From shou at ceh.ac.uk Mon Nov 24 14:44:08 2008 From: shou at ceh.ac.uk (Stewart Houten) Date: Mon, 24 Nov 2008 19:44:08 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement Message-ID: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> Dear all, We will be releasing Bio-Linux 5.0 on the 1st December and would like to invite members of this list to download and try a pre-release version in advance of this. A number of you have already contributed to the development process by testing earlier beta versions and have provided constructive feedback and suggestions so far, for which we are very grateful. If you would like to get BL5 now and have access to a DVD writer, then please download the iso image from below and try it out. The DVD image can be downloaded from: http://nebc.nox.ac.uk/cgi-bin/download_register/register.cgi?a=bio-linux5 We would welcome you to try it out running live or as a full installation, either as a single system or as dual-boot. Of course, we suggest that people make full backups of their current system before doing this. We will be publishing full installation instructions shortly but a detailed guide on creating backups can be found here: http://nebc.nox.ac.uk/envgen/software/archives/000501.html A draft userguide is available from: http://nebc.nox.ac.uk/envgen/software/archives/000589.html We are keen to hear about your first impressions on any aspect of the new system. For example, Do you like the new desktop? Does the system run well on your hardware? Can you find the tools you need? If you have the time to look at the userguide, is there information that you feel is missing? More information about Bio-Linux 5.0 is below, but please contact us if you have any questions or comments. Regards, The NEBC Team Bio-Linux 5.0 is based on Ubuntu 8.04 (LTS) and the Gnome desktop. While the Gnome desktop looks a little different to KDE, we hope that the usability and friendly design will be easy to appreciate and quick to adapt to. In contrast to earlier versions of Bio-Linux, the full Bio-Linux 5.0 system can be installed or run as a Live system from the DVD image. This removes the need for a fixed IP address, network installation and the previous constraints on hardware types. We envision the Live system will find frequent use in teaching courses, demonstrations, or just working when out of the lab. Of course, in Bio-Linux 5.0 we have retained the added value features of the previous versions. So you will find it comes with databases (PostgreSQL and MySQL), a preconfigured firewall, development tools, nightly software updates, disaster-recovery backup and the 60+ bioinformatics packages in our software repository. From jaa53 at cornell.edu Mon Nov 24 15:16:54 2008 From: jaa53 at cornell.edu (Jose Andres) Date: Mon, 24 Nov 2008 15:16:54 -0500 Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement In-Reply-To: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> References: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> Message-ID: Hey, I'll most likely install bioLinux 5 in a new machine. Could you please send me an updated version of the hardware requirements? Cheers, /Jose On Nov 24, 2008, at 14:44, Stewart Houten wrote: > Dear all, > > We will be releasing Bio-Linux 5.0 on the 1st December and would like > to invite members of this list to download and try a pre-release > version in advance of this. A number of you have already contributed > to the development process by testing earlier beta versions and have > provided constructive feedback and suggestions so far, for which we > are very grateful. > > If you would like to get BL5 now and have access to a DVD writer, then > please download the iso image from below and try it out. > > The DVD image can be downloaded from: > http://nebc.nox.ac.uk/cgi-bin/download_register/register.cgi?a=bio- > linux5 > > We would welcome you to try it out running live or as a full > installation, either as a single system or as dual-boot. Of course, > we suggest that people make full backups of their current system > before doing this. We will be publishing full installation > instructions shortly but a detailed guide on creating backups can be > found here: > http://nebc.nox.ac.uk/envgen/software/archives/000501.html > > A draft userguide is available from: > http://nebc.nox.ac.uk/envgen/software/archives/000589.html > > We are keen to hear about your first impressions on any aspect of the > new system. For example, Do you like the new desktop? Does the system > run well on your hardware? Can you find the tools you need? If you > have the time to look at the userguide, is there information that you > feel is missing? > > More information about Bio-Linux 5.0 is below, but please contact us > if you have any questions or comments. > > Regards, > The NEBC Team > > > Bio-Linux 5.0 is based on Ubuntu 8.04 (LTS) and the Gnome > desktop. While the Gnome desktop looks a little different to KDE, we > hope that the usability and friendly design will be easy to appreciate > and quick to adapt to. > > In contrast to earlier versions of Bio-Linux, the full Bio-Linux 5.0 > system can be installed or run as a Live system from the DVD image. > This removes the need for a fixed IP address, network installation and > the previous constraints on hardware types. We envision the Live > system will find frequent use in teaching courses, demonstrations, or > just working when out of the lab. > > Of course, in Bio-Linux 5.0 we have retained the added value features > of the previous versions. So you will find it comes with databases > (PostgreSQL and MySQL), a preconfigured firewall, development tools, > nightly software updates, disaster-recovery backup and the 60+ > bioinformatics packages in our software repository. > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > > -- > 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 shou at ceh.ac.uk Tue Nov 25 08:01:12 2008 From: shou at ceh.ac.uk (Stewart Houten) Date: Tue, 25 Nov 2008 13:01:12 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement In-Reply-To: References: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> Message-ID: <20081125130112.GA7449@ivpcp068.nerc-oxford.ac.uk> Hi Jose, We have been deliberately vague about suggesting hardware requirements as in principle you should have success installing Bio-Linux 5.0 on a wide range of x86 machines. The minimum hardware requirements for Hardy are published on the Ubuntu site here http://www.ubuntu.com/getubuntu/releasenotes/804 Regards, Stewart From vanallsburg at hope.edu Tue Nov 25 13:04:02 2008 From: vanallsburg at hope.edu (Paul Van Allsburg) Date: Tue, 25 Nov 2008 13:04:02 -0500 Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement In-Reply-To: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> References: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> Message-ID: <492C3E12.1060202@hope.edu> Stewart Houten wrote: > Dear all, > > We will be releasing Bio-Linux 5.0 on the 1st December and would like > to invite members of this list to download and try a pre-release > version in advance of this. A number of you have already contributed > to the development process by testing earlier beta versions and have > provided constructive feedback and suggestions so far, for which we > are very grateful. > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > > I Downloaded/installed in VMware Workstation 6.0.5 on Win XP host 2.8Ghz P4 3.5GB ram Biolinux virtual machine configured with 10gig disk & 1gig ram after login I received a crash report: Sorry, the package "gnome-menus 2.22.2-0ubuntu1" failed to install or upgrade I ran the Update Manager to install updates- 316 total (360.7 MB), which completed successfully. Looks great! Thanks, Paul -- Paul Van Allsburg Scientific Computing Specialist Natural Sciences Division, Hope College 35 E. 12th St. Holland, Michigan 49423 616-395-7292 vanallsburg at hope.edu http://www.hope.edu/academic/csm/ From shou at ceh.ac.uk Tue Nov 25 13:22:51 2008 From: shou at ceh.ac.uk (Stewart Houten) Date: Tue, 25 Nov 2008 18:22:51 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement In-Reply-To: <492C3E12.1060202@hope.edu> References: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> <492C3E12.1060202@hope.edu> Message-ID: <20081125182250.GA8909@ivpcp068.nerc-oxford.ac.uk> Hi Paul, On Nov 25, 2008, Paul Van Allsburg wrote: > > I Downloaded/installed in VMware Workstation 6.0.5 > on Win XP host 2.8Ghz P4 3.5GB ram > Biolinux virtual machine configured with 10gig disk & 1gig ram > > after login I received a crash report: > Sorry, the package "gnome-menus 2.22.2-0ubuntu1" failed to install or > upgrade Ah, thanks for pointing this out. I get the same error when the machine does not auto-detect the network properly but not otherwise. I've tracked the issue down and fixed it so I'll be putting an updated image up for download later today. Thank you for trying it out so quickly and for the feedback! Regards, Stewart From nhaigh at sheffield.ac.uk Tue Nov 25 22:10:55 2008 From: nhaigh at sheffield.ac.uk (Nathan S. Watson-Haigh) Date: Wed, 26 Nov 2008 13:10:55 +1000 Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement In-Reply-To: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> References: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> Message-ID: A comment about default user setup. Bio-Linux 5 automatically gives sudo rights to the initial user entered during installation....this may or may not be desired for several reasons. Could the installation be changed to setup a manager account automatically with sudo rights and then have the person doing the install, choose a password for the manager and then setup a normal user account (without sudo rights)? Just a thought. Nath -----Original Message----- From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Stewart Houten Sent: Tuesday, 25 November 2008 5:44 AM To: bio-linux at envgen.nerc-oxford.ac.uk Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement Dear all, We will be releasing Bio-Linux 5.0 on the 1st December and would like to invite members of this list to download and try a pre-release version in advance of this. A number of you have already contributed to the development process by testing earlier beta versions and have provided constructive feedback and suggestions so far, for which we are very grateful. If you would like to get BL5 now and have access to a DVD writer, then please download the iso image from below and try it out. The DVD image can be downloaded from: http://nebc.nox.ac.uk/cgi-bin/download_register/register.cgi?a=bio-linux5 We would welcome you to try it out running live or as a full installation, either as a single system or as dual-boot. Of course, we suggest that people make full backups of their current system before doing this. We will be publishing full installation instructions shortly but a detailed guide on creating backups can be found here: http://nebc.nox.ac.uk/envgen/software/archives/000501.html A draft userguide is available from: http://nebc.nox.ac.uk/envgen/software/archives/000589.html We are keen to hear about your first impressions on any aspect of the new system. For example, Do you like the new desktop? Does the system run well on your hardware? Can you find the tools you need? If you have the time to look at the userguide, is there information that you feel is missing? More information about Bio-Linux 5.0 is below, but please contact us if you have any questions or comments. Regards, The NEBC Team Bio-Linux 5.0 is based on Ubuntu 8.04 (LTS) and the Gnome desktop. While the Gnome desktop looks a little different to KDE, we hope that the usability and friendly design will be easy to appreciate and quick to adapt to. In contrast to earlier versions of Bio-Linux, the full Bio-Linux 5.0 system can be installed or run as a Live system from the DVD image. This removes the need for a fixed IP address, network installation and the previous constraints on hardware types. We envision the Live system will find frequent use in teaching courses, demonstrations, or just working when out of the lab. Of course, in Bio-Linux 5.0 we have retained the added value features of the previous versions. So you will find it comes with databases (PostgreSQL and MySQL), a preconfigured firewall, development tools, nightly software updates, disaster-recovery backup and the 60+ bioinformatics packages in our software repository. _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From shou at ceh.ac.uk Wed Nov 26 08:01:41 2008 From: shou at ceh.ac.uk (Stewart Houten) Date: Wed, 26 Nov 2008 13:01:41 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement In-Reply-To: References: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> Message-ID: <20081126130141.GA10587@ivpcp068.nerc-oxford.ac.uk> Hi Nathan, Good to hear from you. On Nov 26, 2008, Nathan S. Watson-Haigh wrote: > A comment about default user setup. > > Bio-Linux 5 automatically gives sudo rights to the initial user entered > during installation....this may or may not be desired for several reasons. > Could the installation be changed to setup a manager account automatically > with sudo rights and then have the person doing the install, choose a > password for the manager and then setup a normal user account (without sudo > rights)? This probably could be achieved but for several reasons we decided to fit our requirements to the default Ubuntu/ubiquity setup. Our decision was motivated by the fact that the person installing the computer is most likely the owner or dedicated administrator of the machine and after installing the first thing they will need to do is customise the machine, restore backups, add user accounts, setup printers, nfs etc. We thought the default Ubuntu approach served this need very well. Also modifying the installer code (ubiquity) to provide a dialog allowing you to set a manager password is not really an option as the code is not easy to fathom (it is something we considered for another reason) and it would likely be tricky to maintain during future updates to the image. There are other ways around this but we wanted to keep things simple where possible. Unfortunately when you installed you didn't have a copy of our Installation Guide in front of you and in this we have tried (in brief) to address the account setup process and make a suggestion that this admin account be set up with the name manager. If you would like to take a look at this it is now in a temporary location on the web here: http://nebc.nox.ac.uk/bio-linux5/Bio-Linux5_InstallationGuide.pdf Any comments on this document would also be welcome. Cheers, Stewart From j.hadfield at ed.ac.uk Wed Nov 26 08:29:15 2008 From: j.hadfield at ed.ac.uk (Jarrod Hadfield) Date: Wed, 26 Nov 2008 13:29:15 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement In-Reply-To: <20081126130141.GA10587@ivpcp068.nerc-oxford.ac.uk> References: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> <20081126130141.GA10587@ivpcp068.nerc-oxford.ac.uk> Message-ID: Hi Stewart, Could I be taken off the email list, please. Thanks, Jarrod On 26 Nov 2008, at 13:01, Stewart Houten wrote: > Hi Nathan, > > Good to hear from you. > > On Nov 26, 2008, Nathan S. Watson-Haigh > wrote: >> A comment about default user setup. >> >> Bio-Linux 5 automatically gives sudo rights to the initial user >> entered >> during installation....this may or may not be desired for several >> reasons. >> Could the installation be changed to setup a manager account >> automatically >> with sudo rights and then have the person doing the install, choose a >> password for the manager and then setup a normal user account >> (without sudo >> rights)? > > This probably could be achieved but for several reasons we decided to > fit our requirements to the default Ubuntu/ubiquity setup. Our > decision was motivated by the fact that the person installing the > computer is most likely the owner or dedicated administrator of the > machine and after installing the first thing they will need to do is > customise the machine, restore backups, add user accounts, setup > printers, nfs etc. We thought the default Ubuntu approach served this > need very well. > > Also modifying the installer code (ubiquity) to provide a dialog > allowing you to set a manager password is not really an option as the > code is not easy to fathom (it is something we considered for another > reason) and it would likely be tricky to maintain during future > updates to the image. There are other ways around this but we wanted > to keep things simple where possible. > > Unfortunately when you installed you didn't have a copy of our > Installation Guide in front of you and in this we have tried (in > brief) to address the account setup process and make a suggestion that > this admin account be set up with the name manager. If you would like > to take a look at this it is now in a temporary location on the web > here: > > http://nebc.nox.ac.uk/bio-linux5/Bio-Linux5_InstallationGuide.pdf > > Any comments on this document would also be welcome. > > Cheers, > Stewart > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From rwt017 at abdn.ac.uk Wed Nov 26 08:13:50 2008 From: rwt017 at abdn.ac.uk (Tony Travis) Date: Wed, 26 Nov 2008 13:13:50 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement In-Reply-To: <20081126130141.GA10587@ivpcp068.nerc-oxford.ac.uk> References: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> <20081126130141.GA10587@ivpcp068.nerc-oxford.ac.uk> Message-ID: <492D4B8E.8060202@abdn.ac.uk> Stewart Houten wrote: > [...] > Also modifying the installer code (ubiquity) to provide a dialog > allowing you to set a manager password is not really an option as the > code is not easy to fathom (it is something we considered for another > reason) and it would likely be tricky to maintain during future > updates to the image. There are other ways around this but we wanted > to keep things simple where possible. Hello, Stewart. I think there are two different issues to consider: One is the 'live' DVD user, the other is the 'primary' user: When I created 'biobuntu', I set the 'live' DVD user to "manager" using 'reconstructor' to remaster the Ubuntu 6.06.1 LTS 'live' CD. In NuGO we have a mandatory policy of making UID 1000 the local admin "manager", and UID "1001" remote admin "nugo". I think it is unwise to use the 'primary' user account by default, because it is a proxy for "root". I use the same policy on all our servers here, and my laptop! Not tried your latest beta yet, but I have downloaded it :-) Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt From shou at ceh.ac.uk Wed Nov 26 10:39:52 2008 From: shou at ceh.ac.uk (Stewart Houten) Date: Wed, 26 Nov 2008 15:39:52 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 pre-release announcement In-Reply-To: <492D4B8E.8060202@abdn.ac.uk> References: <20081124194408.GA4962@ivpcp068.nerc-oxford.ac.uk> <20081126130141.GA10587@ivpcp068.nerc-oxford.ac.uk> <492D4B8E.8060202@abdn.ac.uk> Message-ID: <20081126153952.GA12003@ivpcp068.nerc-oxford.ac.uk> Hi Tony, > I think there are two different issues to consider: One is the 'live' > DVD user, the other is the 'primary' user: When I created 'biobuntu', I > set the 'live' DVD user to "manager" using 'reconstructor' to remaster > the Ubuntu 6.06.1 LTS 'live' CD. > > In NuGO we have a mandatory policy of making UID 1000 the local admin > "manager", and UID "1001" remote admin "nugo". I think it is unwise to > use the 'primary' user account by default, because it is a proxy for > "root". I use the same policy on all our servers here, and my laptop! Our policy for Bio-Linux is essentially the same but with different names. As a general rule we actively encourage our admins to create separate and unprivileged accounts for all users of the system, and to only use the "manager" account for administration tasks. I have more to add but we should probably take it off the list so I'll write privately. > Not tried your latest beta yet, but I have downloaded it :-) Great. I'd love to hear your comments. Regards, Stewart