases<br clear="none">> (not just LTS or the next Biolinux). But I don't know if doing so will<br clear="none">> mangle things vis-a-vis any Biolinux updater scripts which may be in the<br clear="none">> system.<br clear="none"><br clear="none">You will probably break a lot of packages if you do: It's advisable to<br clear="none">remove all your 'bio-linux*' packages before removing the repositories<br clear="none">or you risk dependency 'hell' :-(<br clear="none"><br clear="none">> Would doing this solve the primary issue of being on a Biolinux upgrade<br clear="none">> path versus an Ubuntu upgrade path?<br clear="none"><br clear="none">Yes, as long as you remove ALL your Bio-Linux packages before removing<br clear="none">the Bio-Linux repositories from your configuration.<br clear="none"><br clear="none">HTH,<br clear="none"><br clear="none"> Tony.<br clear="none"><br clear="none">--<br clear="none">Dr. A.J.Travis, University of Aberdeen, Institute of Biological and<br clear="none">Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen<br clear="none">AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396<br clear="none"><a shape="rect" href="http://www.abdn.ac.uk,/" target="_blank">http://www.abdn.ac.uk, </a>mailto:<a shape="rect" ymailto="mailto:tony.travis@abdn.ac.uk" href="mailto:tony.travis@abdn.ac.uk">tony.travis@abdn.ac.uk</a>, skype:ajtravis<br clear="none"><br clear="none"><br clear="none">The University of Aberdeen is a charity registered in Scotland, No SC013683.<br clear="none">Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.<div class="yqt3444623404" id="yqtfd01073"><br clear="none">_______________________________________________<br clear="none">Bio-Linux-list mailing list<br clear="none"><a shape="rect" ymailto="mailto:Bio-Linux-list@bioinformatics.org" href="mailto:Bio-Linux-list@bioinformatics.org">Bio-Linux-list@bioinformatics.org</a><br clear="none"><a shape="rect" href="http://www.bioinformatics.org/mm/listinfo/bio-linux-list" target="_blank">http://www.bioinformatics.org/mm/listinfo/bio-linux-list</a></div><br><br></div> </div> </div> </div></div></body></html>