From a.travis at abdn.ac.uk Thu Sep 10 13:26:54 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Thu, 10 Sep 2009 18:26:54 +0100 Subject: [Bio-Linux] NuGO-Linux Message-ID: <4AA936DE.2000106@abdn.ac.uk> Hello, NBX/NEBC developers. I've remastered my NuGO-Linux DVD, using the Ubuntu 8.04.3 LTS desktop install CD instead of 8.04.1 LTS, which Bio-Linux 5.0 is based on. There are known problems with 'persistent' USB sessions running from 8.04.1 because of bugs in 'casper' in the Linux kernel used on this 'live' CD. I've also installed the 'official' Ubuntu "usb-creator", which creates 'persistent' USB sticks differently to the "bio-linux-usb-maker" script and avoids the problems of disk corruption that we encountered in Italy. The latest NuGO-Linux iso can be downloaded from: http://nbx1.nugo.org/biobuntu/nugo-linux-20090910.iso Burn the iso to a DVD, and boot it, then use: System/Administration/Create a USB startup disk This version does not have my customised NuGO "umenu.exe" or "wubi.exe" on the iso. I'll add these after testing 'persistent' Linux sessions. Please try this out if you have time, and let me know how you get on. Thanks, 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 lucventurini at gmail.com Thu Sep 10 15:48:44 2009 From: lucventurini at gmail.com (Luca Venturini) Date: Thu, 10 Sep 2009 21:48:44 +0200 Subject: [Bio-Linux] AMD64 packages Message-ID: <1252612124.7144.10.camel@R2D2> Dear BioLinux developers, I would like to ask to you if perchance there is any plan to provide a 64bit repository and/or cd image of BioLinux - it would be great to use this software taking advantage of the 64 bit technology. I would also like to thank you all for the marvelous job you are doing - your repository has made my life easier in installing and discovering new software for my reasearch projects. Thank you for your kind attention. Distint regards Luca Venturini -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.travis at abdn.ac.uk Fri Sep 11 05:48:29 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Fri, 11 Sep 2009 10:48:29 +0100 Subject: [Bio-Linux] AMD64 packages In-Reply-To: <1252612124.7144.10.camel@R2D2> References: <1252612124.7144.10.camel@R2D2> Message-ID: <4AAA1CED.7090405@abdn.ac.uk> Luca Venturini wrote: > Dear BioLinux developers, > I would like to ask to you > if perchance there is any plan to provide a 64bit repository and/or cd > image of BioLinux - it would be great to use this software taking > advantage of the 64 bit technology. > I would also like to thank you all for the marvelous job you are doing - > your repository has made my life easier in installing and discovering > new software for my reasearch projects. > Thank you for your kind attention. Hello, Luca. I've discussed collaborating with NEBC on the 'Debianisation' of Bio-Linux. It will be quite a large effort to create the necessary 'deb-src' packages for Bio-Linux, but this would open up Bio-Linux onto other platforms including 64-bit. One possibility we've discussed is the creation of a 'community' version of Bio-Linux, which I proposed some time ago as my 'biobuntu' blueprint: https://blueprints.launchpad.net/ubuntu/+spec/biobuntu My 'biobuntu' DVD is a port of Bio-Linux 4.0 to Ubuntu 6.06.LTS, using the 32-bit binary deb's from the NEBC repository. We are discussing the possibility of creating an Ubuntu PPA for 'biobuntu', which could form the basis of several custom Bio-Linux derivatives with a common generic 'biobuntu' core. My own interest in this is development of NuGO-Linux for our data sharing project: http://www.nugo.org/nbx I currently use 'biobuntu' on an openMosix Beowulf at RINH: http://bioinformatics.rri.sari.ac.uk 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 lucventurini at gmail.com Fri Sep 11 06:35:33 2009 From: lucventurini at gmail.com (Luca Venturini) Date: Fri, 11 Sep 2009 12:35:33 +0200 Subject: [Bio-Linux] AMD64 packages In-Reply-To: <4AAA1CED.7090405@abdn.ac.uk> References: <1252612124.7144.10.camel@R2D2> <4AAA1CED.7090405@abdn.ac.uk> Message-ID: <1252665333.11215.113.camel@R2D2> Dear Tony, thank you for your quick answer. I had already seen the biobuntu project page some time ago, but the blueprint there seemed to indicate that the project had stopped with the release of the Ubuntu-base BioLinux 5.0. Glad to read it is not so. In particular, the possibility of a Biobuntu PPA is quite interesting, especially for porting this software to 64 bit machines too. I look forward from hearing news about this possibility. For now, however, do you have perchance any advice in installing this software on a 64 bit system? In some months I will probably have to switch from 32 bit to 64 (I plan on a huge upgrade on RAM), so I was looking around for a smooth transition also in this area. Thank you for your kind attention. Bye, Luca Il giorno ven, 11/09/2009 alle 10.48 +0100, Tony Travis ha scritto: > Luca Venturini wrote: > > Dear BioLinux developers, > > I would like to ask to you > > if perchance there is any plan to provide a 64bit repository and/or cd > > image of BioLinux - it would be great to use this software taking > > advantage of the 64 bit technology. > > I would also like to thank you all for the marvelous job you are doing - > > your repository has made my life easier in installing and discovering > > new software for my reasearch projects. > > Thank you for your kind attention. > > Hello, Luca. > > I've discussed collaborating with NEBC on the 'Debianisation' of > Bio-Linux. It will be quite a large effort to create the necessary > 'deb-src' packages for Bio-Linux, but this would open up Bio-Linux onto > other platforms including 64-bit. One possibility we've discussed is the > creation of a 'community' version of Bio-Linux, which I proposed some > time ago as my 'biobuntu' blueprint: > > https://blueprints.launchpad.net/ubuntu/+spec/biobuntu > > My 'biobuntu' DVD is a port of Bio-Linux 4.0 to Ubuntu 6.06.LTS, using > the 32-bit binary deb's from the NEBC repository. We are discussing the > possibility of creating an Ubuntu PPA for 'biobuntu', which could form > the basis of several custom Bio-Linux derivatives with a common generic > 'biobuntu' core. My own interest in this is development of NuGO-Linux > for our data sharing project: > > http://www.nugo.org/nbx > > I currently use 'biobuntu' on an openMosix Beowulf at RINH: > > http://bioinformatics.rri.sari.ac.uk > > 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 > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: From obuckley at ceh.ac.uk Fri Sep 11 06:47:53 2009 From: obuckley at ceh.ac.uk (Oliver Buckley) Date: Fri, 11 Sep 2009 11:47:53 +0100 Subject: [Bio-Linux] Introduction.... Message-ID: <1252666073.6878.6.camel@IVPC228> Hello, My name is Oliver Buckley, I am new member of NEBC and I will be working on the Bio-Linux project. With regard to 64 bit packages, I just wanted to say we are aware of the need for them and will begin work on this imminently! Thanks Oliver From lucventurini at gmail.com Fri Sep 11 06:58:12 2009 From: lucventurini at gmail.com (Luca Venturini) Date: Fri, 11 Sep 2009 12:58:12 +0200 Subject: [Bio-Linux] Introduction.... In-Reply-To: <1252666073.6878.6.camel@IVPC228> References: <1252666073.6878.6.camel@IVPC228> Message-ID: <1252666692.11215.129.camel@R2D2> Dear Oliver, thank you for the splendid news. Regards, Luca Venturini Il giorno ven, 11/09/2009 alle 11.47 +0100, Oliver Buckley ha scritto: > Hello, > > My name is Oliver Buckley, I am new member of NEBC and I will be working > on the Bio-Linux project. > > With regard to 64 bit packages, I just wanted to say we are aware of the > need for them and will begin work on this imminently! > > Thanks > Oliver > > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.travis at abdn.ac.uk Fri Sep 11 07:37:54 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Fri, 11 Sep 2009 12:37:54 +0100 Subject: [Bio-Linux] AMD64 packages In-Reply-To: <1252665333.11215.113.camel@R2D2> References: <1252612124.7144.10.camel@R2D2> <4AAA1CED.7090405@abdn.ac.uk> <1252665333.11215.113.camel@R2D2> Message-ID: <4AAA3692.1020704@abdn.ac.uk> Luca Venturini wrote: > Dear Tony, > thank you for your quick answer. I had already seen > the biobuntu project page some time ago, but the blueprint there seemed > to indicate that the project had stopped with the release of the > Ubuntu-base BioLinux 5.0. Glad to read it is not so. In particular, the > possibility of a Biobuntu PPA is quite interesting, especially for > porting this software to 64 bit machines too. I look forward from > hearing news about this possibility. Hello, Luca. Development of 'biobuntu' did stop when Bio-Linux 5.0 was released, but I attended a meeting between NuGO (European Nutrigenomics Organisation), NTC (Dutch Toxicogenomics Consortium) and NEBC in Oxford last month to discuss collaboration on core features of a Linux-based bioinformatics workstation or server that we can customise for our respective users. One possibility that we discussed was opening up Bio-Linux 'core' development to the Ubuntu developer community, via the blueprints and PPA. My 'biobuntu' blueprint could be a starting point for this, but I also want to develop it for clustering instances via Kerrighed/XtreemOS. Please subscribe to my blueprint if you're interested. > For now, however, do you have perchance any advice in installing this > software on a 64 bit system? In some months I will probably have to > switch from 32 bit to 64 (I plan on a huge upgrade on RAM), so I was > looking around for a smooth transition also in this area. > Thank you for your kind attention. You could use a 32-bit chroot to run a Bio-Linux userland under a 64-bit kernel. I've thought of doing this myself, but I've not actually tried it yet. NuGO currently has 31 NBX Opteron servers, mostly running 32-bit 'biobuntu', but we are upgrading them to "NuGO-Linux" a Bio-Linux 5.0 derivative customised for NuGO. If you're intererested, you can download the latest 'alpha' version of "NuGO-Linux" from: http://nbx1.nugo.org/biobuntu I'm creating USB sticks from this, but we encountered problems using ext2 filesystems on out USB sticks created using bio-linux-usb-maker. If you burn the nugo-linux-20090910.iso to DVD and try to create a USB stick using the hardy backport of Ubuntu "usb-creator" that is installed on it, you need to make a symbolic link to the CD device e.g.: ln -s /dev/scd0 cdrom.iso This is because "usb-creator" doesn't detect the CD/DVD when running in a 'live' session: Something that bio-linux-usb-maker does do very well! 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 a.travis at abdn.ac.uk Fri Sep 11 07:44:43 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Fri, 11 Sep 2009 12:44:43 +0100 Subject: [Bio-Linux] Introduction.... In-Reply-To: <1252666073.6878.6.camel@IVPC228> References: <1252666073.6878.6.camel@IVPC228> Message-ID: <4AAA382B.8090100@abdn.ac.uk> Oliver Buckley wrote: > Hello, > > My name is Oliver Buckley, I am new member of NEBC and I will be working > on the Bio-Linux project. Hello, Oliver. Just a quick post to say hello, and congratulations on your appointment! > With regard to 64 bit packages, I just wanted to say we are aware of the > need for them and will begin work on this imminently! Does this mean that you will now restructure your NEBC repository to provide binary packages for different architectures, or will you just add source packages? One reason why I suggested using the PPA is to get automated builds. 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 lucventurini at gmail.com Fri Sep 11 08:22:56 2009 From: lucventurini at gmail.com (Luca Venturini) Date: Fri, 11 Sep 2009 14:22:56 +0200 Subject: [Bio-Linux] AMD64 packages In-Reply-To: <4AAA3692.1020704@abdn.ac.uk> References: <1252612124.7144.10.camel@R2D2> <4AAA1CED.7090405@abdn.ac.uk> <1252665333.11215.113.camel@R2D2> <4AAA3692.1020704@abdn.ac.uk> Message-ID: <1252671776.11215.132.camel@R2D2> Dear Tony, I have subscribed to the blueprint as you suggested. The link at nugo.org you provided, however, does not exist, at least according to my dns. Bye, Luca Il giorno ven, 11/09/2009 alle 12.37 +0100, Tony Travis ha scritto: > Luca Venturini wrote: > > Dear Tony, > > thank you for your quick answer. I had already seen > > the biobuntu project page some time ago, but the blueprint there seemed > > to indicate that the project had stopped with the release of the > > Ubuntu-base BioLinux 5.0. Glad to read it is not so. In particular, the > > possibility of a Biobuntu PPA is quite interesting, especially for > > porting this software to 64 bit machines too. I look forward from > > hearing news about this possibility. > > Hello, Luca. > > Development of 'biobuntu' did stop when Bio-Linux 5.0 was released, but > I attended a meeting between NuGO (European Nutrigenomics Organisation), > NTC (Dutch Toxicogenomics Consortium) and NEBC in Oxford last month to > discuss collaboration on core features of a Linux-based bioinformatics > workstation or server that we can customise for our respective users. > > One possibility that we discussed was opening up Bio-Linux 'core' > development to the Ubuntu developer community, via the blueprints and > PPA. My 'biobuntu' blueprint could be a starting point for this, but I > also want to develop it for clustering instances via Kerrighed/XtreemOS. > > Please subscribe to my blueprint if you're interested. > > > For now, however, do you have perchance any advice in installing this > > software on a 64 bit system? In some months I will probably have to > > switch from 32 bit to 64 (I plan on a huge upgrade on RAM), so I was > > looking around for a smooth transition also in this area. > > Thank you for your kind attention. > > You could use a 32-bit chroot to run a Bio-Linux userland under a 64-bit > kernel. I've thought of doing this myself, but I've not actually tried > it yet. NuGO currently has 31 NBX Opteron servers, mostly running 32-bit > 'biobuntu', but we are upgrading them to "NuGO-Linux" a Bio-Linux 5.0 > derivative customised for NuGO. If you're intererested, you can download > the latest 'alpha' version of "NuGO-Linux" from: > > http://nbx1.nugo.org/biobuntu > > I'm creating USB sticks from this, but we encountered problems using > ext2 filesystems on out USB sticks created using bio-linux-usb-maker. > > If you burn the nugo-linux-20090910.iso to DVD and try to create a USB > stick using the hardy backport of Ubuntu "usb-creator" that is installed > on it, you need to make a symbolic link to the CD device e.g.: > > ln -s /dev/scd0 cdrom.iso > > This is because "usb-creator" doesn't detect the CD/DVD when running in > a 'live' session: Something that bio-linux-usb-maker does do very well! > > 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 > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Fri Sep 11 09:25:18 2009 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 11 Sep 2009 14:25:18 +0100 Subject: [Bio-Linux] AMD64 packages In-Reply-To: <1252671776.11215.132.camel@R2D2> References: <1252612124.7144.10.camel@R2D2> <4AAA1CED.7090405@abdn.ac.uk> <1252665333.11215.113.camel@R2D2> <4AAA3692.1020704@abdn.ac.uk> <1252671776.11215.132.camel@R2D2> Message-ID: <1252675518.13568.311.camel@barsukas> Hi Luca and Tony, Could I ask that if you are interested in continuing this technical/developer discussion you should move to the developers mailing list: http://nebc.nox.ac.uk/mailman/listinfo/bio-linux-dev The main bio-linux list has a wide readership and is geared towards users who are probably not interested in Ubuntu blueprints or the repository structure. Cheers, TIM From a.travis at abdn.ac.uk Fri Sep 11 09:29:01 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Fri, 11 Sep 2009 14:29:01 +0100 Subject: [Bio-Linux] AMD64 packages In-Reply-To: <1252671776.11215.132.camel@R2D2> References: <1252612124.7144.10.camel@R2D2> <4AAA1CED.7090405@abdn.ac.uk> <1252665333.11215.113.camel@R2D2> <4AAA3692.1020704@abdn.ac.uk> <1252671776.11215.132.camel@R2D2> Message-ID: <4AAA509D.9000100@abdn.ac.uk> Luca Venturini wrote: > Dear Tony, > I have subscribed to the blueprint as you suggested. > The link at nugo.org you provided, however, does not exist, at least > according to my dns. Hello, Luca. The link is correct, but the NuGO web server is not allowing external access to the NBX page for some reason: I've asked the webmaster to investigate. Please try again later. 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 a.travis at abdn.ac.uk Fri Sep 11 09:48:06 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Fri, 11 Sep 2009 14:48:06 +0100 Subject: [Bio-Linux] AMD64 packages In-Reply-To: <1252675518.13568.311.camel@barsukas> References: <1252612124.7144.10.camel@R2D2> <4AAA1CED.7090405@abdn.ac.uk> <1252665333.11215.113.camel@R2D2> <4AAA3692.1020704@abdn.ac.uk> <1252671776.11215.132.camel@R2D2> <1252675518.13568.311.camel@barsukas> Message-ID: <4AAA5516.4010607@abdn.ac.uk> Tim Booth wrote: > Hi Luca and Tony, > > Could I ask that if you are interested in continuing this > technical/developer discussion you should move to the developers mailing > list: > > http://nebc.nox.ac.uk/mailman/listinfo/bio-linux-dev > > The main bio-linux list has a wide readership and is geared towards > users who are probably not interested in Ubuntu blueprints or the > repository structure. Hello, Tim. OK, I've cc'ed this to nbx-dev, just in case anyone there replies... 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 mclange at ucdavis.edu Fri Sep 11 10:53:55 2009 From: mclange at ucdavis.edu (Matthew Lange) Date: Fri, 11 Sep 2009 07:53:55 -0700 Subject: [Bio-Linux] Introduction.... In-Reply-To: <1252666073.6878.6.camel@IVPC228> References: <1252666073.6878.6.camel@IVPC228> Message-ID: <4AAA6483.9000805@ucdavis.edu> An HTML attachment was scrubbed... URL: