[Bio-Linux] Live Bio-Linux not persistent

Fri Jun 20 04:25:23 EDT 2014

Hi Tim,

thanks, it went really well.

There was quite a high attrition rate of sticks when we were booting up - the two most common problems were a file in /var/run no longer being writeable (or absent) and the stick not booting past the splash screen; the stick booting as command line only without xwindows (and me not remembering the command to start it). We lost about 6 to that, but with the extras we had plenty.  They had all worked though as I checked them - was wondering whether these errors are easily fixable in future, or whether it’s safest simply to reclone?

Managed to introduce Linux, do raw sequence processing with .sff files and QIIME, intro to R and process real datasets (NMDS and Adonis, heatmaps and some hypothesis testing) with Phyloseq in 3 hours.  Then a team of sports physios and psychologists put me back together.

Feedback really positive, particularly as they could take all the software, files and operating system away with them - think we’ve got some converts :)

Thanks agin for your help

Cheers

Mike

Mike Cox

Research Associate
Molecular Genetics & Genomics

Genomic Medicine
National Heart and Lung Institute
Guy Scadding Building
Royal Brompton Campus
London SW3 6LY

0207 594 7974

http://www1.imperial.ac.uk/medicine/people/michael.cox1/

* New NHLI short course "Principles of Genomic Medicine" *
http://www1.imperial.ac.uk/nhli/PGM

On 19 Jun 2014, at 12:00, bio-linux-request at nebclists.nerc.ac.uk<mailto:bio-linux-request at nebclists.nerc.ac.uk> wrote:

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Today's Topics:

  1. Re: Live Bio-Linux not persistent (Tim Booth)

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Message: 1
Date: Thu, 19 Jun 2014 11:10:29 +0100
From: Tim Booth <tbooth at ceh.ac.uk>
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Live Bio-Linux not persistent
Message-ID: <1403172629.5184.7.camel at balisaur>
Content-Type: text/plain; charset="UTF-8"

Hi Mike,

Congratulations on that bit of detective work.  I'd not bothered
checking the Grub configuration as it didn't make any difference on our
test machines, or any teaching machines I've used before, but I guess
your machines boot via EFI and therefore do use Grub.

Yes, persistent mode will slow the things down a bit.  Unfortunately
there's no avoiding this, and I think that your fix is quite correct.

As I recall you are teaching today, so I hope it goes well and if you
have any urgent issues please do give me a call.

Cheers,

TIM

On Thu, 2014-06-12 at 12:12 +0100, Cox, Michael J wrote:
Dear All,

I think I fixed this, when I checked /boot/grub/grub.cfg there was no
persistent flag. Adding this to the first menu entry line:

linux /casper/vmlinuz.efi file=/cdrom/preseed/ubuntu.seed boot=casper
persistent quite splash ?

now renders the sticks persistent.  In addition I can now see the data
and tutorials that Tim loaded for me in /home.

It does take a little longer to load and is slow initially, so I have
some concerns that I have done something less than ideal.  Comments
appreciated.

Thanks

Mike

On 12 Jun 2014, at 12:00, <bio-linux-request at nebclists.nerc.ac.uk>
<bio-linux-request at nebclists.nerc.ac.uk> wrote:

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Today's Topics:

 1. Live Bio-Linux not persistent (Cox, Michael J)

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Message: 1
Date: Thu, 12 Jun 2014 09:13:37 +0000
From: "Cox, Michael J" <michael.cox1 at imperial.ac.uk>
To: "bio-linux at nebclists.nerc.ac.uk"
<bio-linux at nebclists.nerc.ac.uk>
Subject: [Bio-Linux] Live Bio-Linux not persistent
Message-ID: <B6B32EFF-5AD6-436B-B760-975F4CCA4864 at imperial.ac.uk>
Content-Type: text/plain; charset="windows-1252"

Hi All,

we?re using live USBs for a course next week that Tim kindly cloned
after installing a couple of R packages and a test dataset.  He?s
now on his hols, so I thought I?d check to see whether the rest of
the list could help me with an issue that I?m having.

On boot, I couldn?t find the data that Tim added.  I?ve checked by
creating a file and the sticks aren?t persistent and files are
removed when the USB stick is.  I did find a reference that
suggested creating a new user and that user account would be
persistent, but no joy, new user and file removed on reboot.

The additional R packages that Tim added to the distribution (dev
version of PhyloSeq) are present and correct, so that at least has
stayed.

I have checked in:

/syslinux/txt.cfg

and this seems correct - the persistent flag is set on the Try
Bio-Linux 7 option:

default live
label live
menu label ^Try Bio-Linux 7 without installing
kernel /casper/vmlinuz.efi
append noprompt cdrom-detect/try-usb=true persistent
file=/cdrom/preseed/ubuntu.seed boot=casper initrd=/casper/initrd.lz
quiet splash  locale=en_GB.UTF-8 --
label live-install
menu label ^Install Bio-Linux 7
kernel /casper/vmlinuz.efi
append noprompt cdrom-detect/try-usb=true persistent
file=/cdrom/preseed/ubuntu.seed boot=casper only-ubiquity
initrd=/casper/initrd.lz quiet splash --
label check
menu label ^Check stick for defects
kernel /casper/vmlinuz.efi
append  boot=casper noprompt integrity-check
initrd=/casper/initrd.lz quiet splash --
label memtest
menu label Test ^memory
kernel /install/mt86plus
label hd
menu label ^Boot from first hard disk
localboot 0x80

This post
http://ubuntuforums.org/showthread.php?t=2124124&p=12551088#post12551088 suggests editing syslinux.cfg (rather than txt.cfg) to make a Ubuntu stick persistent, which I?ve tried, but it booted up exactly as before and again was stubbornly resistant to retaining files.

Can anyone suggest ways to get this working?  Given the fact the R
packages have remained, some aspect of this seems to be
functioning?  I could have the attendees download the data and
course material, but would much rather they left with a copy of
Bio-Linux and all their work and notes in one elegant package.

Thanks very much for your help

Mike

Mike Cox

Research Associate
Molecular Genetics & Genomics

Genomic Medicine
National Heart and Lung Institute
Guy Scadding Building
Royal Brompton Campus
London SW3 6LY

0207 594 7974

http://www1.imperial.ac.uk/medicine/people/michael.cox1/

* New NHLI short course "Principles of Genomic Medicine" *
http://www1.imperial.ac.uk/nhli/PGM

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--
Tim Booth <tbooth at ceh.ac.uk>
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

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