From tbooth at ceh.ac.uk Tue Sep 25 05:20:28 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 25 Sep 2012 10:20:28 +0100 Subject: [Bio-linux-dev] Broken act package In-Reply-To: <5194B53077CB9B4D9BA963852B50909C0D4992@MBX06.ad.oak.ox.ac.uk> References: <5194B53077CB9B4D9BA963852B50909C0D4992@MBX06.ad.oak.ox.ac.uk> Message-ID: <1348564828.3372.352.camel@balisaur> Hi Keith, I should have purged the bio-linux-act package from the server, as the bio-linux-artemis package contains ACT and the bio-linux-act package is just an empty shell. I've now done that and when I try to install bio-linux-act I just get a message saying that bio-linux-artemis provides it, which is as it should be. In your case there should be nothing more to do, unless you still have a problem running ACT. Believe it or not the weather just here has been full sunshine and a light breeze all morning. I can only assume there is some strange microclimate vortex controlling the weather in Wallingford as the rest of the country seems to be getting soaked. Cheers, TIM On Tue, 2012-09-25 at 09:32 +0100, Keith Jolley wrote: > Hi Tim, > > Just tried to install bio-linux-act and it's complaining: > > The following packages have unmet dependencies. > bio-linux-act: Depends: bio-linux-artemis (>= 13.2-0) but it is not going to be installed > E: Broken packages > > > Odd, because bio-linux-artemis 13.2-6 is installed. > > Anyway, I'm in Portugal this week running a course - the weather is a bit better than at home! > > Cheers > Keith -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From tbooth at ceh.ac.uk Wed Sep 26 11:45:33 2012 From: tbooth at ceh.ac.uk (Booth, Timothy G.) Date: Wed, 26 Sep 2012 16:45:33 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) Message-ID: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> Dear Bio-Linux testers, My deadline for the Bio-Linux 7 Beta release has, ahem, slipped a little later than I first anticipated, but I have now finished all the package updates and tested upgrading several machines in-house. As far as I'm aware, once you get through the upgrade, everything works and is ready to use. There is no ISO download just yet, but I invite everyone on this list to try upgrading their Bio-Linux 6 systems in-place. This is the first time in 7 releases that we've been confident to advise upgrading in-place without reinstalling. In short, the upgrade process is fairly complex so I've prepared a script to do all the necessary actions and make it simple for you. If the script doesn't finish for some reason you can simply run it again as many times as you need to. I've fixed all the issues I know about but you may hit other problems - please report and discuss bugs on this list, or even better file a bug report here: https://bugs.launchpad.net/bio-linux *** It should go without saying - don't do this on a critical server just now. Check you have a few GB free disk space before you start. Back up your data first. Really, back up your data first. *** To run the script: 1) Open a terminal 2) download (using wget or otherwise) this script: http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh 3) Run the script: sudo bash ./bl_do_update_to7.sh This will trigger everything off. The script is designed to be run on a Bio-Linux 6 machine but should also be fine if run on a vanilla Ubuntu 12.04 box (or even on regular Ubuntu 10.04) as it first ensures that Ubuntu is upgraded, then installs all the BL stuff, and finally clears up some legacy packages and sets the backdrop. If the new backdrop doesn't appear you probably need to re-run the script again until it does, or until you hit a bug that stops it working. It will take about 2-3 hours to do the full upgrade. You'll periodically need to answer various questions that pop up. Notes and known issues: The initial upgrade from Ubuntu 10.04 to 12.04 can fail if you have additional software sources (eg. PPAs) enabled. You may need to disable these via the "Additional Software Sources" tab in the update manager. The CRAN repositories, FreeNX PPA, and the Google Chrome repository (which is added automatically if you install Chrome) should be OK and the upgrade script deals with them explicitly. The Ubuntu upgrade also produces various warnings, and you may well see a bizarre error box saying "???? ???????? ???? ????". You don't have to worry about this! There's not much I can do about these things as they come from the core Ubuntu packages. I think I've solved the errors where APT would complain about installing unauthenticated packages, but if you see any such errors please let me know. Bio-Linux packages are split between the old repository (on nebc.nerc.ac.uk) and the new Bio-Linux PPA on Launchpad. You'll notice some packages that can't go on Launchpad but don't work on BL6 will be downloaded and installed separately. This is a temporary workaround. After upgrading you'll be using the Unity desktop. This is going to be the default on Bio-Linux 7 as it is the default on Ubuntu. If you don't like it and want to contribute instructions for swapping to Gnome-shell/KDE/Xfce/TWM then I'll gladly share these on the website, but personally I'm sticking with Unity. It's not so bad once you get used to it! Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From daniel.antony.pass at googlemail.com Wed Sep 26 11:54:22 2012 From: daniel.antony.pass at googlemail.com (Daniel Pass) Date: Wed, 26 Sep 2012 16:54:22 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> Message-ID: Cheers Tim, I'll give this a whirl on my laptop this evening. For what it's worth, after a couple of hours of hating Unity, I began to like it and I agree with keeping up with the core ubuntu. It's like when everyone freaks out when they change facebook. Regards Dan On 26 September 2012 16:45, Booth, Timothy G. wrote: > Dear Bio-Linux testers, > > My deadline for the Bio-Linux 7 Beta release has, ahem, slipped a little > later than I first anticipated, but I have now finished all the package > updates and tested upgrading several machines in-house. As far as I'm > aware, once you get through the upgrade, everything works and is ready > to use. There is no ISO download just yet, but I invite everyone on > this list to try upgrading their Bio-Linux 6 systems in-place. This is > the first time in 7 releases that we've been confident to advise > upgrading in-place without reinstalling. > > In short, the upgrade process is fairly complex so I've prepared a > script to do all the necessary actions and make it simple for you. If > the script doesn't finish for some reason you can simply run it again as > many times as you need to. I've fixed all the issues I know about but > you may hit other problems - please report and discuss bugs on this > list, or even better file a bug report here: > > https://bugs.launchpad.net/bio-linux > > *** It should go without saying - don't do this on a critical server > just now. Check you have a few GB free disk space before you start. > Back up your data first. Really, back up your data first. *** > > To run the script: > > 1) Open a terminal > 2) download (using wget or otherwise) this script: > http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh > 3) Run the script: > sudo bash ./bl_do_update_to7.sh > > This will trigger everything off. The script is designed to be run on a > Bio-Linux 6 machine but should also be fine if run on a vanilla Ubuntu > 12.04 box (or even on regular Ubuntu 10.04) as it first ensures that > Ubuntu is upgraded, then installs all the BL stuff, and finally clears > up some legacy packages and sets the backdrop. If the new backdrop > doesn't appear you probably need to re-run the script again until it > does, or until you hit a bug that stops it working. > > It will take about 2-3 hours to do the full upgrade. You'll > periodically need to answer various questions that pop up. > > Notes and known issues: > > The initial upgrade from Ubuntu 10.04 to 12.04 can fail if you have > additional software sources (eg. PPAs) enabled. You may need to disable > these via the "Additional Software Sources" tab in the update manager. > The CRAN repositories, FreeNX PPA, and the Google Chrome repository > (which is added automatically if you install Chrome) should be OK and > the upgrade script deals with them explicitly. > > The Ubuntu upgrade also produces various warnings, and you may well see > a bizarre error box saying "???? ???????? ???? ????". You don't have to > worry about this! There's not much I can do about these things as they > come from the core Ubuntu packages. > > I think I've solved the errors where APT would complain about installing > unauthenticated packages, but if you see any such errors please let me > know. > > Bio-Linux packages are split between the old repository (on > nebc.nerc.ac.uk) and the new Bio-Linux PPA on Launchpad. You'll notice > some packages that can't go on Launchpad but don't work on BL6 will be > downloaded and installed separately. This is a temporary workaround. > > After upgrading you'll be using the Unity desktop. This is going to be > the default on Bio-Linux 7 as it is the default on Ubuntu. If you don't > like it and want to contribute instructions for swapping to > Gnome-shell/KDE/Xfce/TWM then I'll gladly share these on the website, > but personally I'm sticking with Unity. It's not so bad once you get > used to it! > > Cheers, > > TIM > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > -- Daniel Pass Tel: (029208)76680 Mob: 07735658687 http://www.kille-morgan.org.uk Room 0.39, School of Biosciences, Biological Sciences Building, Museum Avenue, Cardiff, CF10 3AT -------------- next part -------------- An HTML attachment was scrubbed... URL: From ajt at minke.ukfsn.org Wed Sep 26 12:01:08 2012 From: ajt at minke.ukfsn.org (Tony Travis) Date: Wed, 26 Sep 2012 17:01:08 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> Message-ID: <506326C4.5010300@minke.ukfsn.org> On 26/09/12 16:54, Daniel Pass wrote: > Cheers Tim, I'll give this a whirl on my laptop this evening. > > For what it's worth, after a couple of hours of hating Unity, I began to > like it and I agree with keeping up with the core ubuntu. It's like when > everyone freaks out when they change facebook. Hi, Dan. I second that - I upgraded Bio-Linux 6 on my laptop to Ubuntu 12.04 LTS using the Ubuntu upgrade process. All working fine now, but I'll also run Tim's script on a vanilla Ubuntu 12.04 LTS server that we've just installed. Won't try it on my laptop until I've backed it up ;-) Bye, Tony. From mikeyj.cox at gmail.com Wed Sep 26 12:02:46 2012 From: mikeyj.cox at gmail.com (Cox, Michael J) Date: Wed, 26 Sep 2012 17:02:46 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> Message-ID: Exciting! Would QIIME 1.5 be included in the update or is that going to take some further fun and games after BL7 is a go? Cheers Mike @mikeyj On 26 Sep 2012, at 16:45, "Booth, Timothy G." wrote: > Dear Bio-Linux testers, > > My deadline for the Bio-Linux 7 Beta release has, ahem, slipped a little > later than I first anticipated, but I have now finished all the package > updates and tested upgrading several machines in-house. As far as I'm > aware, once you get through the upgrade, everything works and is ready > to use. There is no ISO download just yet, but I invite everyone on > this list to try upgrading their Bio-Linux 6 systems in-place. This is > the first time in 7 releases that we've been confident to advise > upgrading in-place without reinstalling. > > In short, the upgrade process is fairly complex so I've prepared a > script to do all the necessary actions and make it simple for you. If > the script doesn't finish for some reason you can simply run it again as > many times as you need to. I've fixed all the issues I know about but > you may hit other problems - please report and discuss bugs on this > list, or even better file a bug report here: > > https://bugs.launchpad.net/bio-linux > > *** It should go without saying - don't do this on a critical server > just now. Check you have a few GB free disk space before you start. > Back up your data first. Really, back up your data first. *** > > To run the script: > > 1) Open a terminal > 2) download (using wget or otherwise) this script: > http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh > 3) Run the script: > sudo bash ./bl_do_update_to7.sh > > This will trigger everything off. The script is designed to be run on a > Bio-Linux 6 machine but should also be fine if run on a vanilla Ubuntu > 12.04 box (or even on regular Ubuntu 10.04) as it first ensures that > Ubuntu is upgraded, then installs all the BL stuff, and finally clears > up some legacy packages and sets the backdrop. If the new backdrop > doesn't appear you probably need to re-run the script again until it > does, or until you hit a bug that stops it working. > > It will take about 2-3 hours to do the full upgrade. You'll > periodically need to answer various questions that pop up. > > Notes and known issues: > > The initial upgrade from Ubuntu 10.04 to 12.04 can fail if you have > additional software sources (eg. PPAs) enabled. You may need to disable > these via the "Additional Software Sources" tab in the update manager. > The CRAN repositories, FreeNX PPA, and the Google Chrome repository > (which is added automatically if you install Chrome) should be OK and > the upgrade script deals with them explicitly. > > The Ubuntu upgrade also produces various warnings, and you may well see > a bizarre error box saying "???? ???????? ???? ????". You don't have to > worry about this! There's not much I can do about these things as they > come from the core Ubuntu packages. > > I think I've solved the errors where APT would complain about installing > unauthenticated packages, but if you see any such errors please let me > know. > > Bio-Linux packages are split between the old repository (on > nebc.nerc.ac.uk) and the new Bio-Linux PPA on Launchpad. You'll notice > some packages that can't go on Launchpad but don't work on BL6 will be > downloaded and installed separately. This is a temporary workaround. > > After upgrading you'll be using the Unity desktop. This is going to be > the default on Bio-Linux 7 as it is the default on Ubuntu. If you don't > like it and want to contribute instructions for swapping to > Gnome-shell/KDE/Xfce/TWM then I'll gladly share these on the website, > but personally I'm sticking with Unity. It's not so bad once you get > used to it! > > Cheers, > > TIM > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev From kelvinjefford at googlemail.com Wed Sep 26 12:15:22 2012 From: kelvinjefford at googlemail.com (Kelvin Jefford) Date: Wed, 26 Sep 2012 13:15:22 -0300 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) - Unity desktop Message-ID: FYI ... You can change the desktop to whichever setting you like ... Unity, Gnome 2, Gnome 3, XFCE, BlackBox ... etc. Might be a bit more complex to change to KDE I'm sure, as the others use the nautilus (gnome) desktop. On the Ubuntu forums you should be able to find out the right info. If you need help, I might be able to find the information for you. Kelvin Jefford On 26/09/2012, Cox, Michael J wrote: > Exciting! > > Would QIIME 1.5 be included in the update or is that going to take some > further fun and games after BL7 is a go? > > Cheers > > Mike > > @mikeyj > > > On 26 Sep 2012, at 16:45, "Booth, Timothy G." wrote: > >> Dear Bio-Linux testers, >> >> My deadline for the Bio-Linux 7 Beta release has, ahem, slipped a little >> later than I first anticipated, but I have now finished all the package >> updates and tested upgrading several machines in-house. As far as I'm >> aware, once you get through the upgrade, everything works and is ready >> to use. There is no ISO download just yet, but I invite everyone on >> this list to try upgrading their Bio-Linux 6 systems in-place. This is >> the first time in 7 releases that we've been confident to advise >> upgrading in-place without reinstalling. >> >> In short, the upgrade process is fairly complex so I've prepared a >> script to do all the necessary actions and make it simple for you. If >> the script doesn't finish for some reason you can simply run it again as >> many times as you need to. I've fixed all the issues I know about but >> you may hit other problems - please report and discuss bugs on this >> list, or even better file a bug report here: >> >> https://bugs.launchpad.net/bio-linux >> >> *** It should go without saying - don't do this on a critical server >> just now. Check you have a few GB free disk space before you start. >> Back up your data first. Really, back up your data first. *** >> >> To run the script: >> >> 1) Open a terminal >> 2) download (using wget or otherwise) this script: >> http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh >> 3) Run the script: >> sudo bash ./bl_do_update_to7.sh >> >> This will trigger everything off. The script is designed to be run on a >> Bio-Linux 6 machine but should also be fine if run on a vanilla Ubuntu >> 12.04 box (or even on regular Ubuntu 10.04) as it first ensures that >> Ubuntu is upgraded, then installs all the BL stuff, and finally clears >> up some legacy packages and sets the backdrop. If the new backdrop >> doesn't appear you probably need to re-run the script again until it >> does, or until you hit a bug that stops it working. >> >> It will take about 2-3 hours to do the full upgrade. You'll >> periodically need to answer various questions that pop up. >> >> Notes and known issues: >> >> The initial upgrade from Ubuntu 10.04 to 12.04 can fail if you have >> additional software sources (eg. PPAs) enabled. You may need to disable >> these via the "Additional Software Sources" tab in the update manager. >> The CRAN repositories, FreeNX PPA, and the Google Chrome repository >> (which is added automatically if you install Chrome) should be OK and >> the upgrade script deals with them explicitly. >> >> The Ubuntu upgrade also produces various warnings, and you may well see >> a bizarre error box saying "???? ???????? ???? ????". You don't have to >> worry about this! There's not much I can do about these things as they >> come from the core Ubuntu packages. >> >> I think I've solved the errors where APT would complain about installing >> unauthenticated packages, but if you see any such errors please let me >> know. >> >> Bio-Linux packages are split between the old repository (on >> nebc.nerc.ac.uk) and the new Bio-Linux PPA on Launchpad. You'll notice >> some packages that can't go on Launchpad but don't work on BL6 will be >> downloaded and installed separately. This is a temporary workaround. >> >> After upgrading you'll be using the Unity desktop. This is going to be >> the default on Bio-Linux 7 as it is the default on Ubuntu. If you don't >> like it and want to contribute instructions for swapping to >> Gnome-shell/KDE/Xfce/TWM then I'll gladly share these on the website, >> but personally I'm sticking with Unity. It's not so bad once you get >> used to it! >> >> Cheers, >> >> TIM >> >> -- >> Tim Booth >> NERC Environmental Bioinformatics Centre >> >> Centre for Ecology and Hydrology >> Maclean Bldg, Benson Lane >> Crowmarsh Gifford >> Wallingford, England >> OX10 8BB >> >> http://nebc.nerc.ac.uk >> +44 1491 69 2705 >> >> -- >> This message (and any attachments) is for the recipient only. NERC >> is subject to the Freedom of Information Act 2000 and the contents >> of this email and any reply you make may be disclosed by NERC unless >> it is exempt from release under the Act. Any material supplied to >> NERC may be stored in an electronic records management system. >> _______________________________________________ >> Bio-Linux-dev mailing list >> Bio-Linux-dev at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > From tony.travis at ed.ac.uk Wed Sep 26 12:45:52 2012 From: tony.travis at ed.ac.uk (Tony Travis) Date: Wed, 26 Sep 2012 17:45:52 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <506326C4.5010300@minke.ukfsn.org> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> Message-ID: <50633140.6090505@ed.ac.uk> On 26/09/12 17:01, Tony Travis wrote: > On 26/09/12 16:54, Daniel Pass wrote: >> Cheers Tim, I'll give this a whirl on my laptop this evening. >> >> For what it's worth, after a couple of hours of hating Unity, I began to >> like it and I agree with keeping up with the core ubuntu. It's like when >> everyone freaks out when they change facebook. > > Hi, Dan. > > I second that - I upgraded Bio-Linux 6 on my laptop to Ubuntu 12.04 LTS > using the Ubuntu upgrade process. All working fine now, but I'll also > run Tim's script on a vanilla Ubuntu 12.04 LTS server that we've just > installed. Won't try it on my laptop until I've backed it up ;-) Hi, Tim. I've just tried your script on a minimal 12.04 LTS server install and everything went well until it tried installing Qiime. Did you try the changes that I suggested before to install Qiime under Bio-Linux? I'll look into it and see if I can come up with a fix. HTH, Tony. > Some packages could not be installed. This may mean that you have > requested an impossible situation or if you are using the unstable > distribution that some required packages have not yet been created > or been moved out of Incoming. > The following information may help to resolve the situation: > > The following packages have unmet dependencies. > bio-linux-qiime : Depends: qiime (>= 1.3.0) but it is not going to be installed > E: Unable to correct problems, you have held broken packages. > Not all packages installed properly - exiting. From tony.travis at ed.ac.uk Wed Sep 26 12:52:54 2012 From: tony.travis at ed.ac.uk (Tony Travis) Date: Wed, 26 Sep 2012 17:52:54 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <50633140.6090505@ed.ac.uk> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> Message-ID: <506332E6.4040101@ed.ac.uk> On 26/09/12 17:45, Tony Travis wrote: > [...] > I'll look into it and see if I can come up with a fix. Hi, Tim. No fix yest, but here's some info that might help: Bye, Tony. > The following packages have unmet dependencies. > bio-linux-qiime : Depends: qiime (>= 1.3.0) but it is not going to be installed > E: Unable to correct problems, you have held broken packages. > Not all packages installed properly - exiting. > root at bifx-rta:/usr/local/src/NEBC/Bio-Linux-upgrade# apt-cache policy qiime > qiime: > Installed: (none) > Candidate: 1.4.0-0ubuntu2 > Version table: > 1.4.0-0ubuntu2 0 > 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages > 1.3.0-3 0 > 500 http://gb.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages > 1.3.0-0ubuntu6 0 > 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages > 1.3.0-0ubuntu5 0 > 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages > 1.2.1-ubuntu5 0 > 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages > root at bifx-rta:/usr/local/src/NEBC/Bio-Linux-upgrade# aptitude install qiime > The following NEW packages will be installed: > qiime{b} > The following packages are RECOMMENDED but will NOT be installed: > cd-hit chimeraslayer python-matplotlib > 0 packages upgraded, 1 newly installed, 0 to remove and 7 not upgraded. > Need to get 4,214 kB of archives. After unpacking 17.5 MB will be used. > The following packages have unmet dependencies: > qiime : Depends: libffi5 (>= 3.0.4) which is a virtual package. > Depends: libgmp3c2 but it is not going to be installed. > Depends: python2.6 which is a virtual package. > Depends: python-pynast but it is not going to be installed. > open: 110; closed: 326; defer: 82; conflict: 340 oThe following actions will resolve these dependencies: > > Remove the following packages: > 1) bio-linux-assembly-conversion-tools > 2) bio-linux-happy > 3) bio-linux-nrdb > 4) bio-linux-ocount > 5) bio-linux-staden > 6) bluez-alsa:i386 > 7) glib-networking:i386 > 8) gstreamer0.10-plugins-base:i386 > 9) gstreamer0.10-plugins-good:i386 > 10) gstreamer0.10-x:i386 > 11) gtk2-engines:i386 > 12) gtk2-engines-murrine:i386 > 13) gtk2-engines-oxygen:i386 > 14) gtk2-engines-pixbuf:i386 > 15) gvfs:i386 > 16) gvfs-libs:i386 > 17) ia32-libs > 18) ia32-libs-multiarch:i386 > 19) ibus-gtk:i386 > 20) libaa1:i386 > 21) libacl1:i386 > 22) libao4:i386 > 23) libasn1-8-heimdal:i386 > 24) libasound2:i386 > 25) libasound2-plugins:i386 > 26) libasyncns0:i386 > 27) libatk1.0-0:i386 > 28) libattr1:i386 > 29) libaudio2:i386 > 30) libaudiofile1:i386 > 31) libavahi-client3:i386 > 32) libavahi-common3:i386 > 33) libavc1394-0:i386 > 34) libbz2-1.0:i386 > 35) libc6:i386 > 36) libcaca0:i386 > 37) libcairo-gobject2:i386 > 38) libcairo2:i386 > 39) libcanberra-gtk-module:i386 > 40) libcanberra-gtk0:i386 > 41) libcanberra0:i386 > 42) libcap2:i386 > 43) libcapi20-3:i386 > 44) libcdparanoia0:i386 > 45) libcomerr2:i386 > 46) libcroco3:i386 > 47) libcups2:i386 > 48) libcupsimage2:i386 > 49) libcurl3:i386 > 50) libdatrie1:i386 > 51) libdb5.1:i386 > 52) libdbus-1-3:i386 > 53) libdbus-glib-1-2:i386 > 54) libdrm-intel1:i386 > 55) libdrm-nouveau1a:i386 > 56) libdrm-radeon1:i386 > 57) libdrm2:i386 > 58) libdv4:i386 > 59) libesd0:i386 > 60) libexif12:i386 > 61) libexpat1:i386 > 62) libffi6:i386 > 63) libflac8:i386 > 64) libfontconfig1:i386 > 65) libfreetype6:i386 > 66) libgail-common:i386 > 67) libgail18:i386 > 68) libgcc1:i386 > 69) libgconf-2-4:i386 > 70) libgcrypt11:i386 > 71) libgd2-xpm:i386 > 72) libgdbm3:i386 > 73) libgdk-pixbuf2.0-0:i386 > 74) libgettextpo0:i386 > 75) libgl1-mesa-dri:i386 > 76) libgl1-mesa-glx:i386 > 77) libglapi-mesa:i386 > 78) libglib2.0-0:i386 > 79) libglu1-mesa:i386 > 80) libgnome-keyring0:i386 > 81) libgnutls26:i386 > 82) libgomp1:i386 > 83) libgpg-error0:i386 > 84) libgphoto2-2:i386 > 85) libgphoto2-port0:i386 > 86) libgpm2:i386 > 87) libgssapi-krb5-2:i386 > 88) libgssapi3-heimdal:i386 > 89) libgstreamer-plugins-base0.10-0:i386 > 90) libgstreamer0.10-0:i386 > 91) libgtk2.0-0:i386 > 92) libgudev-1.0-0:i386 > 93) libhcrypto4-heimdal:i386 > 94) libheimbase1-heimdal:i386 > 95) libheimntlm0-heimdal:i386 > 96) libhx509-5-heimdal:i386 > 97) libibus-1.0-0:i386 > 98) libice6:i386 > 99) libidn11:i386 > 100) libiec61883-0:i386 > 101) libieee1284-3:i386 > 102) libjack-jackd2-0:i386 > 103) libjasper1:i386 > 104) libjpeg-turbo8:i386 > 105) libjpeg8:i386 > 106) libjson0:i386 > 107) libk5crypto3:i386 > 108) libkeyutils1:i386 > 109) libkrb5-26-heimdal:i386 > 110) libkrb5-3:i386 > 111) libkrb5support0:i386 > 112) liblcms1:i386 > 113) libldap-2.4-2:i386 > 114) libllvm3.0:i386 > 115) libltdl7:i386 > 116) libmad0:i386 > 117) libmikmod2:i386 > 118) libmng1:i386 > 119) libmpg123-0:i386 > 120) libmysqlclient18:i386 > 121) libncurses5:i386 > 122) libncursesw5:i386 > 123) libnspr4:i386 > 124) libnss3:i386 > 125) libodbc1:i386 > 126) libogg0:i386 > 127) libopenal1:i386 > 128) liborc-0.4-0:i386 > 129) libp11-kit0:i386 > 130) libpango1.0-0:i386 > 131) libpciaccess0:i386 > 132) libpcre3:i386 > 133) libpixman-1-0:i386 > 134) libpng12-0:i386 > 135) libproxy1:i386 > 136) libpulse-mainloop-glib0:i386 > 137) libpulse0:i386 > 138) libpulsedsp:i386 > 139) libqt4-dbus:i386 > 140) libqt4-declarative:i386 > 141) libqt4-designer:i386 > 142) libqt4-network:i386 > 143) libqt4-opengl:i386 > 144) libqt4-qt3support:i386 > 145) libqt4-script:i386 > 146) libqt4-scripttools:i386 > 147) libqt4-sql:i386 > 148) libqt4-sql-mysql:i386 > 149) libqt4-svg:i386 > 150) libqt4-test:i386 > 151) libqt4-xml:i386 > 152) libqt4-xmlpatterns:i386 > 153) libqtcore4:i386 > 154) libqtgui4:i386 > 155) libqtwebkit4:i386 > 156) libraw1394-11:i386 > 157) libroken18-heimdal:i386 > 158) librsvg2-2:i386 > 159) librsvg2-common:i386 > 160) librtmp0:i386 > 161) libsamplerate0:i386 > 162) libsane:i386 > 163) libsasl2-2:i386 > 164) libsasl2-modules:i386 > 165) libsdl-image1.2:i386 > 166) libsdl-mixer1.2:i386 > 167) libsdl-net1.2:i386 > 168) libsdl-ttf2.0-0:i386 > 169) libsdl1.2debian:i386 > 170) libselinux1:i386 > 171) libshout3:i386 > 172) libslang2:i386 > 173) libsm6:i386 > 174) libsndfile1:i386 > 175) libsoup-gnome2.4-1:i386 > 176) libsoup2.4-1:i386 > 177) libspeex1:i386 > 178) libspeexdsp1:i386 > 179) libsqlite3-0:i386 > 180) libssl0.9.8:i386 > 181) libssl1.0.0:i386 > 182) libstdc++5:i386 > 183) libstdc++6:i386 > 184) libtag1-vanilla:i386 > 185) libtag1c2a:i386 > 186) libtasn1-3:i386 > 187) libtdb1:i386 > 188) libthai0:i386 > 189) libtheora0:i386 > 190) libtiff4:i386 > 191) libtinfo5:i386 > 192) libudev0:i386 > 193) libunistring0:i386 > 194) libusb-0.1-4:i386 > 195) libuuid1:i386 > 196) libv4l-0:i386 > 197) libv4lconvert0:i386 > 198) libvisual-0.4-0:i386 > 199) libvisual-0.4-plugins:i386 > 200) libvorbis0a:i386 > 201) libvorbisenc2:i386 > 202) libvorbisfile3:i386 > 203) libwavpack1:i386 > 204) libwind0-heimdal:i386 > 205) libwrap0:i386 > 206) libx11-6:i386 > 207) libx11-xcb1:i386 > 208) libxau6:i386 > 209) libxaw7:i386 > 210) libxcb-glx0:i386 > 211) libxcb-render0:i386 > 212) libxcb-shm0:i386 > 213) libxcb1:i386 > 214) libxcomposite1:i386 > 215) libxcursor1:i386 > 216) libxdamage1:i386 > 217) libxdmcp6:i386 > 218) libxext6:i386 > 219) libxfixes3:i386 > 220) libxft2:i386 > 221) libxi6:i386 > 222) libxinerama1:i386 > 223) libxml2:i386 > 224) libxmu6:i386 > 225) libxp6:i386 > 226) libxpm4:i386 > 227) libxrandr2:i386 > 228) libxrender1:i386 > 229) libxslt1.1:i386 > 230) libxss1:i386 > 231) libxt6:i386 > 232) libxtst6:i386 > 233) libxv1:i386 > 234) libxxf86vm1:i386 > 235) odbcinst1debian2:i386 > 236) xaw3dg:i386 > 237) zlib1g:i386 > > Keep the following packages at their current version: > 238) qiime [Not Installed] > > Leave the following dependencies unresolved: > 239) libcanberra-gtk0:i386 recommends libcanberra-gtk-module:i386 > 240) libncurses5:i386 recommends libgpm2:i386 > 241) libncursesw5:i386 recommends libgpm2:i386 > 242) libslang2:i386 recommends libpng12-0:i386 > 243) libgl1-mesa-glx:i386 recommends libgl1-mesa-dri:i386 (>= 7.2) > 244) libgphoto2-2:i386 recommends udev:i386 (>= 0.175) > 245) libgphoto2-2:i386 recommends libgphoto2-l10n:i386 (>= 2.4.13-1ubuntu1.2) > 246) libqt4-dbus:i386 recommends qdbus:i386 (= 4:4.8.1-0ubuntu4.2) > 247) libqtgui4:i386 recommends libcups2:i386 > 248) ia32-libs-multiarch:i386 recommends libgl1-mesa-glx:i386 > 249) ia32-libs-multiarch:i386 recommends libgl1-mesa-dri:i386 > > > Accept this solution? [Y/n/q/?] From tony.travis at ed.ac.uk Wed Sep 26 13:56:04 2012 From: tony.travis at ed.ac.uk (Tony Travis) Date: Wed, 26 Sep 2012 18:56:04 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <506332E6.4040101@ed.ac.uk> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> Message-ID: <506341B4.6070702@ed.ac.uk> On 26/09/12 17:52, Tony Travis wrote: > On 26/09/12 17:45, Tony Travis wrote: >> [...] >> I'll look into it and see if I can come up with a fix. Hi, Tim. I downloaded your script: > wget http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh I edited "bio-linux-qiime" out of the list, then ran it locally: > chmod +x bl_master_package_list.sh > ./bl_master_package_list.sh > [...] > E: Unable to locate package estscan2 This is because the adding the PPA failed: > ./bl_do_update_to7.sh: line 55: apt-add-repository: command not found > ./bl_do_update_to7.sh: line 58: apt-add-repository: command not found This, which I didn't notice first time round, I fixed by: aptitude install python-software-properties I modified your installer to run the script without Qiime locally: > root at bifx-rta:/usr/local/src/NEBC/Bio-Linux-upgrade# diff bl_do_update_to7.sh bl_do_update_to7.sh.orig > 138,139c138 > < #runurl "http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh" > < ./bl_master_package_list.sh > --- >> runurl "http://nebc.nerc.ac.uk/downloads/bl7_only/bl_master_package_list.sh" And I got: All done - your system is updated to Bio-Linux 7! Thanks for all your work creating this Bio-Linux 7 update script. Bye, Tony. From tony.travis at ed.ac.uk Wed Sep 26 19:51:47 2012 From: tony.travis at ed.ac.uk (Tony Travis) Date: Thu, 27 Sep 2012 00:51:47 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <506341B4.6070702@ed.ac.uk> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk> Message-ID: <50639513.8090907@ed.ac.uk> On 26/09/12 18:56, Tony Travis wrote: > [...] > And I got: > > All done - your system is updated to Bio-Linux 7! Hi, Tim. You need to install the 'fallback' session to get NX working: aptitude install gnome-session-fallback It would have been installed in a Desktop version, but I started from a vanilla server install with just the SSH service. However, the use-case I'm interested in is installing a Bio-Linux terminal server using an existing 64-bit Ubuntu 12.04 LTS server instance as a starting point. Bye, Tony. From tony.travis at ed.ac.uk Thu Sep 27 06:15:56 2012 From: tony.travis at ed.ac.uk (Tony Travis) Date: Thu, 27 Sep 2012 11:15:56 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <50639513.8090907@ed.ac.uk> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk> <50639513.8090907@ed.ac.uk> Message-ID: <5064275C.2040805@ed.ac.uk> On 27/09/12 00:51, Tony Travis wrote: > On 26/09/12 18:56, Tony Travis wrote: >> [...] >> And I got: >> >> All done - your system is updated to Bio-Linux 7! Hi, Tim. I also had to install Ubuntu desktop to get NX working properly: aptitude install ubuntu-desktop Then remove network manager, which should not be installed on a server: > aptitude purge network-manager network-manager-gnome network-manager-pptp network-manager-pptp-gnome Orphaned dependencies can be removed, and APT integrity checked by: > aptitude -f install Now I have all of Bio-Linux 7 accessible via NX except for Qiime. Bye, Tony. From tbooth at ceh.ac.uk Thu Sep 27 06:34:27 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 27 Sep 2012 11:34:27 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <5064275C.2040805@ed.ac.uk> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk> <50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk> Message-ID: <1348742067.4031.6.camel@balisaur> Hi Tony, Great stuff - I didn't realise that apt-add-repository wasn't on there by default and this has caused you various problems. I'll modify the script to sort that out and I think I can also easily fix the other things you mentioned. The nebc/bio-linux PPA should provide the version of Qiime necessary to install bio-linux-qiime on Ubuntu 12.04. There are a few helper applications that the latest Qiime wants which are not yet packaged for Bio-Linux, but the core features should all work. What happens if you try to install Qiime now that the PPA is added as a package source? (here's how it should be) tbooth at balisaur[tbooth]apt-cache policy qiime qiime: Installed: 1.5.0+repack-2ubuntu4 Candidate: 1.5.0+repack-2ubuntu4 Version table: *** 1.5.0+repack-2ubuntu4 0 500 http://ppa.launchpad.net/nebc/bio-linux/ubuntu/ precise/main amd64 Packages 100 /var/lib/dpkg/status 1.4.0-0ubuntu2 0 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages 1.3.0-3 0 500 http://gb.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages 1.3.0-0ubuntu6 0 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages 1.3.0-0ubuntu5 0 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages 1.2.1-ubuntu5 0 500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages Cheers, TIM On Thu, 2012-09-27 at 11:15 +0100, Tony Travis wrote: > On 27/09/12 00:51, Tony Travis wrote: > > On 26/09/12 18:56, Tony Travis wrote: > >> [...] > >> And I got: > >> > >> All done - your system is updated to Bio-Linux 7! > > Hi, Tim. > > I also had to install Ubuntu desktop to get NX working properly: > > aptitude install ubuntu-desktop > > Then remove network manager, which should not be installed on a server: > > > aptitude purge network-manager network-manager-gnome network-manager-pptp network-manager-pptp-gnome > > Orphaned dependencies can be removed, and APT integrity checked by: > > > aptitude -f install > > Now I have all of Bio-Linux 7 accessible via NX except for Qiime. > > Bye, > > Tony. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From tony.travis at ed.ac.uk Thu Sep 27 06:39:25 2012 From: tony.travis at ed.ac.uk (Tony Travis) Date: Thu, 27 Sep 2012 11:39:25 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <1348742067.4031.6.camel@balisaur> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk> <50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk> <1348742067.4031.6.camel@balisaur> Message-ID: <50642CDD.8040708@ed.ac.uk> On 27/09/12 11:34, Tim Booth wrote: > Hi Tony, > > Great stuff - I didn't realise that apt-add-repository wasn't on there > by default and this has caused you various problems. I'll modify the > script to sort that out and I think I can also easily fix the other > things you mentioned. > > The nebc/bio-linux PPA should provide the version of Qiime necessary to > install bio-linux-qiime on Ubuntu 12.04. There are a few helper > applications that the latest Qiime wants which are not yet packaged for > Bio-Linux, but the core features should all work. What happens if you > try to install Qiime now that the PPA is added as a package source? Hi, Tim. I ran your original script again, but with the PPA enabled, and it installed Qiime without error :-) > All done - your system is updated to Bio-Linux 7! > You may want to run 'sudo apt-get autoremove' if that was suggested above. Thanks! Tony. From daniel.antony.pass at googlemail.com Thu Sep 27 06:51:40 2012 From: daniel.antony.pass at googlemail.com (Daniel Pass) Date: Thu, 27 Sep 2012 11:51:40 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <50642CDD.8040708@ed.ac.uk> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk> <50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk> <1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk> Message-ID: Currently I have only gone the route of Ubuntu12.04 into BL7 on my laptop, but that seemed to work flawlessly although did need a couple of re-runs. Qiime continues to work as before. Im running it on my virtual box now but keeping expectations low after you said there were issues with it before, Tim. It won't let me run the script straight, and keeps forcing the 'upgrade to 12.04' gui on me so letting it do that first so assuming it'll go after that. All of the server install info is really helpful guys. All 4 of ours are in pretty heavy use at the moment, so having the kinks worked out before we do the push is really helpful. Dan On 27 September 2012 11:39, Tony Travis wrote: > On 27/09/12 11:34, Tim Booth wrote: > >> Hi Tony, >> >> Great stuff - I didn't realise that apt-add-repository wasn't on there >> by default and this has caused you various problems. I'll modify the >> script to sort that out and I think I can also easily fix the other >> things you mentioned. >> >> The nebc/bio-linux PPA should provide the version of Qiime necessary to >> install bio-linux-qiime on Ubuntu 12.04. There are a few helper >> applications that the latest Qiime wants which are not yet packaged for >> Bio-Linux, but the core features should all work. What happens if you >> try to install Qiime now that the PPA is added as a package source? >> > > Hi, Tim. > > I ran your original script again, but with the PPA enabled, and it > installed Qiime without error :-) > > All done - your system is updated to Bio-Linux 7! >> You may want to run 'sudo apt-get autoremove' if that was suggested above. >> > > Thanks! > > > Tony. > ______________________________**_________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.**ac.uk > http://nebclists.nerc.ac.uk/**mailman/listinfo/bio-linux-dev > -- Daniel Pass Tel: (029208)76680 Mob: 07735658687 http://www.kille-morgan.org.uk Room 0.39, School of Biosciences, Biological Sciences Building, Museum Avenue, Cardiff, CF10 3AT -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Thu Sep 27 06:57:52 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 27 Sep 2012 11:57:52 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> Message-ID: <1348743472.4031.19.camel@balisaur> Hi Mike, See my reply to Tony. I have Qiime 1.5 happily on my BL7 machine so you should be able to get it on yours. When I run "qiime print_qiime_config -t" I get the following errors due to missing dependencies: ParsInsert is missing clearcut is missing cluster_jobs_fp is missing pplacer is missing rtax is missing usearch is missing * You can install these manually if you need them. If you want them packaged up in a hurry you'll need to put in an NBAF application or bung Tony some cash. * in the case of USearch, unlike UClust, the license prohibits any redistribution. I also get the following errors but as far as I know these things actually work fine, even though the version is unsupported: R is unsupported version BLAST is unsupported version maptplotlib is unsupported version mothur is unsupported version numpy is unsupported version python is unsupported version raxmlHPC needs updating Cheers, TIM On Wed, 2012-09-26 at 17:02 +0100, Cox, Michael J wrote: > Exciting! > > Would QIIME 1.5 be included in the update or is that going to take some further fun and games after BL7 is a go? > > Cheers > > Mike > > @mikeyj > > > On 26 Sep 2012, at 16:45, "Booth, Timothy G." wrote: > > > Dear Bio-Linux testers, > > > > My deadline for the Bio-Linux 7 Beta release has, ahem, slipped a little > > later than I first anticipated, but I have now finished all the package > > updates and tested upgrading several machines in-house. As far as I'm > > aware, once you get through the upgrade, everything works and is ready > > to use. There is no ISO download just yet, but I invite everyone on > > this list to try upgrading their Bio-Linux 6 systems in-place. This is > > the first time in 7 releases that we've been confident to advise > > upgrading in-place without reinstalling. > > > > In short, the upgrade process is fairly complex so I've prepared a > > script to do all the necessary actions and make it simple for you. If > > the script doesn't finish for some reason you can simply run it again as > > many times as you need to. I've fixed all the issues I know about but > > you may hit other problems - please report and discuss bugs on this > > list, or even better file a bug report here: > > > > https://bugs.launchpad.net/bio-linux > > > > *** It should go without saying - don't do this on a critical server > > just now. Check you have a few GB free disk space before you start. > > Back up your data first. Really, back up your data first. *** > > > > To run the script: > > > > 1) Open a terminal > > 2) download (using wget or otherwise) this script: > > http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh > > 3) Run the script: > > sudo bash ./bl_do_update_to7.sh > > > > This will trigger everything off. The script is designed to be run on a > > Bio-Linux 6 machine but should also be fine if run on a vanilla Ubuntu > > 12.04 box (or even on regular Ubuntu 10.04) as it first ensures that > > Ubuntu is upgraded, then installs all the BL stuff, and finally clears > > up some legacy packages and sets the backdrop. If the new backdrop > > doesn't appear you probably need to re-run the script again until it > > does, or until you hit a bug that stops it working. > > > > It will take about 2-3 hours to do the full upgrade. You'll > > periodically need to answer various questions that pop up. > > > > Notes and known issues: > > > > The initial upgrade from Ubuntu 10.04 to 12.04 can fail if you have > > additional software sources (eg. PPAs) enabled. You may need to disable > > these via the "Additional Software Sources" tab in the update manager. > > The CRAN repositories, FreeNX PPA, and the Google Chrome repository > > (which is added automatically if you install Chrome) should be OK and > > the upgrade script deals with them explicitly. > > > > The Ubuntu upgrade also produces various warnings, and you may well see > > a bizarre error box saying "???? ???????? ???? ????". You don't have to > > worry about this! There's not much I can do about these things as they > > come from the core Ubuntu packages. > > > > I think I've solved the errors where APT would complain about installing > > unauthenticated packages, but if you see any such errors please let me > > know. > > > > Bio-Linux packages are split between the old repository (on > > nebc.nerc.ac.uk) and the new Bio-Linux PPA on Launchpad. You'll notice > > some packages that can't go on Launchpad but don't work on BL6 will be > > downloaded and installed separately. This is a temporary workaround. > > > > After upgrading you'll be using the Unity desktop. This is going to be > > the default on Bio-Linux 7 as it is the default on Ubuntu. If you don't > > like it and want to contribute instructions for swapping to > > Gnome-shell/KDE/Xfce/TWM then I'll gladly share these on the website, > > but personally I'm sticking with Unity. It's not so bad once you get > > used to it! > > > > Cheers, > > > > TIM > > > > -- > > Tim Booth > > NERC Environmental Bioinformatics Centre > > > > Centre for Ecology and Hydrology > > Maclean Bldg, Benson Lane > > Crowmarsh Gifford > > Wallingford, England > > OX10 8BB > > > > http://nebc.nerc.ac.uk > > +44 1491 69 2705 > > > > -- > > This message (and any attachments) is for the recipient only. NERC > > is subject to the Freedom of Information Act 2000 and the contents > > of this email and any reply you make may be disclosed by NERC unless > > it is exempt from release under the Act. Any material supplied to > > NERC may be stored in an electronic records management system. > > _______________________________________________ > > Bio-Linux-dev mailing list > > Bio-Linux-dev at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tbooth at ceh.ac.uk Thu Sep 27 07:03:38 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 27 Sep 2012 12:03:38 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk> <50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk> <1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk> Message-ID: <1348743818.4031.24.camel@balisaur> Hi Dan, On Thu, 2012-09-27 at 11:51 +0100, Daniel Pass wrote: > Currently I have only gone the route of Ubuntu12.04 into BL7 on my > laptop, but that seemed to work flawlessly although did need a couple > of re-runs. Qiime continues to work as before. > So you can confirm you now have Qiime 1.5, right? > > Im running it on my virtual box now but keeping expectations low after > you said there were issues with it before, Tim. It won't let me run > the script straight, and keeps forcing the 'upgrade to 12.04' gui on > me so letting it do that first so assuming it'll go after that. > The script can't do its work until the base system is updated to Ubuntu 12.04. This brings with it things like the kernel, Gnome, python, etc. This bit of the update is handled by the Ubuntu upgrade GUI. If you think you are already upgraded to 12.04 but you still get this situation then let me know. Cheers, TIM > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From tony.travis at ed.ac.uk Thu Sep 27 07:04:20 2012 From: tony.travis at ed.ac.uk (Tony Travis) Date: Thu, 27 Sep 2012 12:04:20 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <1348743472.4031.19.camel@balisaur> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <1348743472.4031.19.camel@balisaur> Message-ID: <506432B4.2080509@ed.ac.uk> On 27/09/12 11:57, Tim Booth wrote: > Hi Mike, > > See my reply to Tony. I have Qiime 1.5 happily on my BL7 machine so you > should be able to get it on yours. When I run "qiime print_qiime_config > -t" I get the following errors due to missing dependencies: > > ParsInsert is missing > clearcut is missing > cluster_jobs_fp is missing > pplacer is missing > rtax is missing > usearch is missing * > > You can install these manually if you need them. If you want them > packaged up in a hurry you'll need to put in an NBAF application or bung > Tony some cash. Hi, Tim. Thanks for the plug :-) Mike, if you want some contract work doing please email me off-list: tony.travis at minke-informatics.co.uk Bye, Tony. From daniel.antony.pass at googlemail.com Thu Sep 27 09:52:56 2012 From: daniel.antony.pass at googlemail.com (Daniel Pass) Date: Thu, 27 Sep 2012 14:52:56 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <1348743818.4031.24.camel@balisaur> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk> <50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk> <1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk> <1348743818.4031.24.camel@balisaur> Message-ID: I'm pretty certain I'm on qiime1.5 , but my laptop is at home so cant check till tonight. I've finished the VM box upgrade now, from BL6 to BL7. I knew it was going to do the ubuntu upgrade first, just thought it was going to be in the shell and thought the gui was getting in the way, but no problems! On the VM Qiime is 1.5, galaxy is going and I have a lovely grasshoper and biolinux logo. No issues in install other than qiime freaking out that my r-core was too new and it stopped the script. apt-get remove'd and then the script ran through to the end. Do you plan to change around the unity hotlinks for the final distro? I imagine a folder of links to bioinformatics programs would be useful to new users, and unity is a bit annoying in the no hierarchical menus. Maybe as Galaxy is the flagship, pin that to the main menu, and drop ubuntuone etc Dan On 27 September 2012 12:03, Tim Booth wrote: > Hi Dan, > > On Thu, 2012-09-27 at 11:51 +0100, Daniel Pass wrote: > > Currently I have only gone the route of Ubuntu12.04 into BL7 on my > > laptop, but that seemed to work flawlessly although did need a couple > > of re-runs. Qiime continues to work as before. > > > So you can confirm you now have Qiime 1.5, right? > > > > Im running it on my virtual box now but keeping expectations low after > > you said there were issues with it before, Tim. It won't let me run > > the script straight, and keeps forcing the 'upgrade to 12.04' gui on > > me so letting it do that first so assuming it'll go after that. > > > The script can't do its work until the base system is updated to Ubuntu > 12.04. This brings with it things like the kernel, Gnome, python, etc. > This bit of the update is handled by the Ubuntu upgrade GUI. > > If you think you are already upgraded to 12.04 but you still get this > situation then let me know. > > Cheers, > > TIM > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > -- Daniel Pass Tel: (029208)76680 Mob: 07735658687 http://www.kille-morgan.org.uk Room 0.39, School of Biosciences, Biological Sciences Building, Museum Avenue, Cardiff, CF10 3AT -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Thu Sep 27 11:59:53 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 27 Sep 2012 16:59:53 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <5064275C.2040805@ed.ac.uk> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk> <50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk> Message-ID: <1348761593.4031.60.camel@balisaur> Hi, I've tweaked the script based on Tony's reports. Testers can re-run the upgrade if they like and the extra couple of packages that NX wants will be installed. Note that after the upgrade you now have "runurl" on the system so you can do this in one step, rather then two, if you like: sudo runurl http://nebc.nerc.ac.uk/downloads/bl7_only/bl_do_update_to7.sh Details... > This is because the adding the PPA failed: > > > ./bl_do_update_to7.sh: line 55: apt-add-repository: command not > found > > ./bl_do_update_to7.sh: line 58: apt-add-repository: command not > found > This, which I didn't notice first time round, I fixed by: > aptitude install python-software-properties The script now handles this properly and installs the package first > You need to install the 'fallback' session to get NX working: > > aptitude install gnome-session-fallback > > I also had to install Ubuntu desktop to get NX working properly: > > aptitude install ubuntu-desktop These are both now in the master package list > Then remove network manager, which should not be installed on a server: > > > aptitude purge network-manager network-manager-gnome network-manager-pptp network-manager-pptp-gnome I've tweaked the script to install both the above packages with "--no-install-recommends" so that should get NX working for everyone while not upsetting servers with network-manager and friends. I think that was all for now. Cheers, TIM -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From tbooth at ceh.ac.uk Thu Sep 27 12:50:01 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 27 Sep 2012 17:50:01 +0100 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk> <50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk> <1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk> <1348743818.4031.24.camel@balisaur> Message-ID: <1348764601.4031.80.camel@balisaur> Hi Dan, I'm looking into how best to customise the default panel on the Unity Dash. The things that come up when you click the Ubuntu logo at the top (AKA the BFB - big freakin button) are called 'lenses' - the Home lens, the Applications lens, the Files lens etc. I looked at what it would take to make my own bioinformatics lens - there are full instructions - and it might be worth a shot but then it might take weeks to perfect and I'd like a quicker solution. The Home lens with the smart search is pretty neat, but some of the others aren't even very good for Ubuntu, never mind Bio-Linux. How the heck is it generating "Apps available for Download" in the Applications lens? It seems to pick some totally random packages, then, if you click one, next time you look it generates another random selection. How pointless! I agree that having a folder of app links and putting Galaxy in the side bar is probably the quickest way to get something acceptable, though it's not ideal. > Cheers, TIM > Do you plan to change around the unity hotlinks for the final distro? > I imagine a folder of links to bioinformatics programs would be useful > to new users, and unity is a bit annoying in the > no hierarchical menus. Maybe as Galaxy is the flagship, pin that to > the main menu, and drop ubuntuone etc > > > Dan > > > On 27 September 2012 12:03, Tim Booth wrote: > Hi Dan, > > On Thu, 2012-09-27 at 11:51 +0100, Daniel Pass wrote: > > Currently I have only gone the route of Ubuntu12.04 into BL7 > on my > > laptop, but that seemed to work flawlessly although did need > a couple > > of re-runs. Qiime continues to work as before. > > > > So you can confirm you now have Qiime 1.5, right? > > > > Im running it on my virtual box now but keeping expectations > low after > > you said there were issues with it before, Tim. It won't let > me run > > the script straight, and keeps forcing the 'upgrade to > 12.04' gui on > > me so letting it do that first so assuming it'll go after > that. > > > > The script can't do its work until the base system is updated > to Ubuntu > 12.04. This brings with it things like the kernel, Gnome, > python, etc. > This bit of the update is handled by the Ubuntu upgrade GUI. > > If you think you are already upgraded to 12.04 but you still > get this > situation then let me know. > > Cheers, > > TIM > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > -- > This message (and any attachments) is for the recipient only. > NERC > is subject to the Freedom of Information Act 2000 and the > contents > of this email and any reply you make may be disclosed by NERC > unless > it is exempt from release under the Act. Any material supplied > to > NERC may be stored in an electronic records management system. > > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > > > > > > -- > > > > Daniel Pass > > Tel: (029208)76680 > Mob: 07735658687 > http://www.kille-morgan.org.uk > > Room 0.39, > School of Biosciences, > Biological Sciences Building, > Museum Avenue, > Cardiff, > CF10 3AT > > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From raonyguimaraes at gmail.com Sat Sep 29 09:14:29 2012 From: raonyguimaraes at gmail.com (=?ISO-8859-1?Q?Raony_Guimaraes_Corr=EAa_Do_Carmo_Lisboa_Cardenas?=) Date: Sat, 29 Sep 2012 10:14:29 -0300 Subject: [Bio-linux-dev] Upgrade to Bio-Linux 7 (at last) In-Reply-To: <1348764601.4031.80.camel@balisaur> References: <1DCCED50D0696A498958BA6B254456E2223BA7FB43@nerckwmb1.ad.nerc.ac.uk> <506326C4.5010300@minke.ukfsn.org> <50633140.6090505@ed.ac.uk> <506332E6.4040101@ed.ac.uk> <506341B4.6070702@ed.ac.uk> <50639513.8090907@ed.ac.uk> <5064275C.2040805@ed.ac.uk> <1348742067.4031.6.camel@balisaur> <50642CDD.8040708@ed.ac.uk> <1348743818.4031.24.camel@balisaur> <1348764601.4031.80.camel@balisaur> Message-ID: Hello Tim and everyone else! Since you said "should also be fine if run on a vanilla Ubuntu 12.04 box (or even on regular Ubuntu 10.04)" I decided to give a try for the new version of Ubuntu Studio 12.04 64 bits that comes with Xfce and all the cool stuff for Audio ,Graphics ,Video , Photographyand Publishing already installed. So far no regrets, the panels and menus are looking very similar with the old gnome 2 style, very nice look and feel and I loved the very minimalistic button on the top left that give you access to everything you need inside a single menu. (Also with the bioinformatics submenu) Of course you can always install Unity if you think this will improve your productivity. (not my case) :P The bl_do_update_to7.shworked really well and I'm glad to have all the ecosystem from Ubuntu Studio 12.04 back on my laptop this time mixed all the packages from Biolinux 7. Before trying this I upgraded my old version of Biolinux 6 and this gave me the feeeling that I just got a brand new Ubuntu 12.04/Unity without anything special or specific for Bioinformatics. I know the packages were installled but the feeling was not the same. (I hope/imagine you guys will make a good artwork before the official release to make it looks more like Biolinux, am I right ?) For me, the biggest difference of Biolinux 6 was the menu full of apps for bioinformatics already installed that may be I would never really discover by myself and that I could simply give a try without fearing breaking my system when installing it. Let alone the fact I could show off to my friends all the cool stuff I had installed for doing my research and analysis. :D Thank you a lot for this guys! Another thing I would like to suggest is a categorization of all the apps installed related with Bioinformatics. Ubuntu Studio once again, did a really good job splitting into Audio, Photography, Graphics and Video. Would be nice to have something like that for Biolinux, ex: DNA, RNA, Protein, NGS ... and so on ... just a suggestion. One of the things would be really nice to have in Biolinux is a meta package Same way Ubuntu Studio has, so everyone could convert his Ubuntu based distro in Biolinux. https://launchpad.net/ubuntu/+source/ubuntustudio-meta https://help.ubuntu.com/community/Ubuntu%20Studio%20Upgrade%20from%20Ubuntu Thank you all and keep the good work! Regards. Atenciosamente, C------0 Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas G--------1 T--------1 msn/gtalk: raonyguimaraes at gmail.com A-------0 skype: raonyguimaraes C----0 phone: +55 31 93404152 1 0--G Member @ LGC - Laboratory of Clinical Genomics 1-----T Bachelor in Biomedical Informatics - USP Ribeir?o Preto 1--------A PhD Student in Bioinformatics - UFMG 0---------C 1--------G Creator of the Brazilian Portal of Biomedical Informatics and Medicina do Futuro 1-----G www.informaticabiomedica.org / www.medicinadofuturo.com.br T G--0 Research Interests: Personalized Medicine and Pharmacogenomics A------0 http://lattes.cnpq.br/0263349039132540 T--------1 C--------0 "Bioinformatics: We Can Change The World..." On Thu, Sep 27, 2012 at 1:50 PM, Tim Booth wrote: > Hi Dan, > > I'm looking into how best to customise the default panel on the Unity > Dash. The things that come up when you click the Ubuntu logo at the top > (AKA the BFB - big freakin button) are called 'lenses' - the Home lens, > the Applications lens, the Files lens etc. I looked at what it would > take to make my own bioinformatics lens - there are full instructions - > and it might be worth a shot but then it might take weeks to perfect and > I'd like a quicker solution. > > The Home lens with the smart search is pretty neat, but some of the > others aren't even very good for Ubuntu, never mind Bio-Linux. How the > heck is it generating "Apps available for Download" in the Applications > lens? It seems to pick some totally random packages, then, if you click > one, next time you look it generates another random selection. How > pointless! > > I agree that having a folder of app links and putting Galaxy in the side > bar is probably the quickest way to get something acceptable, though > it's not ideal. > > > Cheers, > > TIM > > > Do you plan to change around the unity hotlinks for the final distro? > > I imagine a folder of links to bioinformatics programs would be useful > > to new users, and unity is a bit annoying in the > > no hierarchical menus. Maybe as Galaxy is the flagship, pin that to > > the main menu, and drop ubuntuone etc > > > > > > Dan > > > > > > On 27 September 2012 12:03, Tim Booth wrote: > > Hi Dan, > > > > On Thu, 2012-09-27 at 11:51 +0100, Daniel Pass wrote: > > > Currently I have only gone the route of Ubuntu12.04 into BL7 > > on my > > > laptop, but that seemed to work flawlessly although did need > > a couple > > > of re-runs. Qiime continues to work as before. > > > > > > > So you can confirm you now have Qiime 1.5, right? > > > > > > Im running it on my virtual box now but keeping expectations > > low after > > > you said there were issues with it before, Tim. It won't let > > me run > > > the script straight, and keeps forcing the 'upgrade to > > 12.04' gui on > > > me so letting it do that first so assuming it'll go after > > that. > > > > > > > The script can't do its work until the base system is updated > > to Ubuntu > > 12.04. This brings with it things like the kernel, Gnome, > > python, etc. > > This bit of the update is handled by the Ubuntu upgrade GUI. > > > > If you think you are already upgraded to 12.04 but you still > > get this > > situation then let me know. > > > > Cheers, > > > > TIM > > > > > > > -- > > Tim Booth > > NERC Environmental Bioinformatics Centre > > > > Centre for Ecology and Hydrology > > Maclean Bldg, Benson Lane > > Crowmarsh Gifford > > Wallingford, England > > OX10 8BB > > > > http://nebc.nerc.ac.uk > > +44 1491 69 2705 > > -- > > This message (and any attachments) is for the recipient only. > > NERC > > is subject to the Freedom of Information Act 2000 and the > > contents > > of this email and any reply you make may be disclosed by NERC > > unless > > it is exempt from release under the Act. Any material supplied > > to > > NERC may be stored in an electronic records management system. > > > > _______________________________________________ > > Bio-Linux-dev mailing list > > Bio-Linux-dev at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > > > > > > > > > > > > -- > > > > > > > > Daniel Pass > > > > Tel: (029208)76680 > > Mob: 07735658687 > > http://www.kille-morgan.org.uk > > > > Room 0.39, > > School of Biosciences, > > Biological Sciences Building, > > Museum Avenue, > > Cardiff, > > CF10 3AT > > > > > > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: