From bradshej at gmail.com Fri Apr 15 21:44:49 2011 From: bradshej at gmail.com (John Bradsher) Date: Sat, 16 Apr 2011 01:44:49 +0000 Subject: [Bio-Linux] odd and confounding behavior with BioLinux distros 5 and 6 Message-ID: I have recently turned on to BioLinux 6, and I run it daily on one machine with an Intel Core i5 processor. I have been interested to install BL6 on an older Pentium 4 machine. First, understand that I've been successful installing Ubuntu Linux 10.10 on this older machine, so I'm fairly confident that the processor is able to do the trick. The trouble comes when I insert the disk for BL6, I repeatedly get the error "x86 is expected, but found only i686 processor. Find a kernel appropriate for your processor." OK, so I found alternative means to boot with BL6, only to be foiled again: the machine is old enough that I have no option to boot from a USB key, though options for onboard NIC and cardbus NIC are present (I don't understand what boot options these represent). So I can't use the USB boot option (or at least my understanding of this jargon is poor enough that I'd profit from a bit of explanation if booting from the USB key is possible somehow). So, I considered this conundrum a bit, and concluded that I'd prefer to put an archival copy of BioLinux 5 on the machine, then choose from the options from the GRUB menu. Here is where it gets really interesting. So I download and burn the DVD-ROM, then insert and attempt to boot. I went into the BIOS and specified the boot order (verified numerous times), only to realize that the machine now refuses to boot from the DVD-ROM!! I don't get it. It boots straight from the hard disk copy of ubuntu 10.10. I will add that during the time I've been looking at BL6, I have manually downloaded a few of the packages for BL6 from the nebc site. Among these are the welcome page with Craig Venter's Institute advertised proudly. For the booting process, I don't really know what's keeping the DVD-ROM from working properly. Could it be one or more of the packages that identify the boot process as a (BL6) updated version of what's in the boot (DVD-ROM) drive? If so, is there any way to remove the offending packages, and get the archived (BL5) version of the software on the GRUB menu? Thanks, John Bradsher -- John Bradsher -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.travis at abdn.ac.uk Sat Apr 16 13:20:17 2011 From: a.travis at abdn.ac.uk (Tony Travis) Date: Sat, 16 Apr 2011 18:20:17 +0100 Subject: [Bio-Linux] odd and confounding behavior with BioLinux distros 5 and 6 In-Reply-To: References: Message-ID: <4DA9CFD1.4070606@abdn.ac.uk> On 16/04/11 02:44, John Bradsher wrote: > I have recently turned on to BioLinux 6, and I run it daily on one > machine with an Intel Core i5 processor. I have been interested to > install BL6 on an older Pentium 4 machine. First, understand that I've > been successful installing Ubuntu Linux 10.10 on this older machine, so > I'm fairly confident that the processor is able to do the trick. The > trouble comes when I insert the disk for BL6, I repeatedly get the error > "x86 is expected, but found only i686 processor. Find a kernel > appropriate for your processor." >[...] Hi, John. The Core i5 is a 64-bit processor (x86_64) and is capable of running Bio-Linux 6, which is based on 64-bit Ubuntu 10.04, but the Pentium 4 is only a 32-bit processor (i686) and is not capable of running it. The previous version of Bio-Linux 5 was based on 32-bit Ubuntu 8.04 that would run on a Pentium 4. HTH, 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 From bradshej at gmail.com Sat Apr 16 17:57:20 2011 From: bradshej at gmail.com (John Bradsher) Date: Sat, 16 Apr 2011 17:57:20 -0400 Subject: [Bio-Linux] odd and confounding behavior with BioLinux distros 5 and 6 In-Reply-To: <4DA9CFD1.4070606@abdn.ac.uk> References: <4DA9CFD1.4070606@abdn.ac.uk> Message-ID: Hello Tony: Well, thanks for the confirmation on that. I had suspected this, even if some of the specs for the Pentium 4 suggest that it has the 64-bit architecture. However, the real problem comes from being unable to boot from the disk with the BL5 iso image. As I stated before, I can only imagine that this results from having the more recent ubuntu 10.10 kernel running on the Pentium 4 machine. Is there any reason this should happen? Is there any workaround for the problem? Thanks, John Bradsher On Sat, Apr 16, 2011 at 1:20 PM, Tony Travis wrote: > On 16/04/11 02:44, John Bradsher wrote: > >> I have recently turned on to BioLinux 6, and I run it daily on one >> machine with an Intel Core i5 processor. I have been interested to >> install BL6 on an older Pentium 4 machine. First, understand that I've >> been successful installing Ubuntu Linux 10.10 on this older machine, so >> I'm fairly confident that the processor is able to do the trick. The >> trouble comes when I insert the disk for BL6, I repeatedly get the error >> "x86 is expected, but found only i686 processor. Find a kernel >> appropriate for your processor." >> [...] >> > > Hi, John. > > The Core i5 is a 64-bit processor (x86_64) and is capable of running > Bio-Linux 6, which is based on 64-bit Ubuntu 10.04, but the Pentium 4 is > only a 32-bit processor (i686) and is not capable of running it. The > previous version of Bio-Linux 5 was based on 32-bit Ubuntu 8.04 that would > run on a Pentium 4. > > HTH, > > 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 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -- John Bradsher -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.travis at abdn.ac.uk Sat Apr 16 19:18:29 2011 From: a.travis at abdn.ac.uk (Tony Travis) Date: Sun, 17 Apr 2011 00:18:29 +0100 Subject: [Bio-Linux] odd and confounding behavior with BioLinux distros 5 and 6 In-Reply-To: References: <4DA9CFD1.4070606@abdn.ac.uk> Message-ID: <4DAA23C5.8090805@abdn.ac.uk> On 16/04/11 22:57, John Bradsher wrote: > Hello Tony: > Well, thanks for the confirmation on that. I had suspected this, even if > some of the specs for the Pentium 4 suggest that it has the 64-bit > architecture. Hi, John. Sorry, I should have said that *most* Pentium 4's are 32-bit, and I suspect that your's is a 32-bit one. Intel did ship versions of the Pentium 4 with 64-bit extensions and, the 'Core' chipsets are derived from Pentium processors anyway. You are quite right that some of the 'high-end' Pentium 4's were in fact 64-bit, but not the ones used in 'commodity' PC's. They were used in high-end workstations or servers. > However, the real problem comes from being unable to boot from the disk > with the BL5 iso image. As I stated before, I can only imagine that this > results from having the more recent ubuntu 10.10 kernel running on the > Pentium 4 machine. Is there any reason this should happen? Is there any > workaround for the problem? I'm a bit confused, because if you boot off the Bio-Linux 5 'live' DVD, you will be running a 32-bit Ubuntu 8.04 kernel even if you have a 10.10 kernel installed on your hard disk. The DVD does not read files off the hard disk. All it does is use the swap file if one is present. HTH, 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 From bradshej at gmail.com Sun Apr 17 16:29:21 2011 From: bradshej at gmail.com (John Bradsher) Date: Sun, 17 Apr 2011 20:29:21 +0000 Subject: [Bio-Linux] odd and confounding behavior with BioLinux distros 5 and 6 In-Reply-To: <4DAA23C5.8090805@abdn.ac.uk> References: <4DA9CFD1.4070606@abdn.ac.uk> <4DAA23C5.8090805@abdn.ac.uk> Message-ID: Hello Tony: Yes, the sequence and process as you see it in the last response is exactly what I'd expect should happen. But, alas, that doesn't happen, which is the source of my confusion. I've entered the BIOS several times and specified the boot order, but I always get the same thing: booting only to ubuntu 10.10, even with the bio-linux 5 iso in the boot drive. Any insights would be welcome. Thanks, John Bradsher On Sat, Apr 16, 2011 at 11:18 PM, Tony Travis wrote: > On 16/04/11 22:57, John Bradsher wrote: > >> Hello Tony: >> Well, thanks for the confirmation on that. I had suspected this, even if >> some of the specs for the Pentium 4 suggest that it has the 64-bit >> architecture. >> > > Hi, John. > > Sorry, I should have said that *most* Pentium 4's are 32-bit, and I suspect > that your's is a 32-bit one. Intel did ship versions of the Pentium 4 with > 64-bit extensions and, the 'Core' chipsets are derived from Pentium > processors anyway. You are quite right that some of the 'high-end' Pentium > 4's were in fact 64-bit, but not the ones used in 'commodity' PC's. They > were used in high-end workstations or servers. > > > However, the real problem comes from being unable to boot from the disk >> with the BL5 iso image. As I stated before, I can only imagine that this >> results from having the more recent ubuntu 10.10 kernel running on the >> Pentium 4 machine. Is there any reason this should happen? Is there any >> workaround for the problem? >> > > I'm a bit confused, because if you boot off the Bio-Linux 5 'live' DVD, you > will be running a 32-bit Ubuntu 8.04 kernel even if you have a 10.10 kernel > installed on your hard disk. The DVD does not read files off the hard disk. > All it does is use the swap file if one is present. > > > HTH, > > 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 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -- John Bradsher -------------- next part -------------- An HTML attachment was scrubbed... URL: From humberto at hpcf.upr.edu Sun Apr 17 17:11:15 2011 From: humberto at hpcf.upr.edu (Humberto Ortiz-Zuazaga) Date: Sun, 17 Apr 2011 17:11:15 -0400 Subject: [Bio-Linux] odd and confounding behavior with BioLinux distros 5 and 6 In-Reply-To: References: <4DA9CFD1.4070606@abdn.ac.uk> <4DAA23C5.8090805@abdn.ac.uk> Message-ID: <4DAB5773.30706@hpcf.upr.edu> Hi John. If you misburn the ISO it will fall back to the next available boot drive. Perhaps you can consult a local linux user group? :-) On 4/17/11 4:29 PM, John Bradsher wrote: > Hello Tony: > > Yes, the sequence and process as you see it in the last response is > exactly what I'd expect should happen. But, alas, that doesn't happen, > which is the source of my confusion. I've entered the BIOS several times > and specified the boot order, but I always get the same thing: booting > only to ubuntu 10.10, even with the bio-linux 5 iso in the boot drive. > Any insights would be welcome. > Thanks, > > John Bradsher > > On Sat, Apr 16, 2011 at 11:18 PM, Tony Travis > wrote: > > On 16/04/11 22:57, John Bradsher wrote: > > Hello Tony: > Well, thanks for the confirmation on that. I had suspected this, > even if > some of the specs for the Pentium 4 suggest that it has the 64-bit > architecture. > > > Hi, John. > > Sorry, I should have said that *most* Pentium 4's are 32-bit, and I > suspect that your's is a 32-bit one. Intel did ship versions of the > Pentium 4 with 64-bit extensions and, the 'Core' chipsets are > derived from Pentium processors anyway. You are quite right that > some of the 'high-end' Pentium 4's were in fact 64-bit, but not the > ones used in 'commodity' PC's. They were used in high-end > workstations or servers. > > > However, the real problem comes from being unable to boot from > the disk > with the BL5 iso image. As I stated before, I can only imagine > that this > results from having the more recent ubuntu 10.10 kernel running > on the > Pentium 4 machine. Is there any reason this should happen? Is > there any > workaround for the problem? > > > I'm a bit confused, because if you boot off the Bio-Linux 5 'live' > DVD, you will be running a 32-bit Ubuntu 8.04 kernel even if you > have a 10.10 kernel installed on your hard disk. The DVD does not > read files off the hard disk. All it does is use the swap file if > one is present. > > > HTH, > > 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 > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > > -- > John Bradsher > > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Humberto Ortiz Zuazaga Programmer-Archaeologist From a.travis at abdn.ac.uk Sun Apr 17 17:30:36 2011 From: a.travis at abdn.ac.uk (Tony Travis) Date: Sun, 17 Apr 2011 22:30:36 +0100 Subject: [Bio-Linux] odd and confounding behavior with BioLinux distros 5 and 6 In-Reply-To: References: <4DA9CFD1.4070606@abdn.ac.uk> <4DAA23C5.8090805@abdn.ac.uk> Message-ID: <4DAB5BFC.5050400@abdn.ac.uk> On 17/04/11 21:29, John Bradsher wrote: > Hello Tony: > > Yes, the sequence and process as you see it in the last response is > exactly what I'd expect should happen. But, alas, that doesn't happen, > which is the source of my confusion. I've entered the BIOS several times > and specified the boot order, but I always get the same thing: booting > only to ubuntu 10.10, even with the bio-linux 5 iso in the boot drive. > Any insights would be welcome. Hi, John. Check that you actually have a DVD reader on your 'old' P4 system! I've been caught out before now by assuming that a CD/DVD reader was fitted when, in fact, it was only a CD reader ;-) Check that other CD's will boot on your P4 system in case there's a problem with your CD/DVD reader. You could try the well-known UBCD: http://www.ultimatebootcd.com/ If that boots OK from a CD, try burning a copy to a DVD and see if that also boots. It should do if your P4 CD/DVD reader is working properly, but you might find some DVD-/+RW media incompatible with an old reader. As a last resort, you could try disconnecting the hard disk, just to see if the Bio-Linux 6 DVD will boot at all on your P4 system. If it does, then your BIOS settings could be wrong. HTH, 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 From farhat.habib at gmail.com Tue Apr 26 09:51:34 2011 From: farhat.habib at gmail.com (Farhat Habib) Date: Tue, 26 Apr 2011 19:21:34 +0530 Subject: [Bio-Linux] Taverna Message-ID: Hi, The current version of Taverna in Biolinux is 1.7 whereas the current Taverna version is 2.2. Is there any plan to upgrade Taverna in Biolinux to the latest version? Thanks, Farhat -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Tue Apr 26 10:04:02 2011 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 26 Apr 2011 15:04:02 +0100 Subject: [Bio-Linux] Taverna In-Reply-To: References: Message-ID: <1303826642.3295.123.camel@barsukas> Hi Farhat, It would be very good to have an updated Taverna package, but right now this is fairly low on the list of my priorities. Taverna 2.x is not structured the same way as Taverna 1.x so it's unfortunately not just a question of putting the new Taverna code into a package. If anyone else on the list is waiting on an updated Taverna let me know and I'll make it a higher priority, otherwise I'm not likely to get around to it until after our round of courses in June. Cheers, TIM On Tue, 2011-04-26 at 14:51 +0100, Farhat Habib wrote: > Hi, > > > The current version of Taverna in Biolinux is 1.7 whereas the current > Taverna version is 2.2. Is there any plan to upgrade Taverna in > Biolinux to the latest version? > > > Thanks, > Farhat -- 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 farhat.habib at gmail.com Tue Apr 26 10:09:12 2011 From: farhat.habib at gmail.com (Farhat Habib) Date: Tue, 26 Apr 2011 19:39:12 +0530 Subject: [Bio-Linux] Taverna In-Reply-To: <1303826642.3295.123.camel@barsukas> References: <1303826642.3295.123.camel@barsukas> Message-ID: Not a major issue. I will just install it externally then. Thanks for the quick response. -Farhat -- Farhat Habib, PhD Scientist-C, Center of Excellence in Epigenetics Indian Institute of Science Education & Research, Sai Trinity Building, Garware Circle, Sutarwadi, Pashan, Pune-411 021. http://www.iiserpune.ac.in/~farhat Twitter: @far_hat Office: +91 20 2590 8080 On Tue, Apr 26, 2011 at 7:34 PM, Tim Booth wrote: > Hi Farhat, > > It would be very good to have an updated Taverna package, but right now > this is fairly low on the list of my priorities. Taverna 2.x is not > structured the same way as Taverna 1.x so it's unfortunately not just a > question of putting the new Taverna code into a package. > > If anyone else on the list is waiting on an updated Taverna let me know > and I'll make it a higher priority, otherwise I'm not likely to get > around to it until after our round of courses in June. > > Cheers, > > TIM > > On Tue, 2011-04-26 at 14:51 +0100, Farhat Habib wrote: > > Hi, > > > > > > The current version of Taverna in Biolinux is 1.7 whereas the current > > Taverna version is 2.2. Is there any plan to upgrade Taverna in > > Biolinux to the latest version? > > > > > > Thanks, > > Farhat > > -- > 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 mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: