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<div>Hi Tim,</div>
<div><br>
</div>
<div>thanks, it went really well. </div>
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>Feedback really positive, particularly as they could take all the software, files and operating system away with them - think we’ve got some converts :)</div>
<div><br>
</div>
<div>Thanks agin for your help</div>
<div><br>
</div>
<div>Cheers</div>
<div><br>
</div>
<div>Mike</div>
<div><br>
</div>
<div><br>
</div>
<br>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
Mike Cox<br>
<br>
Research Associate<br>
Molecular Genetics & Genomics</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<br>
</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
Genomic Medicine<br>
National Heart and Lung Institute<br>
Guy Scadding Building<br>
Royal Brompton Campus<br>
London SW3 6LY<br>
<br>
0207 594 7974</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<br>
<a href="http://www1.imperial.ac.uk/medicine/people/michael.cox1/">http://www1.imperial.ac.uk/medicine/people/michael.cox1/</a></div>
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<br>
</div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
* New NHLI short course "Principles of Genomic Medicine" *<br>
<a href="http://www1.imperial.ac.uk/nhli/PGM">http://www1.imperial.ac.uk/nhli/PGM</a><br>
<br>
</div>
</span></div>
</div>
</div>
</div>
<br>
<div>
<div>On 19 Jun 2014, at 12:00, <a href="mailto:bio-linux-request@nebclists.nerc.ac.uk">
bio-linux-request@nebclists.nerc.ac.uk</a> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Send Bio-Linux mailing list submissions to<br>
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To subscribe or unsubscribe via the World Wide Web, visit<br>
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When replying, please edit your Subject line so it is more specific<br>
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Today's Topics:<br>
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1. Re: Live Bio-Linux not persistent (Tim Booth)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 19 Jun 2014 11:10:29 +0100<br>
From: Tim Booth <tbooth@ceh.ac.uk><br>
To: bio-linux@nebclists.nerc.ac.uk<br>
Subject: Re: [Bio-Linux] Live Bio-Linux not persistent<br>
Message-ID: <1403172629.5184.7.camel@balisaur><br>
Content-Type: text/plain; charset="UTF-8"<br>
<br>
Hi Mike,<br>
<br>
Congratulations on that bit of detective work. I'd not bothered<br>
checking the Grub configuration as it didn't make any difference on our<br>
test machines, or any teaching machines I've used before, but I guess<br>
your machines boot via EFI and therefore do use Grub.<br>
<br>
Yes, persistent mode will slow the things down a bit. Unfortunately<br>
there's no avoiding this, and I think that your fix is quite correct.<br>
<br>
As I recall you are teaching today, so I hope it goes well and if you<br>
have any urgent issues please do give me a call.<br>
<br>
Cheers,<br>
<br>
TIM<br>
<br>
On Thu, 2014-06-12 at 12:12 +0100, Cox, Michael J wrote:<br>
<blockquote type="cite">Dear All, <br>
<br>
<br>
I think I fixed this, when I checked /boot/grub/grub.cfg there was no<br>
persistent flag. Adding this to the first menu entry line:<br>
<br>
<br>
linux /casper/vmlinuz.efi file=/cdrom/preseed/ubuntu.seed boot=casper<br>
persistent quite splash ?<br>
<br>
<br>
now renders the sticks persistent. In addition I can now see the data<br>
and tutorials that Tim loaded for me in /home. <br>
<br>
<br>
It does take a little longer to load and is slow initially, so I have<br>
some concerns that I have done something less than ideal. Comments<br>
appreciated.<br>
<br>
<br>
Thanks<br>
<br>
<br>
Mike<br>
<br>
<br>
<br>
On 12 Jun 2014, at 12:00, <bio-linux-request@nebclists.nerc.ac.uk><br>
<bio-linux-request@nebclists.nerc.ac.uk> wrote:<br>
<br>
<blockquote type="cite">Send Bio-Linux mailing list submissions to<br>
bio-linux@nebclists.nerc.ac.uk<br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux<br>
or, via email, send a message with subject or body 'help' to<br>
bio-linux-request@nebclists.nerc.ac.uk<br>
<br>
You can reach the person managing the list at<br>
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When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Bio-Linux digest..."<br>
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<br>
Today's Topics:<br>
<br>
1. Live Bio-Linux not persistent (Cox, Michael J)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 12 Jun 2014 09:13:37 +0000<br>
From: "Cox, Michael J" <michael.cox1@imperial.ac.uk><br>
To: "bio-linux@nebclists.nerc.ac.uk"<br>
<bio-linux@nebclists.nerc.ac.uk><br>
Subject: [Bio-Linux] Live Bio-Linux not persistent<br>
Message-ID: <B6B32EFF-5AD6-436B-B760-975F4CCA4864@imperial.ac.uk><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Hi All,<br>
<br>
we?re using live USBs for a course next week that Tim kindly cloned<br>
after installing a couple of R packages and a test dataset. He?s<br>
now on his hols, so I thought I?d check to see whether the rest of<br>
the list could help me with an issue that I?m having.<br>
<br>
On boot, I couldn?t find the data that Tim added. I?ve checked by<br>
creating a file and the sticks aren?t persistent and files are<br>
removed when the USB stick is. I did find a reference that<br>
suggested creating a new user and that user account would be<br>
persistent, but no joy, new user and file removed on reboot.<br>
<br>
The additional R packages that Tim added to the distribution (dev<br>
version of PhyloSeq) are present and correct, so that at least has<br>
stayed.<br>
<br>
I have checked in:<br>
<br>
/syslinux/txt.cfg<br>
<br>
and this seems correct - the persistent flag is set on the Try<br>
Bio-Linux 7 option:<br>
<br>
default live<br>
label live<br>
menu label ^Try Bio-Linux 7 without installing<br>
kernel /casper/vmlinuz.efi<br>
append noprompt cdrom-detect/try-usb=true persistent<br>
file=/cdrom/preseed/ubuntu.seed boot=casper initrd=/casper/initrd.lz<br>
quiet splash locale=en_GB.UTF-8 --<br>
label live-install<br>
menu label ^Install Bio-Linux 7<br>
kernel /casper/vmlinuz.efi<br>
append noprompt cdrom-detect/try-usb=true persistent<br>
file=/cdrom/preseed/ubuntu.seed boot=casper only-ubiquity<br>
initrd=/casper/initrd.lz quiet splash --<br>
label check<br>
menu label ^Check stick for defects<br>
kernel /casper/vmlinuz.efi<br>
append boot=casper noprompt integrity-check<br>
initrd=/casper/initrd.lz quiet splash --<br>
label memtest<br>
menu label Test ^memory<br>
kernel /install/mt86plus<br>
label hd<br>
menu label ^Boot from first hard disk<br>
localboot 0x80<br>
<br>
This post<br>
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.<br>
<br>
Can anyone suggest ways to get this working? Given the fact the R<br>
packages have remained, some aspect of this seems to be<br>
functioning? I could have the attendees download the data and<br>
course material, but would much rather they left with a copy of<br>
Bio-Linux and all their work and notes in one elegant package.<br>
<br>
Thanks very much for your help<br>
<br>
Mike<br>
<br>
<br>
Mike Cox<br>
<br>
Research Associate<br>
Molecular Genetics & Genomics<br>
<br>
Genomic Medicine<br>
National Heart and Lung Institute<br>
Guy Scadding Building<br>
Royal Brompton Campus<br>
London SW3 6LY<br>
<br>
0207 594 7974<br>
<br>
http://www1.imperial.ac.uk/medicine/people/michael.cox1/<br>
<br>
* New NHLI short course "Principles of Genomic Medicine" *<br>
http://www1.imperial.ac.uk/nhli/PGM<br>
<br>
<br>
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<br>
-- <br>
Tim Booth <tbooth@ceh.ac.uk><br>
NERC Environmental Bioinformatics Centre <br>
<br>
Centre for Ecology and Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB <br>
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http://nebc.nerc.ac.uk<br>
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