From gawbul at gmail.com Sun Aug 3 17:09:57 2014 From: gawbul at gmail.com (Steve Moss) Date: Sun, 3 Aug 2014 22:09:57 +0100 Subject: [Bio-linux-dev] upgrade_to_8.sh Message-ID: Dear Tim, I was looking through the upgrade_to_8.sh script and noticed you use the PYVERS function to check the version of the operating system. I wondered what the rationale was behind that? Could there be any cases where people who upgrade their python version pre-14.04 pass the test for 14.04 when they shouldn't? Had you thought about checking /etc/debian_version instead? Precise lists wheezy/sid, where as Trusty lists jessie/sid. You could also parse the output of lsb_release - d? e.g. lsb_release -d | cut -d " " -f 2 gives 14.04.1. Cheers, Steve -- Steve Moss about.me/gawbul [image: Steve Moss on about.me] -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at abdn.ac.uk Mon Aug 4 07:12:17 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Mon, 4 Aug 2014 12:12:17 +0100 Subject: [Bio-linux-dev] MATE Message-ID: <53DF6A91.4090400@abdn.ac.uk> Hi, Tim. Neither your Bio-Linux 8 update script or .iso install: "mate-users-admin" This is useful if you are administering a headless server via "x2go" or if you decide to adopt the MATE desktop on a server/desktop with limited support for hardware accelerated graphics. I upgraded two of my Bio-Linux 7 garage servers to Bio-Linux 8 yesterday and got a warning from the Ubuntu 14.04 LTS installer that I would be better off sticking to the 12.04 LTS release because the graphics would be very slow under Ubuntu 14.04 LTS... They weren't kidding: The 14.04 LTS Unity desktop was unusable on my servers, so I switched to MATE on the console instead. What do you mean "I shouldn't use a GUI to administer a server" ;-) 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 cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Mon Aug 4 09:44:18 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 4 Aug 2014 14:44:18 +0100 Subject: [Bio-linux-dev] upgrade_to_8.sh In-Reply-To: References: Message-ID: <1407159858.6360.74.camel@balisaur> Hi Steve, The lsb_release think makes the most logical sense, but what I couldn't work out was what this would be set to on a partially upgraded system, or one upgraded without using the official upgrade tool. Does it get set at the start of the upgrade or at the end or in the middle? To be honest I can't really remember my rationale when I wrote the upgrade_to_7 script, and my method is probably not the best, but since it seemed to work well I just decided to stick with it for the upgrade_to_8 script. If people report problems I'll change it. Cheers, TIM On Sun, 2014-08-03 at 22:09 +0100, Steve Moss wrote: > Dear Tim, > > > I was looking through the upgrade_to_8.sh script and noticed you use > the PYVERS function to check the version of the operating system. I > wondered what the rationale was behind that? Could there be any cases > where people who upgrade their python version pre-14.04 pass the test > for 14.04 when they shouldn't? > > > Had you thought about checking /etc/debian_version instead? Precise > lists wheezy/sid, where as Trusty lists jessie/sid. You could also > parse the output of lsb_release - d? e.g. lsb_release -d | cut -d " " > -f 2 gives 14.04.1. > > > Cheers, > > > Steve > -- > > Steve Moss > about.me/gawbul > Steve Moss on about.me > -- 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 Mon Aug 4 09:55:03 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 4 Aug 2014 14:55:03 +0100 Subject: [Bio-linux-dev] MATE In-Reply-To: <53DF6A91.4090400@abdn.ac.uk> References: <53DF6A91.4090400@abdn.ac.uk> Message-ID: <1407160503.6360.80.camel@balisaur> Hi Tony, I ported the MATE packages over from Sid, and there is no mate-users-admin in Debian at all. Given that Ubuntu has some specific requirements about how users are added (eg. default groups) I'm not sure if this reflects an actual issue with this bit of MATE or just that the Debian packagers never got around to adding it. My inclination would be to add an icon which runs "/usr/bin/unity-control-center user-accounts" since this would give everyone the same options for account maintenance. I'll see if I can work out how to make that appear in the MATE control panel. Cheers, TIM On Mon, 2014-08-04 at 12:12 +0100, Tony Travis wrote: > Hi, Tim. > > Neither your Bio-Linux 8 update script or .iso install: > > "mate-users-admin" > > This is useful if you are administering a headless server via "x2go" or > if you decide to adopt the MATE desktop on a server/desktop with limited > support for hardware accelerated graphics. > > I upgraded two of my Bio-Linux 7 garage servers to Bio-Linux 8 yesterday > and got a warning from the Ubuntu 14.04 LTS installer that I would be > better off sticking to the 12.04 LTS release because the graphics would > be very slow under Ubuntu 14.04 LTS... > > They weren't kidding: The 14.04 LTS Unity desktop was unusable on my > servers, so I switched to MATE on the console instead. > > What do you mean "I shouldn't use a GUI to administer a server" ;-) > > 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 cl?raichte ann an Alba, ?ir. SC013683. > _______________________________________________ > 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 Mon Aug 4 11:37:30 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 4 Aug 2014 16:37:30 +0100 Subject: [Bio-linux-dev] MATE In-Reply-To: <1407160503.6360.80.camel@balisaur> References: <53DF6A91.4090400@abdn.ac.uk> <1407160503.6360.80.camel@balisaur> Message-ID: <1407166650.6360.94.camel@balisaur> Hi Tony, Sorry, I may be talking nonsense there. The application is lurking in mate-system-tools but doesn't work due to a typo in the package build. Should be an easy fix after all. Cheers, TIM On Mon, 2014-08-04 at 14:55 +0100, Tim Booth wrote: > Hi Tony, > > I ported the MATE packages over from Sid, and there is no > mate-users-admin in Debian at all. Given that Ubuntu has some specific > requirements about how users are added (eg. default groups) I'm not sure > if this reflects an actual issue with this bit of MATE or just that the > Debian packagers never got around to adding it. > > My inclination would be to add an icon which runs > "/usr/bin/unity-control-center user-accounts" since this would give > everyone the same options for account maintenance. I'll see if I can > work out how to make that appear in the MATE control panel. > > Cheers, > > TIM > > On Mon, 2014-08-04 at 12:12 +0100, Tony Travis wrote: > > Hi, Tim. > > > > Neither your Bio-Linux 8 update script or .iso install: > > > > "mate-users-admin" > > > > This is useful if you are administering a headless server via "x2go" or > > if you decide to adopt the MATE desktop on a server/desktop with limited > > support for hardware accelerated graphics. > > > > I upgraded two of my Bio-Linux 7 garage servers to Bio-Linux 8 yesterday > > and got a warning from the Ubuntu 14.04 LTS installer that I would be > > better off sticking to the 12.04 LTS release because the graphics would > > be very slow under Ubuntu 14.04 LTS... > > > > They weren't kidding: The 14.04 LTS Unity desktop was unusable on my > > servers, so I switched to MATE on the console instead. > > > > What do you mean "I shouldn't use a GUI to administer a server" ;-) > > > > 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 cl?raichte ann an Alba, ?ir. SC013683. > > _______________________________________________ > > 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 tony.travis at abdn.ac.uk Fri Aug 15 09:39:19 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Fri, 15 Aug 2014 14:39:19 +0100 Subject: [Bio-linux-dev] java-6-openjdk Message-ID: <53EE0D87.8070303@abdn.ac.uk> Hi, Tim. I just ran your 'indempotent' BL8 upgrade script again and realised that unconditionally purging "java-6-openjdk" might not be such a good idea after all... We need it to run the "Structure" GUI, which doesn't work properly with "java-7-openjdk": http://pritchardlab.stanford.edu/structure.html I think there might be other programs that need java-6 too. I'll let you know about any problems I encounter. BTW, I've left java-7 as the default Java - I only use java-6 for particular programs that need it, by specifying the full path to java-6 in a wrapper script. 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 cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Fri Aug 15 09:52:22 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 15 Aug 2014 14:52:22 +0100 Subject: [Bio-linux-dev] java-6-openjdk In-Reply-To: <53EE0D87.8070303@abdn.ac.uk> References: <53EE0D87.8070303@abdn.ac.uk> Message-ID: <1408110742.7724.168.camel@balisaur> Hi Tony, This doesn't stop the script being idempotent, but I agree that its not really designed to be run once the upgrade is done and you have started reconfiguring things. I judged that having programs run with the old Java, which triggers nasty glitches, slowdowns and bugs in things like Artemis and Taverna, was more of a risk than upsetting any things which really need Java 6, but I may have been wrong so do keep me posted if you find further problems. Cheers, TIM On Fri, 2014-08-15 at 14:39 +0100, Tony Travis wrote: > Hi, Tim. > > I just ran your 'indempotent' BL8 upgrade script again and realised that > unconditionally purging "java-6-openjdk" might not be such a good idea > after all... > > We need it to run the "Structure" GUI, which doesn't work properly with > "java-7-openjdk": > > http://pritchardlab.stanford.edu/structure.html > > I think there might be other programs that need java-6 too. I'll let you > know about any problems I encounter. BTW, I've left java-7 as the > default Java - I only use java-6 for particular programs that need it, > by specifying the full path to java-6 in a wrapper script. > > 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 cl?raichte ann an Alba, ?ir. SC013683. > _______________________________________________ > 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