[Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)

[Cox, Michael J]

Thanks Tony, Thanks Tim

Internet restored.  Ran the update script and the package list script and will forward both to you Tim, the list of things not installed is quite long - includes galaxy, raxml and a number of r-cran packages.  

We can get around NX for the moment, I'll get people using putty or winSCP in the meantime, but it's really helpful for a number of the users that are used to desktop environments.  After sorting the network connection, NX now working, but it seems much slower than it was and various bits of the desktop are missing, sidebar the most noticeable.  

Users definitely have ssh permissions as per http://nebc.nerc.ac.uk/tools/bio-linux/accessing-bio-linux - interesting list of stuff after recent NX login in auth.log one of which seems to be related to a constant keychain message and the screen-saver lock, which doesn't clear with entering the user's password.  

No problem with citation Tim - very welcome!  Will contact with files off list.

Thanks again for your help

Mike






On 11 Oct 2012, at 11:05, Tony Travis <tony.travis at ed.ac.uk> wrote:

> On 11/10/12 09:29, Mike Cox wrote:
>> [...]
>> I don't have the BioLinux background, so I suspect that I still have a
>> partial install.  Is there a way to compare what should be installed and
>> what I actually have?
> 
> Hi, Mike.
> 
> I've got a simple script to compare what's installed on a system relative to the distribution manifest generated from an iso image or on two Debian/Ubuntu systems. I tried posting it to this list before, but it was blocked by the automatic moderation policy. Let me know if you want a copy and I'll email it to you directly.
> 
>> NX also not yet working (users attempting to access get a message saying
>> 'access disabled by host').  Attempted to follow Tony's suggestions
>> above - installed Fallback (which hadn't been installed), installed
>> ubuntu-desktop (or so  thought) and purged network-manager, breaking my
>> internet connection.
> 
> Was NX working before the upgrade?
> 
> Our NX is broken, because much of "ubuntu-desktop" consists of recommended packages that are not installed by default. In particular, there is no logout button on the Gnome fall-back desktop and only the system font is available and it renders very badly on the NX desktop. I'm working on these problems and will post an update about what I discover.
> 
>> This fool suggests the update isn't quite
>> fool-proof yet - I should be a professional caving canary ;)
>> Also I left my keys at home, which means my laptop is locked in a
>> drawer. I'm fairly sure you can't help with this, but a lend of a jemmy
>> would be useful. Today is fired.
> 
> Personally, I think creating a Bio-Linux 7 terminal server would be quite useful. We're not quite there yet, but Tim's efforts have brought us within reach of that goal and *any* contribution you can make about using Bio-Linux in this way would be very useful. Bio-Linux is as much about building a community as it is about creating a Linux distribution.
> 
>> Any reccommendations?  Everything is backed up in case a full install is
>> required - but we have a lot of users, so that would be a pain.
> 
> Check /var/log/auth.log to see what is happening when people try to connect via NX. Make sure nx and the users are permitted to login via SSH. Check the ~/.nx folder.
> 
> If you create a temporary account for me with sudo rights I'll login and check it out for you (please contact me at my company email if you want me to do this: tony.travis at minke-informatics.co.uk).
> 
> Bye,
> 
>  Tony.
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