From m.l.ostrowski at warwick.ac.uk Thu Jan 11 11:05:03 2007 From: m.l.ostrowski at warwick.ac.uk (Martin Ostrowski) Date: Thu, 11 Jan 2007 16:05:03 +0000 Subject: [Bio-Linux] How to add more disk space to my Biolinux Message-ID: Hello, By any chance is there a guide to adding more disk space to my Biolinux box? Thanks for any advice, Martin From asmo at ceh.ac.uk Fri Jan 12 04:55:22 2007 From: asmo at ceh.ac.uk (Ashley Morley) Date: Fri, 12 Jan 2007 09:55:22 +0000 Subject: [Bio-Linux] How to add more disk space to my Biolinux Message-ID: Hi Martin, Your Dell Precision 670 machine supports up to 4 internal hardrives, and you are currently using two 80GB (7200rpm) SATA drives installed. If you want to increase capacity, then you can order up to two more internal hard drives from Dell (your current spec below) and install them (or maybe order larger drives if required). The Dell website for ordering these items is http://accessories.us.dell.com/sna/productlisting.aspx?c=uk&category_id=6210&cs=ukdhs1&l=en&~ck=anav DELL 80 GB (7200 RPM) SATA2 Hard Drive for Dell Precision /670 Minitower Systems Usually Ships: 5-7 Days Manufacturer Part: 400-11744 Dell Part: 400-11744 Price ?39.00 I would suggest you use Dell components so that Dell remains your one contact for warranty issues. Instructions for installing the drives should come with the item, but I am sure your IT department would be able to advise on that. You could also use an external hard drive. Perhaps another user has experience of using one? Hope this helps Ashley >>> m.l.ostrowski at warwick.ac.uk 16:05 11 January 2007January 2007 >>> Hello, By any chance is there a guide to adding more disk space to my Biolinux box? Thanks for any advice, Martin _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From tbooth at ceh.ac.uk Fri Jan 12 05:31:25 2007 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 12 Jan 2007 10:31:25 +0000 Subject: [Bio-Linux] How to add more disk space to my Biolinux In-Reply-To: References: Message-ID: <1168597886.15297.101.camel@ivpcp044.nerc-oxford.ac.uk> Hi Martin, As I recently bought an external USB2+FireWire drive for use with Linux, I'll add a quick reply. If you want to go for an external drive then all the ones you can get from Dabs/Amazon/PC World etc. etc. will work on Linux after being reformatted. All external drives are slow compared to internal SATA ones but FireWire is faster than USB2. As I only use my drive for large, rarely accessed files and backups I have no problem with the speed and am very happy with it. A couple of people have now asked about this, so it may well be time to add some info to the website. There is no one-size-fits-all answer but I'd say that in general you want to start by asking these questions: * How much extra space do you want? * How much money do you have? * Is this space for a particular project/person or do you just want to beef up the machine in general? * Does the storage need to be fast? * How are you going to manage backups? (Network backup? Removable media? Extend the Bio-Linux double-drive system?) * If thinking about an external drive, do you want to move this between machines? Do you want to share data with Mac/Windows? Cheers, TIM On Fri, 2007-01-12 at 09:55 +0000, Ashley Morley wrote: > Hi Martin, > > Your Dell Precision 670 machine supports up to 4 internal hardrives, > and you are currently using two 80GB (7200rpm) SATA drives installed. > > If you want to increase capacity, then you can order up to two more > internal hard drives from Dell (your current spec below) and install > them (or maybe order larger drives if required). The Dell website for > ordering these items is > > http://accessories.us.dell.com/sna/productlisting.aspx?c=uk&category_id=6210&cs=ukdhs1&l=en&~ck=anav > > DELL > 80 GB (7200 RPM) SATA2 Hard Drive for Dell Precision /670 Minitower Systems > Usually Ships: 5-7 Days > Manufacturer Part: 400-11744 > Dell Part: 400-11744 > Price ?39.00 > > I would suggest you use Dell components so that Dell remains your one contact for warranty issues. Instructions for installing the drives should come with the item, but I am sure your IT department would be able to advise on that. > > You could also use an external hard drive. Perhaps another user has experience of using one? > > Hope this helps > Ashley > > > > >>> m.l.ostrowski at warwick.ac.uk 16:05 11 January 2007January 2007 >>> > Hello, > > By any chance is there a guide to adding more disk space to my Biolinux box? > > Thanks for any advice, > > Martin > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NEBC at CEH Oxford From M.Ostrowski at warwick.ac.uk Fri Jan 12 07:29:18 2007 From: M.Ostrowski at warwick.ac.uk (Ostrowski, Martin) Date: Fri, 12 Jan 2007 12:29:18 -0000 Subject: [Bio-Linux] How to add more disk space to my Biolinux References: <1168597886.15297.101.camel@ivpcp044.nerc-oxford.ac.uk> Message-ID: Hi Tim and Ashley, I was thinking along the lines of beefing up the double drive system of the standard Biolinux in one of two ways: 1. installing another internal HD on a fast BUS and moving portions of /var/db to the new drive. We have a lot of disk space used for public and private sequence databases, some of which are accessed for BLAST. Since these databases are also held elsewhere they do not need to be backed up so this could free up a lot of space for users files and reduce the amount of regular work for the machine. 2. replacing the 2 x 80 GB HDs with 2 x 160, or 320 GB. I think that the first option would be the best because it is the cheapest and sounds simple. I was hoping for a good guide or some tips for formating disks for linux and transferring the partitions to reduce the risk of deleting everything. Cheers, Martin -----Original Message----- From: bio-linux-bounces at envgen.nerc-oxford.ac.uk on behalf of Tim Booth Sent: Fri 12/01/2007 10:31 To: Bio-Linux help and discussion Subject: Re: [Bio-Linux] How to add more disk space to my Biolinux Hi Martin, As I recently bought an external USB2+FireWire drive for use with Linux, I'll add a quick reply. If you want to go for an external drive then all the ones you can get from Dabs/Amazon/PC World etc. etc. will work on Linux after being reformatted. All external drives are slow compared to internal SATA ones but FireWire is faster than USB2. As I only use my drive for large, rarely accessed files and backups I have no problem with the speed and am very happy with it. A couple of people have now asked about this, so it may well be time to add some info to the website. There is no one-size-fits-all answer but I'd say that in general you want to start by asking these questions: * How much extra space do you want? * How much money do you have? * Is this space for a particular project/person or do you just want to beef up the machine in general? * Does the storage need to be fast? * How are you going to manage backups? (Network backup? Removable media? Extend the Bio-Linux double-drive system?) * If thinking about an external drive, do you want to move this between machines? Do you want to share data with Mac/Windows? Cheers, TIM On Fri, 2007-01-12 at 09:55 +0000, Ashley Morley wrote: > Hi Martin, > > Your Dell Precision 670 machine supports up to 4 internal hardrives, > and you are currently using two 80GB (7200rpm) SATA drives installed. > > If you want to increase capacity, then you can order up to two more > internal hard drives from Dell (your current spec below) and install > them (or maybe order larger drives if required). The Dell website for > ordering these items is > > http://accessories.us.dell.com/sna/productlisting.aspx?c=uk&category_id=6210&cs=ukdhs1&l=en&~ck=anav > > DELL > 80 GB (7200 RPM) SATA2 Hard Drive for Dell Precision /670 Minitower Systems > Usually Ships: 5-7 Days > Manufacturer Part: 400-11744 > Dell Part: 400-11744 > Price ?39.00 > > I would suggest you use Dell components so that Dell remains your one contact for warranty issues. Instructions for installing the drives should come with the item, but I am sure your IT department would be able to advise on that. > > You could also use an external hard drive. Perhaps another user has experience of using one? > > Hope this helps > Ashley > > > > >>> m.l.ostrowski at warwick.ac.uk 16:05 11 January 2007January 2007 >>> > Hello, > > By any chance is there a guide to adding more disk space to my Biolinux box? > > Thanks for any advice, > > Martin > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NEBC at CEH Oxford _______________________________________________ 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 Jan 12 08:56:29 2007 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 12 Jan 2007 13:56:29 +0000 Subject: [Bio-Linux] How to add more disk space to my Biolinux In-Reply-To: References: <1168597886.15297.101.camel@ivpcp044.nerc-oxford.ac.uk> Message-ID: <1168610189.15297.133.camel@ivpcp044.nerc-oxford.ac.uk> Hi Martin, On Fri, 2007-01-12 at 12:29 +0000, Ostrowski, Martin wrote: > Hi Tim and Ashley, > > I was thinking along the lines of beefing up the double drive system > of the standard Biolinux in one of two ways: > > 1. installing another internal HD on a fast BUS and moving portions > of /var/db to the new drive. We have a lot of disk space used for > public and private sequence databases, some of which are accessed for > BLAST. Since these databases are also held elsewhere they do not need > to be backed up so this could free up a lot of space for users files > and reduce the amount of regular work for the machine. > You mean /home/db, right? This is probably the more sensible approach given what you need the space for, and that backups are taken care of. > 2. replacing the 2 x 80 GB HDs with 2 x 160, or 320 GB. > > I think that the first option would be the best because it is the > cheapest and sounds simple. I was hoping for a good guide or some tips > for formating disks for linux and transferring the partitions to > reduce the risk of deleting everything. Well there is the relevant HOWTO: http://tldp.org/HOWTO/Hard-Disk-Upgrade/index.html But this is a little old and, while not actually wrong, it's not how I would do things - I'd use a Knoppix bootable CD to avoid the complexities of cloning a running system, GNU parted for the partitioning and Rsync to copy the files. Also that HOWTO talks about LILO but we use GRUB, so you'd need to get to grips with the GRUB installer to make your new disk actually boot. Moving the entire operating system to a new disk, whatever OS you use, is always a bit tricky! There is also the option of reinstalling from scratch on the new disks (the standard installation script will cause /home to expand into all the extra free disk space), then putting in the old drive and copying the user accounts and /home over. If you have a logbook of changes you made to the system configuration you can go through and make them again - it depends how much you customised. One advantage of this is that the latest Bio-Linux image will install Debian 4.0 "Etch". This is the newest release and will be officially announced by Debian in the next few weeks. It is possible to upgrade machines in-place, and Stewart will be sending out instructions for this, but if you are going to be changing the disks anyway and want the update then it may be easier to reinstall. All swings and roundabouts really - and probably a moot point as I suspect you will go for easy option 1! Cheers, TIM From gawi at ceh.ac.uk Mon Jan 15 12:13:44 2007 From: gawi at ceh.ac.uk (Gareth Wilson) Date: Mon, 15 Jan 2007 17:13:44 +0000 Subject: [Bio-Linux] FAO YAMAP users Message-ID: Hello, This is to let you know that a new version of YAMAP (v.1.0.1) is available. In order to update your current version, you will need to run the following commands in a terminal: apt-get update apt-get install bio-linux-yamap In order to perform the update, you will require 'sudo'. If you don't have 'sudo' rights, you may need to ask your sys-admin for assistance. When the new version is installed, it is important to remove your old yamap configuration files (stored in the .yamap directory in your home directory). New config files will automatically be copied across when you run the new version for the first time. Cheers, Gareth Wilson. DISCLAIMER: This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed. From shou at ceh.ac.uk Fri Jan 26 09:07:51 2007 From: shou at ceh.ac.uk (Stewart Houten) Date: Fri, 26 Jan 2007 14:07:51 +0000 Subject: [Bio-Linux] barf Message-ID: <20070126140751.GA10067@ivpcp068.nerc-oxford.ac.uk> From Michael.Cox at liverpool.ac.uk Fri Jan 26 10:49:16 2007 From: Michael.Cox at liverpool.ac.uk (Cox, Mike) Date: Fri, 26 Jan 2007 15:49:16 -0000 Subject: [Bio-Linux] barf References: <20070126140751.GA10067@ivpcp068.nerc-oxford.ac.uk> Message-ID: Hiya Stewart, Shall I give you a bucket? :) Mike Mike Cox -------------------------------- Postdoctoral Research Associate Division of Genomics and Molecular Microbiology School of Biological Sciences University of Liverpool Crown Street Liverpool L69 7ZB Office 0151 7954576 Lab 0151 7954580 -----Original Message----- From: bio-linux-bounces at envgen.nox.ac.uk on behalf of Stewart Houten Sent: Fri 1/26/2007 2:07 PM To: bio-linux at envgen.nerc-oxford.ac.uk Subject: [Bio-Linux] barf _______________________________________________ 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... 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