From tony.travis at abdn.ac.uk Tue Jul 1 08:38:15 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Tue, 1 Jul 2014 13:38:15 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <53B17B4E.6040008@abdn.ac.uk> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> <1404119740.4956.3.camel@balisaur> <53B1338B.3090207@abdn.ac.uk> <1404128782.4956.49.camel@balisaur> <53B15613.4060300@abdn.ac.uk> <53B159EA.6080404@abdn.ac.uk> <1404137870.24510.3.camel@balisaur> <53B17B4E.6040008@abdn.ac.uk> Message-ID: <53B2ABB7.10209@abdn.ac.uk> On 30/06/14 15:59, Tony Travis wrote: > On 30/06/14 15:17, Tim Booth wrote: >> [...] >>> I also noticed that on the 'greeter' screen the (dotted) version of the >>> current desktop wallpaper is not stretched or zoomed to fill the screen >>> as it was before on a 1600x900 external monitor connected to my laptop. >> >> No idea what I need to do to fix this. I'll see if I can reproduce the >> problem. Yes, I do want to make the system make a good impression if I >> can. > > Hi, Tim. > > The problem only seems to happen when booting: If I just logout/in, the > greeter doesn't have the BL desktop wallpaper - Just the default one... Hi, Tim. Same problem on the lock screen - This only happens if you use an external monitor on a laptop, but it didn't happen on the same laptop and external monitor under BL7. I've been trying out the x2go 'MATE' desktop, which works well, but I think might be improved if you change the default 96dpi font rendering resolution to 106dpi. The bold fonts don't work very well at 96dpi. The appearance of text on the MATE desktop at 106dpi is similar to text on the default Unity desktop. The 96dpi font rendering resolution is for 1024x768 monitors, but has been adopted as a default for X11. I also changed the font rendering to use "Subpixel smoothing (LCD's)". Tested remote MATE sessions on my work desktop workstation "wildcat" via the LAN and on my workstation "minke" at home via ADSL. BTW, I owe you a beer: Your "aptitude keep-all" fixed the post-install problems on "minke", so I've now upgraded three machines successfully. 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 Tue Jul 1 09:14:18 2014 From: tbooth at ceh.ac.uk (Booth, Timothy G.) Date: Tue, 1 Jul 2014 14:14:18 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <53B2ABB7.10209@abdn.ac.uk> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> <1404119740.4956.3.camel@balisaur> <53B1338B.3090207@abdn.ac.uk> <1404128782.4956.49.camel@balisaur> <53B15613.4060300@abdn.ac.uk> <53B159EA.6080404@abdn.ac.uk> <1404137870.24510.3.camel@balisaur> <53B17B4E.6040008@abdn.ac.uk>,<53B2ABB7.10209@abdn.ac.uk> Message-ID: <8C33D34D431A974EAEA913101DDA1944073056FE05@nerckwmbc.ad.nerc.ac.uk> Hi Tony, Thanks for the comments. I'm glad that aptitude is now happy. You may yet earn back the beer with your testing efforts so I won't place my order just yet. :-) I'll plug an external monitor into my laptop tomorrow and see what I can see. I have a "pristine" 14.04 system for comparison, so if the problem exists on that it will be safe to assume there is an open bug somewhere. If not, I'll try and work out what I stuffed up. Regarding the MATE desktop DPI settings, can you tell me what I need to modify in my package to make that happen? Cheers, TIM ________________________________________ From: Tony Travis [tony.travis at abdn.ac.uk] Sent: 01 July 2014 13:38 To: bio-linux-dev at nebclists.nerc.ac.uk Subject: Re: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing On 30/06/14 15:59, Tony Travis wrote: > On 30/06/14 15:17, Tim Booth wrote: >> [...] >>> I also noticed that on the 'greeter' screen the (dotted) version of the >>> current desktop wallpaper is not stretched or zoomed to fill the screen >>> as it was before on a 1600x900 external monitor connected to my laptop. >> >> No idea what I need to do to fix this. I'll see if I can reproduce the >> problem. Yes, I do want to make the system make a good impression if I >> can. > > Hi, Tim. > > The problem only seems to happen when booting: If I just logout/in, the > greeter doesn't have the BL desktop wallpaper - Just the default one... Hi, Tim. Same problem on the lock screen - This only happens if you use an external monitor on a laptop, but it didn't happen on the same laptop and external monitor under BL7. I've been trying out the x2go 'MATE' desktop, which works well, but I think might be improved if you change the default 96dpi font rendering resolution to 106dpi. The bold fonts don't work very well at 96dpi. The appearance of text on the MATE desktop at 106dpi is similar to text on the default Unity desktop. The 96dpi font rendering resolution is for 1024x768 monitors, but has been adopted as a default for X11. I also changed the font rendering to use "Subpixel smoothing (LCD's)". Tested remote MATE sessions on my work desktop workstation "wildcat" via the LAN and on my workstation "minke" at home via ADSL. BTW, I owe you a beer: Your "aptitude keep-all" fixed the post-install problems on "minke", so I've now upgraded three machines successfully. 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 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 abdn.ac.uk Tue Jul 1 11:06:34 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Tue, 1 Jul 2014 16:06:34 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ready for Beta-testing In-Reply-To: <8C33D34D431A974EAEA913101DDA1944073056FE05@nerckwmbc.ad.nerc.ac.uk> References: <1403869758.6513.73.camel@balisaur> <53AEE12F.9060006@abdn.ac.uk> <53AEE28D.8020502@abdn.ac.uk> <1404119740.4956.3.camel@balisaur> <53B1338B.3090207@abdn.ac.uk> <1404128782.4956.49.camel@balisaur> <53B15613.4060300@abdn.ac.uk> <53B159EA.6080404@abdn.ac.uk> <1404137870.24510.3.camel@balisaur> <53B17B4E.6040008@abdn.ac.uk>, <53B2ABB7.10209@abdn.ac.uk> <8C33D34D431A974EAEA913101DDA1944073056FE05@nerckwmbc.ad.nerc.ac.uk> Message-ID: <53B2CE7A.8090605@abdn.ac.uk> On 01/07/14 14:14, Booth, Timothy G. wrote: > Hi Tony, > > Thanks for the comments. I'm glad that aptitude is now happy. You > may yet earn back the beer with your testing efforts so I won't place > my order just yet. :-) Hi, Tim. I didn't know that the "aptitude -f" problems were caused by packages that "aptitude" itself had marked for auto-removal during installation. As you say, "aptitude" is a bit too clever for it's own good: The same might be said about people who use it ;-) > I'll plug an external monitor into my laptop tomorrow and see what I > can see. I have a "pristine" 14.04 system for comparison, so if the > problem exists on that it will be safe to assume there is an open bug > somewhere. If not, I'll try and work out what I stuffed up. The boot/lock screen seems to clone the last-used wallpaper image, but superimposes a dot grid on it. > Regarding the MATE desktop DPI settings, can you tell me what I need > to modify in my package to make that happen? On reflection, I don't think it's a good idea to change the MATE font rendering from the default of 96dpi because X11 uses 96dpi by default. The main reason that the default fonts look so bad in MATE seems to be the way that MATE uses 'hinting' when rendering fonts - see: System / Preferences / Appearance / Fonts / Rendering / Details The fonts look a lot better if you set 'Hinting' = None, which is what I believe Ubuntu does. The font settings are configured by "mate-appearance-properties", which can also be used to install new themes from the command-line. I don't know if you can set the default font rendering per theme, though. To get a MATE desktop that has similar fonts to the default Unity desktop, I increased the size of all the MATE fonts from 10 to 11pt, and the Fixed width font from 11 to 12pt. I also set the colours in Gnome Terminal to default black on light yellow, instead of colours from the current theme. I think this is more legible that white. I'm now ready to get back to work using BL8 for bioinformatics :-) 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 daniel.antony.pass at googlemail.com Wed Jul 9 05:54:09 2014 From: daniel.antony.pass at googlemail.com (Daniel Pass) Date: Wed, 9 Jul 2014 10:54:09 +0100 Subject: [Bio-linux-dev] Biolinux live tour? Message-ID: I just saw that Ubuntu does a HTML5 'live tour' of their latest distro which is smooth as hell: http://www.ubuntu.com/tour/en/ You can click around, search the dash lens, even use firefox! The whole thing is on launchpad: https://launchpad.net/ubuntu-online-tour. If you click on anything real, like the music player it pops up saying "this is just a demo, download the real thing here:" I don't know if it's straightforward to throw the BioLinux dash and style on it, but thought if it is, it could be a cool advertising tool. Make people less scared of booting up scary linux. -- Daniel Pass Tel: (029208)76680 Mob: 07735658687 http://www.kille-morgan.org.uk Room 2.44, School of Biosciences, Biological Sciences Building, Museum Avenue, Cardiff, CF10 3AT -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at abdn.ac.uk Tue Jul 15 07:32:46 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Tue, 15 Jul 2014 12:32:46 +0100 Subject: [Bio-linux-dev] upgrade8 idempotence Message-ID: <53C5115E.30104@abdn.ac.uk> Hi, Tim. Things are looking good now, and the Biostrings problem has gone away. One remaining problem is that your script seems to install and remove "python-software-properties" - Is that what you intended to happen? Bye, Tony. > The following NEW packages will be installed > python-software-properties > 0 to upgrade, 1 to newly install, 0 to remove and 0 not to upgrade. > Need to get 0 B/19.6 kB of archives. > After this operation, 137 kB of additional disk space will be used. > Selecting previously unselected package python-software-properties. > (Reading database ... 369450 files and directories currently installed.) > Preparing to unpack .../python-software-properties_0.92.37.1_all.deb ... > Unpacking python-software-properties (0.92.37.1) ... > Setting up python-software-properties (0.92.37.1) ... > Reading package lists... Done > Building dependency tree > Reading state information... Done > Calculating upgrade... Done > 0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade. > > Verifying that everything installed... > All good! > Scrubbing Java6 packages now we have 7 as default > Reading package lists... Done > Building dependency tree > Reading state information... Done > Package 'openjdk-6-jre' is not installed, so not removed > Package 'openjdk-6-jre-headless' is not installed, so not removed > Package 'openjdk-6-jre-lib' is not installed, so not removed > 0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade. > Scrubbing HAL as it is obsolete and triggers ugly errors > Reading package lists... Done > Building dependency tree > Reading state information... Done > Package 'hal' is not installed, so not removed > 0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade. > Reading package lists... Done > Building dependency tree > Reading state information... Done > The following packages will be REMOVED > python-software-properties* -- 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 Tue Jul 15 07:53:39 2014 From: tbooth at ceh.ac.uk (Booth, Timothy G.) Date: Tue, 15 Jul 2014 12:53:39 +0100 Subject: [Bio-linux-dev] upgrade8 idempotence In-Reply-To: <53C5115E.30104@abdn.ac.uk> References: <53C5115E.30104@abdn.ac.uk> Message-ID: <8C33D34D431A974EAEA913101DDA194407315C3FAE@nerckwmbc.ad.nerc.ac.uk> Hi Tony, Ah yes, software-properties-common replaces this package for our purposes, but I neglected to change this in bl_master_package_list.txt so it gets re-installed. I'll push an updated version shortly. Still having some issues with the live USB - it seems to be hideously slow when a casper-rw partition is enabled. I'm looking to see if I can use f2fs and if this will improve matters. Cheers, TIM ________________________________________ From: Tony Travis [tony.travis at abdn.ac.uk] Sent: 15 July 2014 12:32 To: Bio-Linux technical discussion Subject: [Bio-linux-dev] upgrade8 idempotence Hi, Tim. Things are looking good now, and the Biostrings problem has gone away. One remaining problem is that your script seems to install and remove "python-software-properties" - Is that what you intended to happen? Bye, Tony. > The following NEW packages will be installed > python-software-properties > 0 to upgrade, 1 to newly install, 0 to remove and 0 not to upgrade. > Need to get 0 B/19.6 kB of archives. > After this operation, 137 kB of additional disk space will be used. > Selecting previously unselected package python-software-properties. > (Reading database ... 369450 files and directories currently installed.) > Preparing to unpack .../python-software-properties_0.92.37.1_all.deb ... > Unpacking python-software-properties (0.92.37.1) ... > Setting up python-software-properties (0.92.37.1) ... > Reading package lists... Done > Building dependency tree > Reading state information... Done > Calculating upgrade... Done > 0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade. > > Verifying that everything installed... > All good! > Scrubbing Java6 packages now we have 7 as default > Reading package lists... Done > Building dependency tree > Reading state information... Done > Package 'openjdk-6-jre' is not installed, so not removed > Package 'openjdk-6-jre-headless' is not installed, so not removed > Package 'openjdk-6-jre-lib' is not installed, so not removed > 0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade. > Scrubbing HAL as it is obsolete and triggers ugly errors > Reading package lists... Done > Building dependency tree > Reading state information... Done > Package 'hal' is not installed, so not removed > 0 to upgrade, 0 to newly install, 0 to remove and 0 not to upgrade. > Reading package lists... Done > Building dependency tree > Reading state information... Done > The following packages will be REMOVED > python-software-properties* -- 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 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 abdn.ac.uk Tue Jul 15 08:17:40 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Tue, 15 Jul 2014 13:17:40 +0100 Subject: [Bio-linux-dev] upgrade8 idempotence In-Reply-To: <8C33D34D431A974EAEA913101DDA194407315C3FAE@nerckwmbc.ad.nerc.ac.uk> References: <53C5115E.30104@abdn.ac.uk> <8C33D34D431A974EAEA913101DDA194407315C3FAE@nerckwmbc.ad.nerc.ac.uk> Message-ID: <53C51BE4.7030509@abdn.ac.uk> On 15/07/14 12:53, Booth, Timothy G. wrote: > Hi Tony, > > Ah yes, software-properties-common replaces this package for our > purposes, but I neglected to change this in > bl_master_package_list.txt so it gets re-installed. I'll push an > updated version shortly. Still having some issues with the live USB > - it seems to be hideously slow when a casper-rw partition is > enabled. I'm looking to see if I can use f2fs and if this will > improve matters. Hi, Tim. Is it anything to do with your mount options? Are you using "noatime"? 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 Tue Jul 15 08:56:43 2014 From: tbooth at ceh.ac.uk (Booth, Timothy G.) Date: Tue, 15 Jul 2014 13:56:43 +0100 Subject: [Bio-linux-dev] upgrade8 idempotence In-Reply-To: <53C51BE4.7030509@abdn.ac.uk> References: <53C5115E.30104@abdn.ac.uk> <8C33D34D431A974EAEA913101DDA194407315C3FAE@nerckwmbc.ad.nerc.ac.uk>, <53C51BE4.7030509@abdn.ac.uk> Message-ID: <8C33D34D431A974EAEA913101DDA194407315C3FB0@nerckwmbc.ad.nerc.ac.uk> Hi Tony, Casper does the mounting using its internal magic. I'm sure "noatime" was getting set before on BL7 but I'll check and hack as necessary. TIM ________________________________________ From: Tony Travis [tony.travis at abdn.ac.uk] Sent: 15 July 2014 13:17 To: bio-linux-dev at nebclists.nerc.ac.uk Subject: Re: [Bio-linux-dev] upgrade8 idempotence On 15/07/14 12:53, Booth, Timothy G. wrote: > Hi Tony, > > Ah yes, software-properties-common replaces this package for our > purposes, but I neglected to change this in > bl_master_package_list.txt so it gets re-installed. I'll push an > updated version shortly. Still having some issues with the live USB > - it seems to be hideously slow when a casper-rw partition is > enabled. I'm looking to see if I can use f2fs and if this will > improve matters. Hi, Tim. Is it anything to do with your mount options? Are you using "noatime"? 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 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 Fri Jul 25 12:26:50 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 25 Jul 2014 17:26:50 +0100 Subject: [Bio-linux-dev] Bio-Linux 8 ISO ready for Beta-testing In-Reply-To: <1403869758.6513.73.camel@balisaur> References: <1403869758.6513.73.camel@balisaur> Message-ID: <1406305610.14667.63.camel@balisaur> Dear Devs, I hit a few unexpected glitches making the new Bio-Linux 8 ISO, particularly due to the way the keyboard layouts are handled in the new Ubuntu (a total mess!) and to various other unexpected changes under the hood of the system. I also wanted to ensure I could release both .ISO and .OVA versions at the same time. The OVA is auto-built from the ISO using the fantastic Packer tool so from now on it should always be completely in sync. I've now put a beta version (8.0.1-beta) up on http://nebc.nerc.ac.uk/downloads/ Aside from a few cosmetic fixes, this is final and I expect to put up a final 8.0.2 early next week and to announce it to the world along with the new web content. In particular, if you were to install from this -beta image I can promise you will not have to re-install as all further fixes will be handled via package updates. The upgrade script described below has now been tested by several people and glitches fixed, so I'm considering it final and will announce it along with the ISO next week. Release errata for 8.0.1-beta: * The bioinformatics menu on the Dash still doesn't work, but once I fix it I'll put out a package update and it will start working. * Booting directly from USB with persistence enabled seems slow. I'm working to see if I can speed this up. Once booted it's usable. * There may still be some issues with keyboard setup. Once you have the system installed and you make an account you can set it up no problem. * The OVA needs more testing and may not work yet on VMWare or Parallels. * I've not credited the new background images properly. I'm rectifying this right now! Have a good weekend! TIM On Fri, 2014-06-27 at 12:49 +0100, Tim Booth wrote: > Dear Bio-Linux-Dev subscribers, > > It took longer than I planned, but I'm pleased to announce that the > Bio-Linux 8 upgrade script (aka update to Ubuntu Trusty 14.04) is now > available for testing. I have tried the script out on several machines > here including my own, and nothing has blown up (much). However, as > with any major upgrade you should be sure you have a reliable backup > before proceeding. And as with any beta test you should be prepared for > glitches, so don't run the upgrade 2 hours before you need your machine > for some critical analysis! Please discuss any problems on this list > and I will endeavour to respond helpfully as quickly as I can. > > Notes: > > * There is no ISO or OVA download yet, so you can't test > installing Bio-Linux 8 from scratch or running a "Live" boot. > This is coming! > * The bioinformatics menu in the Dash doesn't work, due to fundamental > changes to the way this actually works under the hood. You can still > search for tools but you can't just get a nice list of bioinf stuff > - I'm working on this. Switch to MATE desktop to get a working > bioinformatics menu (see below). > * You should be able to run the script on a vanilla Ubuntu 14.04 box to > Bio-Linux-ify it (minus a few things like default firewall > settings and sudo/ssh/postgresql config) > * All the bioinf packages have been updated for the new release, > but testing is still ongoing so there may be issues > * None of the docs and tutorials are updated yet, but things are > broadly unchanged so experienced user shouldn't be baffled. > * NX is nixed, and x2go is go for remote desktops! Please test > this and let me know what you think. The lightweight MATE > desktop is provided as it works well with x2go. > * You should see one of a selection of lovely new desktop > wallpapers. I will credit the submitters of those on the > website when the other release material goes up. > > To actually do the upgrade: > > sudo runurl http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh > > (or if the runurl command isn't found, just download the script and do > "sudo sh upgrade8.sh" ). > > Enjoy, and let me know how you get on. > > 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