From tbooth at ceh.ac.uk  Wed May  5 10:20:32 2010
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 05 May 2010 15:20:32 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
Message-ID: <1273069232.26016.428.camel@barsukas>

Dear Bio-Linux testers,

I'm pleased and relieved to send out the first Beta of Bio-Linux 6
(build 6.0.13).  I hope you enjoy it and look forward to the feedback
and discussion.  Please download the ISO from here:

http://nebc.nerc.ac.uk/downloads/bl_beta_release/

This can be burned to a DVD in the usual way (see
http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/dvdtrouble).  While
there will be some changes in the final release, this will not
necessitate re-installation so please do go ahead and install this
version if you can. 

Main changes from BL5 (to recap):

     1. Based on new Ubuntu "Lucid Lynx"
     2. 64-bit system
     3. General fixes and cleanups
     4. Many new packages, documentation and sample data added since the
        initial BL5 release
     5. FreeNX installed as standard
     6. More reliable operation in live mode (we hope)

Miscellaneous useful info:

        If you boot the DVD and immediately see a message that you have
        an "i686 processor" this means that your machine is not 64-bit
        capable.  Most modern machines are, but some (notably netbooks)
        are still 32-bit only.
        
        After installation, run 'apt-get update' and 'apt-get install
        ubuntu-restricted-extras' if you want to install a range of
        things like Flash player and Microsoft fonts.
        
        If you do not have DHCP, after entering your network options
        manually you need to click the little network icon and select
        "Auto eth0" to apply them.
        
        Java on the system is now OpenJDK.  This should work perfectly
        well, but Sun JDK is also available if you need it.

Known issues in Bio-Linux Beta 1 (build 6.0.13):

     1. No ARB or YAMAP packages included yet.  These will come soon.
     2. CRAN repository for Lucid not yet available, so the R packages
        are those supplied by Ubuntu, version 2.10.  For the final
        release R 2.11 will be included.
     3. This version is based off Ubuntu 10.04RC1, not the official
        Ubuntu 10.04 release.  This should not cause any problems.
     4. Making a bootable USB stick directly from the DVD is untested
        and probably broken.
     5. Ugly errors may appear on screen part way through booting.  This
        seems to be an issue with with the the Ubuntu RC1 so it should
        go away in the next beta release.  The errors can be ignored.
     6. The default backup system (that dumps backups to a second drive,
        if available) is untested at this point, though it should work
        as before.
     7. No Handlebar demo on live image.  Some text on the website
        advertises this as a feature but it isn't included yet.
     8. Various wish-list items still to implement - more on these in a
        later mail.
     9. Ubuntu branding appears on the login screen and installer.
    10. The installer progress bar goes up to well over 100% before
        completing.
    11. The Firestarter firewall needs to be configured manually by
        running Firestarter under the System->Administration menu.
    12. The DVD will *always* boot in English with a UK keyboard.  You
        can select something else during installation or set a new
        keboard in Gnome.
    13. The remote admin account (user nebc) can't administer the
        machine until you do "sudo usermod -g root nebc".

There are also release notes produced by Ubuntu, including a list of
known issues with the underlying system, here:

http://www.ubuntu.com/getubuntu/releasenotes/1004

Happy testing!

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+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 a.travis at abdn.ac.uk  Wed May  5 13:57:35 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Wed, 05 May 2010 18:57:35 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <1273069232.26016.428.camel@barsukas>
References: <1273069232.26016.428.camel@barsukas>
Message-ID: <4BE1B18F.6000909@abdn.ac.uk>

On 05/05/10 15:20, Tim Booth wrote:
> Dear Bio-Linux testers,
>
> I'm pleased and relieved to send out the first Beta of Bio-Linux 6
> (build 6.0.13).  I hope you enjoy it and look forward to the feedback
> and discussion.  Please download the ISO from here:
>
> http://nebc.nerc.ac.uk/downloads/bl_beta_release/
>
> This can be burned to a DVD in the usual way (see
> http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/dvdtrouble).  While
> there will be some changes in the final release, this will not
> necessitate re-installation so please do go ahead and install this
> version if you can.

Hello, Tim.

I started upgrading "bobcat" to vanilla Ubuntu 10.04 LTS amd64 over the 
weekend, because I wasn't sure when you would release your first beta!

So, I've now downloaded Bio-Linux 6 (build 6.0.13) and installed it on:

   bobcat.rri.sari.ac.uk

[I've left your "nebc" back-door open if you wahnt to have a look]

First impressions are good - FreeNX works out of the box :-)

One minor issue is that the progress indicator goes > 100% when the 
installer is copying files onto the hard disk. Not important, but might 
confuse/alarm some users installing for the first time. It's probably 
just because your root filesystem is larger than the default Ubuntu.

> [...]
>       6. The default backup system (that dumps backups to a second drive,
>          if available) is untested at this point, though it should work
>          as before.

Hmm... you're not using my improved 'ETOH' backup script, and your 
"Setup Backup Disk" on the Desktop is only using and ext2 filesystem:

> - Found an empty disk on /dev/sdb...
> - Would you like to reformat disk /dev/sdb for backups? [y|n] y
> - This may take a few minutes...
> Warning: The resulting partition is not properly aligned for best performance.
>
> mke2fs 1.41.11 (14-Mar-2010)
> Filesystem label=
> OS type: Linux
> Block size=4096 (log=2)
> Fragment size=4096 (log=2)
> Stride=0 blocks, Stripe width=0 blocks
> 30531584 inodes, 122096389 blocks
> 6104819 blocks (5.00%) reserved for the super user
> First data block=0
> Maximum filesystem blocks=4294967296
> 3727 block groups
> 32768 blocks per group, 32768 fragments per group
> 8192 inodes per group
> Superblock backups stored on blocks:
> 	32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208,
> 	4096000, 7962624, 11239424, 20480000, 23887872, 71663616, 78675968,
> 	102400000

Otherwise, looks great + Thanks for releasing your Beta before we 
completed our Beowulf upgrade ;-)

I still have to work out how to share one instance of Bio-Linux with 
everything in /usr/local via NFS to a cluster of computers. Previously, 
I only installed Bio-Linux on "bobcat", and then shared /usr/local.

I'll let you know how we get on in a 'server' environment.

Bye,

   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/~ajt


From tbooth at ceh.ac.uk  Thu May  6 04:42:22 2010
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 06 May 2010 09:42:22 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <4BE1B18F.6000909@abdn.ac.uk>
References: <1273069232.26016.428.camel@barsukas> <4BE1B18F.6000909@abdn.ac.uk>
Message-ID: <1273135342.26016.452.camel@barsukas>

Hi Tony,

Thanks for testing this so quickly.

> [I've left your "nebc" back-door open if you wahnt to have a look]

This door is only half open (issue 13) but I'll not have a look unless
there is something particular you want to show me.

> First impressions are good - FreeNX works out of the box :-)

Excellent - I need to sort out the icons which don't seem to be
appearing in the menu, but I'm sure you've spotted the client is also
sitting under /usr/NX/bin/nxclient

> One minor issue is that the progress indicator goes > 100% when the 
> installer is copying files onto the hard disk. Not important, but might 
> confuse/alarm some users installing for the first time. It's probably 
> just because your root filesystem is larger than the default Ubuntu.

See known issue 10

> > [...]
> >       6. The default backup system (that dumps backups to a second drive,
> >          if available) is untested at this point, though it should work
> >          as before.
> 
> Hmm... you're not using my improved 'ETOH' backup script, and your 
> "Setup Backup Disk" on the Desktop is only using and ext2 filesystem:

See known issue 6.  The backup system does need reviewing.  I don't
think ext3 journalling is necessary or appropriate for a drive that only
holds dump files, though I may be mistaken.

> I still have to work out how to share one instance of Bio-Linux with 
> everything in /usr/local via NFS to a cluster of computers. Previously, 
> I only installed Bio-Linux on "bobcat", and then shared /usr/local.

I'd hoped to be further down the line towards using more standard
packages - ie. nothing put in /usr/local - by now but unfortunately this
has not worked out.  Hopefully you'll find a workaround.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+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 a.travis at abdn.ac.uk  Thu May  6 04:59:52 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 06 May 2010 09:59:52 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <1273069232.26016.428.camel@barsukas>
References: <1273069232.26016.428.camel@barsukas>
Message-ID: <4BE28508.5060402@abdn.ac.uk>

On 05/05/10 15:20, Tim Booth wrote:
> Dear Bio-Linux testers,
>
> I'm pleased and relieved to send out the first Beta of Bio-Linux 6
> (build 6.0.13).  I hope you enjoy it and look forward to the feedback
> and discussion.  Please download the ISO from here:
>
> http://nebc.nerc.ac.uk/downloads/bl_beta_release/
>[...]

Hello, Tim.

Although the NX client is installed, it's not on the menu and I think it 
would also be useful to install the NX session administrator tool.

I wonder why you populate /usr/local/bin with symbolic links into 
/usr/local/bioinf?

This makes it difficult to preserve 'local' installations, because it's 
complex to merge an old version of /usr/local/bin.

According to the FHS:

"The /usr/local hierarchy is for use by the system administrator when 
installing software locally. It needs to be safe from being overwritten 
when the system software is updated. It may be used for programs and 
data that are shareable amongst a group of hosts, but not found in /usr"

Why not just have /usr/local/bioinf/bin and put that on the PATH?

In our system, we do share /usr/local amongst a group of hosts. This 
makes it difficult to install bio-Linux on all the hosts. Previously, 
I've installed Bio-Linux on one host, and shared /usr/local from that 
one with other 'vanilla' installations of the same release of Ubuntu.

What I plan to do is create a "bio-linux-client" deb that will install 
all the necessary dependencies for making use of a shared /usr/local 
from a Bio-Linux 'server' instance with Bio-Linux 'clients'.

Re: security, I recommend that you install "fail2ban", and "rkhunter".

Bye,

   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/~ajt


From a.travis at abdn.ac.uk  Thu May  6 05:22:48 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 06 May 2010 10:22:48 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <1273135342.26016.452.camel@barsukas>
References: <1273069232.26016.428.camel@barsukas> <4BE1B18F.6000909@abdn.ac.uk>
	<1273135342.26016.452.camel@barsukas>
Message-ID: <4BE28A68.2020004@abdn.ac.uk>

On 06/05/10 09:42, Tim Booth wrote:
> [...]
>> Hmm... you're not using my improved 'ETOH' backup script, and your
>> "Setup Backup Disk" on the Desktop is only using and ext2 filesystem:
>
> See known issue 6.  The backup system does need reviewing.  I don't
> think ext3 journalling is necessary or appropriate for a drive that only
> holds dump files, though I may be mistaken.

If the system crashes during a dump, I believe it is just as important 
to be able to redo any pending disk transactions on a backup drive as it 
is on a working disk. Not only that, ext4 allows for a much faster 
'fsck' check. I've created two backup drives on our system as ext4:

   /backup1 # 500GB RAID1  OS
   /backup2 # 2.0TB RAID10 /export

I'm using two backup drives to minimise how long the databases are shut 
down for during dumps, and to decouple disk accesses. I'm dividing the 
available disk space 50:50 between active filesystems and ETOH backups.

>> I still have to work out how to share one instance of Bio-Linux with
>> everything in /usr/local via NFS to a cluster of computers. Previously,
>> I only installed Bio-Linux on "bobcat", and then shared /usr/local.
>
> I'd hoped to be further down the line towards using more standard
> packages - ie. nothing put in /usr/local - by now but unfortunately this
> has not worked out.  Hopefully you'll find a workaround.

I don't want to break compatibility with Bio-Linux, so I'll merge our 
old /usr/local with Bio-Linux 6 manually. I'm now looking forward to 
getting our system back in production with Bio-Linux 6, which I think 
this is a major milestone in the development of Bio-Linux.

Thanks for all your hard work at NEBC!

Bye,

   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/~ajt


From tbooth at ceh.ac.uk  Thu May  6 06:24:15 2010
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 06 May 2010 11:24:15 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <4BE28508.5060402@abdn.ac.uk>
References: <1273069232.26016.428.camel@barsukas> <4BE28508.5060402@abdn.ac.uk>
Message-ID: <1273141455.26016.484.camel@barsukas>

Hi Tony,

> Re: security, I recommend that you install "fail2ban", and "rkhunter".

I'm not touching fail2ban with a ten foot pole.  Mistyped your password?
Temporary DNS issue?  Banned forever!!  Some servers here at CEH had it
on and it was nothing but trouble - banning localhost was a favourite
trick.  I've yet to see it configured in a way that actually does what
it is supposed to do.

By default, newly created users cannot log in with ssh, so we hope that
anyone enabling ssh access on their account will set a decent password.
I do need to check that this restriction is also honoured by NX.

I'll take a look at rkhunter though I believe it is prone to false
alarms.  I'll definitely put chkrootkit back on - I think it was
standard on BL5.

> If the system crashes during a dump, I believe it is just as important
> to be able to redo any pending disk transactions on a backup drive as
> it is on a working disk. 

If the system crashes during a dump then the latest dump file is
truncated and useless in any case, and if you're writing other files to
that drive then you're not using it in the "normal" way, but I'll go
ahead and change it to ext4 as it makes no odds to me, and as you say it
will save time if fsck is run.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+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 a.travis at abdn.ac.uk  Thu May  6 06:32:54 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 06 May 2010 11:32:54 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <1273135342.26016.452.camel@barsukas>
References: <1273069232.26016.428.camel@barsukas> <4BE1B18F.6000909@abdn.ac.uk>
	<1273135342.26016.452.camel@barsukas>
Message-ID: <4BE29AD6.7020305@abdn.ac.uk>

Hello, Tim.

A minor point: there is no space after the command-line prompt:

   "manager at bobcat[manager]"

instead of:

   "manager at bobcat[manager] "

Bye,

   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/~ajt


From a.travis at abdn.ac.uk  Thu May  6 07:06:26 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 06 May 2010 12:06:26 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <1273141455.26016.484.camel@barsukas>
References: <1273069232.26016.428.camel@barsukas> <4BE28508.5060402@abdn.ac.uk>
	<1273141455.26016.484.camel@barsukas>
Message-ID: <4BE2A2B2.8050108@abdn.ac.uk>

On 06/05/10 11:24, Tim Booth wrote:
> Hi Tony,
>
>> Re: security, I recommend that you install "fail2ban", and "rkhunter".
>
> I'm not touching fail2ban with a ten foot pole.  Mistyped your password?
> Temporary DNS issue?  Banned forever!!  Some servers here at CEH had it
> on and it was nothing but trouble - banning localhost was a favourite
> trick.  I've yet to see it configured in a way that actually does what
> it is supposed to do.

Hello, Tim.

Well, it's very easy to configure 'fail2ban' to allow logins from 
localhost unconditionally, and systems are unbanned after 10mins by 
default. We've used it on the Beowulf and all our NBX's without any 
problem and it is a serious defence against 'brute-force' attacks. It's 
also recommended by DIT (Directorate of Information Technology) at the 
University of Aberdeen for any Internet-facing servers.

> By default, newly created users cannot log in with ssh, so we hope that
> anyone enabling ssh access on their account will set a decent password.
> I do need to check that this restriction is also honoured by NX.
>
> I'll take a look at rkhunter though I believe it is prone to false
> alarms.  I'll definitely put chkrootkit back on - I think it was
> standard on BL5.

I use both, and I think they are both useful.

>> If the system crashes during a dump, I believe it is just as important
>> to be able to redo any pending disk transactions on a backup drive as
>> it is on a working disk.
>
> If the system crashes during a dump then the latest dump file is
> truncated and useless in any case, and if you're writing other files to
> that drive then you're not using it in the "normal" way, but I'll go
> ahead and change it to ext4 as it makes no odds to me, and as you say it
> will save time if fsck is run.

Not true if it's a small, incremental: I think journalling is good!

More seriously, if you continue to use your existing dump script, and 
you have a problem during your weekly level 0 dump then you've lost 
everything except your last level 9. I can't live with that, which is 
why I modified your backup script to use an ETOH dump schedule.

My version does quarterly base-line level 0 dumps, and two separate TOH 
rotations of weekly and daily incremental dumps. It's based on the ETOH 
scheme from: Preston, W.C and Skelly, H. (2002), Backups and recovery, 
USENIX/SAGE, Berkeley. ISBN 1-931971-02-1. pp11-12.

   http://etoh.wopr.net/ex.abstract.html

Bye,

   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/~ajt
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: backup
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20100506/4412c6ee/attachment.ksh>

From tbooth at ceh.ac.uk  Thu May  6 11:59:23 2010
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 06 May 2010 16:59:23 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <4BE29AD6.7020305@abdn.ac.uk>
References: <1273069232.26016.428.camel@barsukas>
	<4BE1B18F.6000909@abdn.ac.uk>	<1273135342.26016.452.camel@barsukas>
	<4BE29AD6.7020305@abdn.ac.uk>
Message-ID: <1273161563.26016.521.camel@barsukas>

But what a waste of a precious column ;-)

Should be fixed by apt-get upgrade (bio-linux-zsh version 1-9).

Cheers,

TIM

On Thu, 2010-05-06 at 11:32 +0100, Tony Travis wrote:
> Hello, Tim.
> 
> A minor point: there is no space after the command-line prompt:
> 
>    "manager at bobcat[manager]"
> 
> instead of:
> 
>    "manager at bobcat[manager] "
> 
> Bye,
> 
>    Tony.
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+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 bioinformatics.lists at gmail.com  Fri May  7 13:13:17 2010
From: bioinformatics.lists at gmail.com (Dan Swan)
Date: Fri, 7 May 2010 18:13:17 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <1273141455.26016.484.camel@barsukas>
References: <1273069232.26016.428.camel@barsukas> <4BE28508.5060402@abdn.ac.uk>
	<1273141455.26016.484.camel@barsukas>
Message-ID: <r2md606310d1005071013qaa9ca192jab286409c726e1af@mail.gmail.com>

All,

> I'll take a look at rkhunter though I believe it is prone to false
> alarms. ?I'll definitely put chkrootkit back on - I think it was
> standard on BL5.

rkhunter is completely ignorant of OS updates, so will start to
trickle warning emails after any update to a binary on it's watchlist,
so you have to run it with --propupd when it starts to complain.

I've never managed to get chkrootkit to not report errors to me.
Even correctly configured to ignore certain . directories it still
sends me a warning email every day to check files, even though it
reports an entirely blank list. It's a known bug and has been present
in Ubuntu for *some time* and persists with Lucid.

regards,

Dan

-- 
Bioinformatics Support Unit  || http://bsu.ncl.ac.uk/
Institute for Cell and Molecular Biosciences,
Faculty of Medical Sciences, Framlington Place,
Newcastle University, Newcastle, NE2 4HH
Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A - Mon/Wed)
Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.25/G.26 - Thu/Fri)
Website: http://bsu.ncl.ac.uk/support
Twitter: http://twitter.com/nclbsu


From a.travis at abdn.ac.uk  Fri May  7 13:36:29 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Fri, 07 May 2010 18:36:29 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <1273161563.26016.521.camel@barsukas>
References: <1273069232.26016.428.camel@barsukas>	<4BE1B18F.6000909@abdn.ac.uk>	<1273135342.26016.452.camel@barsukas>	<4BE29AD6.7020305@abdn.ac.uk>
	<1273161563.26016.521.camel@barsukas>
Message-ID: <4BE44F9D.3080008@abdn.ac.uk>

On 06/05/10 16:59, Tim Booth wrote:
> But what a waste of a precious column ;-)
>
> Should be fixed by apt-get upgrade (bio-linux-zsh version 1-9).

Hello, Tim.

I think it is a mistake to give root a umask of 0077. This causes no end 
of problems, and I told you about that before when we changed it on our 
prototype Kerrighed Beowulf "kitcat": I suggest giving root a umask of 
0022 as is 'normal'. Fair enough if you want to give users a default 
umask of 22 to prevent accidental disclosure of data, but it *really* 
gets in the way for root, and you end up subverting the umask to give 
everyone access to something that root is installing/creating anyway.

I had problems installing the second instance of Bio-Linux 6 without 
existing partitions. This might be a bug in the Ubuntu 10.04 RC you 
remastered: Bio-Linux 6 installed fine when I created the partitions 
manually outside the installer using the Disk Utility. Unless I did 
that, the installer complained that no partitions or filesystems had 
been defined even when I DID define them using the installer.

Re: not sharing /usr/local, the work-around I came come up with is to 
put all our stuff in /opt/local, and share that between machines. I have 
done this before because it's a bit awkward when /usr is an automount 
point. I don't think deb's should put things in /usr/local, but I 
realise that is necessary to get Bio-Linux 6 released quickly.

The dual head nodes of our Beowulf are now running Bio-Linux 6 :-)

Bye,

   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/~ajt


From Simon.Wagstaff at liverpool.ac.uk  Fri May  7 15:03:45 2010
From: Simon.Wagstaff at liverpool.ac.uk (Wagstaff, Simon)
Date: Fri, 7 May 2010 20:03:45 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <1273069232.26016.428.camel@barsukas>
References: <1273069232.26016.428.camel@barsukas>
Message-ID: <DC62E1323AF0C24A99A7A3FE6019CD4D5D3C84F8C2@STAFFMBX1.livad.liv.ac.uk>

Hi Tim,
I also had problems installing BL-6 on disk without existing partitions but I was able to create partitions in the installer successfully.

Simon

-----Original Message-----
From: bio-linux-dev-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-dev-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
Sent: 05 May 2010 15:21
To: bio-linux-dev at nebclists.nerc.ac.uk
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release

Dear Bio-Linux testers,

I'm pleased and relieved to send out the first Beta of Bio-Linux 6
(build 6.0.13).  I hope you enjoy it and look forward to the feedback
and discussion.  Please download the ISO from here:

http://nebc.nerc.ac.uk/downloads/bl_beta_release/

This can be burned to a DVD in the usual way (see
http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/dvdtrouble).  While
there will be some changes in the final release, this will not
necessitate re-installation so please do go ahead and install this
version if you can. 

Main changes from BL5 (to recap):

     1. Based on new Ubuntu "Lucid Lynx"
     2. 64-bit system
     3. General fixes and cleanups
     4. Many new packages, documentation and sample data added since the
        initial BL5 release
     5. FreeNX installed as standard
     6. More reliable operation in live mode (we hope)

Miscellaneous useful info:

        If you boot the DVD and immediately see a message that you have
        an "i686 processor" this means that your machine is not 64-bit
        capable.  Most modern machines are, but some (notably netbooks)
        are still 32-bit only.
        
        After installation, run 'apt-get update' and 'apt-get install
        ubuntu-restricted-extras' if you want to install a range of
        things like Flash player and Microsoft fonts.
        
        If you do not have DHCP, after entering your network options
        manually you need to click the little network icon and select
        "Auto eth0" to apply them.
        
        Java on the system is now OpenJDK.  This should work perfectly
        well, but Sun JDK is also available if you need it.

Known issues in Bio-Linux Beta 1 (build 6.0.13):

     1. No ARB or YAMAP packages included yet.  These will come soon.
     2. CRAN repository for Lucid not yet available, so the R packages
        are those supplied by Ubuntu, version 2.10.  For the final
        release R 2.11 will be included.
     3. This version is based off Ubuntu 10.04RC1, not the official
        Ubuntu 10.04 release.  This should not cause any problems.
     4. Making a bootable USB stick directly from the DVD is untested
        and probably broken.
     5. Ugly errors may appear on screen part way through booting.  This
        seems to be an issue with with the the Ubuntu RC1 so it should
        go away in the next beta release.  The errors can be ignored.
     6. The default backup system (that dumps backups to a second drive,
        if available) is untested at this point, though it should work
        as before.
     7. No Handlebar demo on live image.  Some text on the website
        advertises this as a feature but it isn't included yet.
     8. Various wish-list items still to implement - more on these in a
        later mail.
     9. Ubuntu branding appears on the login screen and installer.
    10. The installer progress bar goes up to well over 100% before
        completing.
    11. The Firestarter firewall needs to be configured manually by
        running Firestarter under the System->Administration menu.
    12. The DVD will *always* boot in English with a UK keyboard.  You
        can select something else during installation or set a new
        keboard in Gnome.
    13. The remote admin account (user nebc) can't administer the
        machine until you do "sudo usermod -g root nebc".

There are also release notes produced by Ubuntu, including a list of
known issues with the underlying system, here:

http://www.ubuntu.com/getubuntu/releasenotes/1004

Happy testing!

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+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-dev mailing list
Bio-Linux-dev at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev


From a.travis at abdn.ac.uk  Fri May  7 15:49:31 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Fri, 07 May 2010 20:49:31 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <4BE44F9D.3080008@abdn.ac.uk>
References: <1273069232.26016.428.camel@barsukas>	<4BE1B18F.6000909@abdn.ac.uk>	<1273135342.26016.452.camel@barsukas>	<4BE29AD6.7020305@abdn.ac.uk>	<1273161563.26016.521.camel@barsukas>
	<4BE44F9D.3080008@abdn.ac.uk>
Message-ID: <4BE46ECB.7050505@abdn.ac.uk>

On 07/05/10 18:36, Tony Travis wrote:
> [...]
> 0022 as is 'normal'. Fair enough if you want to give users a default
> umask of 22 to prevent accidental disclosure of data, but it *really*
>[...]

Hello, Tim.

Oops! I meant:

Fair enough if you *don't* want to give users a default
umask of 22 to prevent accidental disclosure of data...

Bye,

   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/~ajt


From tbooth at ceh.ac.uk  Mon May 10 08:07:19 2010
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 10 May 2010 13:07:19 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <4BE44F9D.3080008@abdn.ac.uk>
References: <1273069232.26016.428.camel@barsukas>
	<4BE1B18F.6000909@abdn.ac.uk>	<1273135342.26016.452.camel@barsukas>
	<4BE29AD6.7020305@abdn.ac.uk>	<1273161563.26016.521.camel@barsukas>
	<4BE44F9D.3080008@abdn.ac.uk>
Message-ID: <1273493239.15465.40.camel@barsukas>

Hi Tony,

Right, I'm back on Bio-Linux development after a long weekend.

> I think it is a mistake to give root a umask of 0077. This causes no end 
> of problems,

Absolutely, and I thought I'd fixed this by adding "Defaults
umask_override" to the file /etc/sudoers.d/10_umask_override.  So if you
do:

% sudo bash
# umask

You should get the result "0022".  This also applies to gksu.  So could
you please confirm that this is the result on your machine and, if so,
where you are seeing the more restrictive umask being applied.

> 
> I had problems installing the second instance of Bio-Linux 6 without 
> existing partitions. This might be a bug in the Ubuntu 10.04 RC 

A quick Google search doesn't turn up any bug reports.  I'll ask Oliver
to see if he can reproduce this and see if 10.04 final fixes it,
otherwise I'll add something to the release notes.

> Re: not sharing /usr/local, the work-around I came come up with is to 
> put all our stuff in /opt/local, and share that between machines. I have 
> done this before because it's a bit awkward when /usr is an automount 
> point. I don't think deb's should put things in /usr/local, but I 
> realise that is necessary to get Bio-Linux 6 released quickly.

Yes, I agree totally.  We've nearly managed to expunge /home/db from
existence.  The next target is /usr/local/bioinf/config_files.  After
that, we can start chipping away at /usr/local and probably
move /usr/local/bioinf to /opt/bioinf.  It's not going to happen
quickly, though.

> The dual head nodes of our Beowulf are now running Bio-Linux 6 :-)

Nice one.  I hope your users like the new system.

Cheers,

TIM


-- 
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 tbooth at ceh.ac.uk  Mon May 10 09:21:31 2010
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 10 May 2010 14:21:31 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <DC62E1323AF0C24A99A7A3FE6019CD4D5D3C84F8C2@STAFFMBX1.livad.liv.ac.uk>
References: <1273069232.26016.428.camel@barsukas>
	<DC62E1323AF0C24A99A7A3FE6019CD4D5D3C84F8C2@STAFFMBX1.livad.liv.ac.uk>
Message-ID: <1273497691.15465.44.camel@barsukas>

Hi,

Oliver has tried installing onto an unpartitioned disk just now and had
no problems, so at the moment we can't reproduce this one.  If any other
testers see it please let me know exactly what happens.

Cheers,

TIM

On Fri, 2010-05-07 at 20:03 +0100, Wagstaff, Simon wrote:
> Hi Tim,
> I also had problems installing BL-6 on disk without existing partitions but I was able to create partitions in the installer successfully.



-- 
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 a.travis at abdn.ac.uk  Mon May 10 10:31:15 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Mon, 10 May 2010 15:31:15 +0100
Subject: [Bio-linux-dev] Bio-Linux 6 Beta 1 release
In-Reply-To: <1273493239.15465.40.camel@barsukas>
References: <1273069232.26016.428.camel@barsukas>	
	<4BE1B18F.6000909@abdn.ac.uk>	<1273135342.26016.452.camel@barsukas>	
	<4BE29AD6.7020305@abdn.ac.uk>	<1273161563.26016.521.camel@barsukas>	
	<4BE44F9D.3080008@abdn.ac.uk> <1273493239.15465.40.camel@barsukas>
Message-ID: <4BE818B3.5040509@abdn.ac.uk>

On 10/05/10 13:07, Tim Booth wrote:
> [...]
> % sudo bash
> # umask
>
> You should get the result "0022".  This also applies to gksu.  So could
> you please confirm that this is the result on your machine and, if so,
> where you are seeing the more restrictive umask being applied.

Hello, Tim.

I normally use "sudo -i", which simulates a root login:

 > manager at topcat[/manager] sudo bash 
  [ 3:17PM]
 > root at topcat:~# umask
 > 0022
 > root at topcat:~# exit
 > manager at topcat[/manager] sudo -i 
  [ 3:17PM]
 > root at topcat:~# umask
 > 0077

I've copied /etc/skel/.profile to /root/.profile and modified it to 
override the default umask and added /opt/local/[s]bin to the PATH:

root at topcat:~# diff -Naur /etc/skel/.profile /root/.profile
--- /etc/skel/.profile	2010-04-19 03:15:58.000000000 +0100
+++ /root/.profile	2010-05-10 15:20:51.086746274 +0100
@@ -6,7 +6,7 @@

  # the default umask is set in /etc/profile; for setting the umask
  # for ssh logins, install and configure the libpam-umask package.
-#umask 022
+umask 022

  # if running bash
  if [ -n "$BASH_VERSION" ]; then
@@ -20,3 +20,5 @@
  if [ -d "$HOME/bin" ] ; then
      PATH="$HOME/bin:$PATH"
  fi
+
+PATH=$PATH:/opt/local/sbin:/opt/local/bin

> [...]
>> The dual head nodes of our Beowulf are now running Bio-Linux 6 :-)
>
> Nice one.  I hope your users like the new system.

They can't get in yet - NIS and the automounter are not quite ready, but 
should be running by tomorrow.

Bye,

   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/~ajt


From tbooth at ceh.ac.uk  Mon May 10 11:48:37 2010
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 10 May 2010 16:48:37 +0100
Subject: [Bio-linux-dev] Path and umask for root on BL6
In-Reply-To: <4BE818B3.5040509@abdn.ac.uk>
References: <1273069232.26016.428.camel@barsukas>
	<4BE1B18F.6000909@abdn.ac.uk>	<1273135342.26016.452.camel@barsukas>
	<4BE29AD6.7020305@abdn.ac.uk>	<1273161563.26016.521.camel@barsukas>
	<4BE44F9D.3080008@abdn.ac.uk> <1273493239.15465.40.camel@barsukas>
	<4BE818B3.5040509@abdn.ac.uk>
Message-ID: <1273506517.15465.66.camel@barsukas>

OK, looking through the rebuilder script for BL, it is set up to
explicitly preserve /root/.profile which suggests that the file should
contain something important.  However, there is no /root/.profile either
in the BL6 image or in the old BL5 image, suggesting it got lost in the
wash some time ago.

I have added the the /root/.profile shown below to the next iteration of
the image.

note - It seems that Ubuntu by default puts /usr/sbin and /sbin into the
path for any admin user as well as for root.  I don't know where you
would put the setting if you happened to want this to happen in the same
way for /opt/local/sbin.

>>>contents of /root/.bashrc

#Because the default umask is 077, and this is rarely suitable for root,
#ensure it is set to the more normal 022
umask 022

# if running bash
if [ -n "$BASH_VERSION" ]; then
    # include .bashrc if it exists
    if [ -f "$HOME/.bashrc" ]; then
        . "$HOME/.bashrc"
    fi
fi

# set PATH so it includes user's private bin if it exists
if [ -d "$HOME/bin" ] ; then
    PATH="$HOME/bin:$PATH"
fi

<<<SNIP

On Mon, 2010-05-10 at 15:31 +0100, Tony Travis wrote:
> On 10/05/10 13:07, Tim Booth wrote:
> > [...]
> > % sudo bash
> > # umask
> >
> > You should get the result "0022".  This also applies to gksu.  So could
> > you please confirm that this is the result on your machine and, if so,
> > where you are seeing the more restrictive umask being applied.
> 
> Hello, Tim.
> 
> I normally use "sudo -i", which simulates a root login:
> 
>  > manager at topcat[/manager] sudo bash 
>   [ 3:17PM]
>  > root at topcat:~# umask
>  > 0022
>  > root at topcat:~# exit
>  > manager at topcat[/manager] sudo -i 
>   [ 3:17PM]
>  > root at topcat:~# umask
>  > 0077
> 
> I've copied /etc/skel/.profile to /root/.profile and modified it to 
> override the default umask and added /opt/local/[s]bin to the PATH:
> 
> root at topcat:~# diff -Naur /etc/skel/.profile /root/.profile
> --- /etc/skel/.profile	2010-04-19 03:15:58.000000000 +0100
> +++ /root/.profile	2010-05-10 15:20:51.086746274 +0100
> @@ -6,7 +6,7 @@
> 
>   # the default umask is set in /etc/profile; for setting the umask
>   # for ssh logins, install and configure the libpam-umask package.
> -#umask 022
> +umask 022
> 
>   # if running bash
>   if [ -n "$BASH_VERSION" ]; then
> @@ -20,3 +20,5 @@
>   if [ -d "$HOME/bin" ] ; then
>       PATH="$HOME/bin:$PATH"
>   fi
> +
> +PATH=$PATH:/opt/local/sbin:/opt/local/bin
> 
> > [...]
> >> The dual head nodes of our Beowulf are now running Bio-Linux 6 :-)
> >
> > Nice one.  I hope your users like the new system.
> 
> They can't get in yet - NIS and the automounter are not quite ready, but 
> should be running by tomorrow.
> 
> Bye,
> 
>    Tony.
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+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 a.travis at abdn.ac.uk  Sun May 16 11:36:29 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Sun, 16 May 2010 16:36:29 +0100
Subject: [Bio-linux-dev] bio-linux-backups
Message-ID: <4BF010FD.2020208@abdn.ac.uk>

Hello, Tim.

Your latest bio-linux-backups deb has clobbered by ETOH backup on our 
NBX's. My fault, I suppose, for using the same name for my backup :-(

Bye,

   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/~ajt


From tbooth at ceh.ac.uk  Mon May 17 04:32:34 2010
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 17 May 2010 09:32:34 +0100
Subject: [Bio-linux-dev] bio-linux-backups
In-Reply-To: <4BF010FD.2020208@abdn.ac.uk>
References: <4BF010FD.2020208@abdn.ac.uk>
Message-ID: <1274085154.15465.224.camel@barsukas>

Hi Tony,

Yes, I changed the setup script to run 'mkfs.ext4' instead of
'mkfs.ext3' as you suggested.  There's not much I can do about the
standard behaviour of Dpkg in overwriting packaged files, but for the
benefit of everyone on this list who may find it useful, here's how to
protect your custom files with dpkg-divert:

sudo dpkg-divert --divert /usr/bin/example.distrib --rename /usr/bin/example

Now the .distrib file will be overwritten by any package updates, and
you are free to put your own version into /usr/bin/example knowing that
it is safe from any clobbering.

Cheers,

TIM

On Sun, 2010-05-16 at 16:36 +0100, Tony Travis wrote:
> Hello, Tim.
> 
> Your latest bio-linux-backups deb has clobbered by ETOH backup on our 
> NBX's. My fault, I suppose, for using the same name for my backup :-(
> 
> Bye,
> 
>    Tony.
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+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 a.travis at abdn.ac.uk  Mon May 17 05:23:14 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Mon, 17 May 2010 10:23:14 +0100
Subject: [Bio-linux-dev] bio-linux-backups
In-Reply-To: <1274085154.15465.224.camel@barsukas>
References: <4BF010FD.2020208@abdn.ac.uk> <1274085154.15465.224.camel@barsukas>
Message-ID: <4BF10B02.3040700@abdn.ac.uk>

On 17/05/10 09:32, Tim Booth wrote:
> Hi Tony,
>
> Yes, I changed the setup script to run 'mkfs.ext4' instead of
> 'mkfs.ext3' as you suggested.  There's not much I can do about the
> standard behaviour of Dpkg in overwriting packaged files, but for the
> benefit of everyone on this list who may find it useful, here's how to
> protect your custom files with dpkg-divert:
>
> sudo dpkg-divert --divert /usr/bin/example.distrib --rename /usr/bin/example
>
> Now the .distrib file will be overwritten by any package updates, and
> you are free to put your own version into /usr/bin/example knowing that
> it is safe from any clobbering.

Hello, Tim.

Thanks for the tip - Didn't know about that, but a far simpler solution 
for me is simply to uninstall bio-linux-backups and anyone who follows 
your advice to use "backup2l" will have to do the same. I've restored my 
ETOH backup script on our NBX's. Your script does a level 0 dump on 
Sunday followed by a level 9 on Monday, which only provides two-days of 
redundancy to recover accidentally deleted or modified files. My simple 
'ETOH' extension to your backup script provides up to three months.

Bye,

   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/~ajt


From btiwari at ceh.ac.uk  Wed May 19 04:25:18 2010
From: btiwari at ceh.ac.uk (Tiwari, Bela)
Date: Wed, 19 May 2010 09:25:18 +0100
Subject: [Bio-linux-dev] New Beta 2 release of Bio-Linux 6 - ARB package is
	now available
Message-ID: <1DCCED50D0696A498958BA6B254456E20874F9312F@nerckwmb1.ad.nerc.ac.uk>

Dear testers,

A second Beta version of the Bio-Linux ISO is now available at the same
location as before:

http://nebc.nerc.ac.uk/downloads/bl_beta_release/

The version number is 6.0.17.  If you already installed the 6.0.13
version then there is no reason to get this release.  Most fixes will
become available through package updates, and when the final Bio-Linux 6
release is made next month I'll prepare a summary of things that
beta-testers should do to get any new features and tweaks that have been
added since Beta 1.

Changes between Beta 1 (6.0.13) and Beta 2 (6.0.17):

      * ARB package is now installed by default
      * Base system is Ubuntu 10.04 final (as opposed to RC)
      * Some new branding
      * Fixed umask for root (added umask 022 to /root/.bashrc)
      * The USB-maker script has been tested and should be able to clone
        a running live DVD or USB stick
      * APT is configured to run nightly updates for security patches
        and Bio-Linux packages
      * Various other fixes and small enhancements
      * All latest bioinformatics packages included

Known issues with this release:

Something is up with the graphics on the bootup and shutdown screens.
Sometimes you see an Ubuntu logo, sometimes a Bio-Linux logo, sometimes
a load of text.  This should not affect the operation of the system.

The link to the UserGuide still points at a file for the Bio-Linux 5.0 Userguide. You may also be requested for a password when you open the guide (you can cancel the message box and still see the document). This file will be updated for the final release.

No YAMAP package on this release.

Cheers,

TIM

--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre
at CEH Wallingford
+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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20100519/42224f76/attachment.html>

From a.travis at abdn.ac.uk  Wed May 19 10:22:41 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Wed, 19 May 2010 15:22:41 +0100
Subject: [Bio-linux-dev] bio-linux-backups
In-Reply-To: <1274085154.15465.224.camel@barsukas>
References: <4BF010FD.2020208@abdn.ac.uk> <1274085154.15465.224.camel@barsukas>
Message-ID: <4BF3F431.7050101@abdn.ac.uk>

On 17/05/10 09:32, Tim Booth wrote:
> Hi Tony,
>
> Yes, I changed the setup script to run 'mkfs.ext4' instead of
> 'mkfs.ext3' as you suggested.
>[...]

Hello, Tim.

Although /backups itself is now on an ext4 filesystem, your "backup" 
script" does not detect or dump Bio-Linux on ext4 filesystems ;-)

Attached is a patch to show the differences between your backup script 
and mine: I have a configuration file in /etc/default, and use ETOH.

Bye,

   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/~ajt
-------------- next part --------------
A non-text attachment was scrubbed...
Name: backup.diff
Type: text/x-patch
Size: 2439 bytes
Desc: not available
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20100519/16bc983e/attachment.bin>

From joachim.jacob at vib.be  Fri May 21 03:43:32 2010
From: joachim.jacob at vib.be (Joachim Jacob)
Date: Fri, 21 May 2010 09:43:32 +0200
Subject: [Bio-linux-dev] Bio-Linux-dev Digest, Vol 6, Issue 7
In-Reply-To: <mailman.1.1274353201.15352.bio-linux-dev@nebclists.nerc.ac.uk>
References: <mailman.1.1274353201.15352.bio-linux-dev@nebclists.nerc.ac.uk>
Message-ID: <4BF639A4.30403@vib.be>

Hello,

I have used *Biolinux 5* for a three day training session I organized at
VIB (www.bits.vib.be).
It helped us a lot - thanks. During the training we started with
installing Biolinux5 as a virtual machine (virtualbox).
Updates were not performed. This vm was used during the whole course.

One question though: although the emboss GUI was present, we had to
install emboss again to make it work.
$ sudo apt-get install emboss

The original installation was apparently not found.

Also: we required for perl two additional packages:
perl-class-inspector and
libfile-slurp-perl

Thanks and regards,
Joachim.


On 20/05/10 13:00, bio-linux-dev-request at nebclists.nerc.ac.uk wrote:
> Send Bio-Linux-dev mailing list submissions to
> 	bio-linux-dev at nebclists.nerc.ac.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> or, via email, send a message with subject or body 'help' to
> 	bio-linux-dev-request at nebclists.nerc.ac.uk
>
> You can reach the person managing the list at
> 	bio-linux-dev-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux-dev digest..."
>
>
> Today's Topics:
>
>    1. Re: bio-linux-backups (Tony Travis)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 19 May 2010 15:22:41 +0100
> From: Tony Travis <a.travis at abdn.ac.uk>
> Subject: Re: [Bio-linux-dev] bio-linux-backups
> To: bio-linux-dev at nebclists.nerc.ac.uk
> Message-ID: <4BF3F431.7050101 at abdn.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> On 17/05/10 09:32, Tim Booth wrote:
>   
>> Hi Tony,
>>
>> Yes, I changed the setup script to run 'mkfs.ext4' instead of
>> 'mkfs.ext3' as you suggested.
>> [...]
>>     
> Hello, Tim.
>
> Although /backups itself is now on an ext4 filesystem, your "backup" 
> script" does not detect or dump Bio-Linux on ext4 filesystems ;-)
>
> Attached is a patch to show the differences between your backup script 
> and mine: I have a configuration file in /etc/default, and use ETOH.
>
> Bye,
>
>    Tony.
>   

-- 

BITS logo    
*
Joachim Jacob, PhD. <http://be.linkedin.com/in/joachimjacob>*
Bioinformatics Trainer
BITS - www.bits.vib.be <http://www.bits.vib.be/>    
VIB - www.vib.be <http://www.vib.be/>

VIB headquarters, Rijvisschestraat 120, BE-9052 Gent, Belgium  (see map
<http://maps.google.be/maps/ms?ie=UTF8&hl=nl&msa=0&msid=110984434447938768012.00047d0caa7a96a740597&ll=51.017345,3.707585&spn=0.022003,0.043731&t=h&z=15>)
Tel.: +32 9 244 66 11     Fax.: +32 9 244 66 10


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20100521/cb05538b/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: logo-default.jpg
Type: image/jpeg
Size: 14628 bytes
Desc: not available
URL: <http://www.bioinformatics.org/pipermail/bio-linux-devel/attachments/20100521/cb05538b/attachment.jpg>

From tbooth at ceh.ac.uk  Mon May 24 12:22:01 2010
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 24 May 2010 17:22:01 +0100
Subject: [Bio-linux-dev] EMBOSS and Perl libraries
In-Reply-To: <4BF639A4.30403@vib.be>
References: <mailman.1.1274353201.15352.bio-linux-dev@nebclists.nerc.ac.uk>
	<4BF639A4.30403@vib.be>
Message-ID: <1274718121.23154.21.camel@barsukas>

Hi Joachim,

Thanks for the feedback.

I'm not sure why you would have had that problem with EMBOSS, but we've
substantially changed the way EMBOSS is packaged since BL5 so the
problem may well have simply gone away.  We can no longer provide the
EMBOSS KMenus (the GUI that used to appear when you selected a single
app from the Applications menu) so you'd now have to use JEmboss as the
GUI in any case.  I'll make sure this is tested on the live image.

The two Perl packages are very small so I've added them to the default
image for the final release at your suggestion.

Cheers,

TIM

On Fri, 2010-05-21 at 08:43 +0100, Joachim Jacob wrote:
> Hello,
> 
> I have used Biolinux 5 for a three day training session I organized at
> VIB (www.bits.vib.be).
> It helped us a lot - thanks. During the training we started with
> installing Biolinux5 as a virtual machine (virtualbox).
> Updates were not performed. This vm was used during the whole course.
> 
> One question though: although the emboss GUI was present, we had to
> install emboss again to make it work.
> $ sudo apt-get install emboss
> 
> The original installation was apparently not found.
> 
> Also: we required for perl two additional packages:
> perl-class-inspector and
> libfile-slurp-perl
> 
> Thanks and regards,
> Joachim.
> 
> 
> On 20/05/10 13:00, bio-linux-dev-request at nebclists.nerc.ac.uk wrote: 
> > Send Bio-Linux-dev mailing list submissions to
> > 	bio-linux-dev at nebclists.nerc.ac.uk
> > 
> > To subscribe or unsubscribe via the World Wide Web, visit
> > 	http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > or, via email, send a message with subject or body 'help' to
> > 	bio-linux-dev-request at nebclists.nerc.ac.uk
> > 
> > You can reach the person managing the list at
> > 	bio-linux-dev-owner at nebclists.nerc.ac.uk
> > 
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Bio-Linux-dev digest..."
> > 
> > 
> > Today's Topics:
> > 
> >    1. Re: bio-linux-backups (Tony Travis)
> > 
> > 
> > ----------------------------------------------------------------------
> > 
> > Message: 1
> > Date: Wed, 19 May 2010 15:22:41 +0100
> > From: Tony Travis <a.travis at abdn.ac.uk>
> > Subject: Re: [Bio-linux-dev] bio-linux-backups
> > To: bio-linux-dev at nebclists.nerc.ac.uk
> > Message-ID: <4BF3F431.7050101 at abdn.ac.uk>
> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> > 
> > On 17/05/10 09:32, Tim Booth wrote:
> >   
> > > Hi Tony,
> > > 
> > > Yes, I changed the setup script to run 'mkfs.ext4' instead of
> > > 'mkfs.ext3' as you suggested.
> > > [...]
> > >     
> > Hello, Tim.
> > 
> > Although /backups itself is now on an ext4 filesystem, your "backup" 
> > script" does not detect or dump Bio-Linux on ext4 filesystems ;-)
> > 
> > Attached is a patch to show the differences between your backup script 
> > and mine: I have a configuration file in /etc/default, and use ETOH.
> > 
> > Bye,
> > 
> >    Tony.
> >   
> 
> -- 
> 
> BITS logo     
> 
> Joachim Jacob, PhD.
> Bioinformatics Trainer
> BITS - www.bits.vib.be     
> VIB - www.vib.be
> VIB headquarters, Rijvisschestraat 120, BE-9052 Gent, Belgium  (see
> map)
> Tel.: +32 9 244 66 11     Fax.: +32 9 244 66 10 
> 
> 
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+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 tbooth at ceh.ac.uk  Mon May 24 12:35:55 2010
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 24 May 2010 17:35:55 +0100
Subject: [Bio-linux-dev] bio-linux-backups
In-Reply-To: <4BF3F431.7050101@abdn.ac.uk>
References: <4BF010FD.2020208@abdn.ac.uk>
	<1274085154.15465.224.camel@barsukas>  <4BF3F431.7050101@abdn.ac.uk>
Message-ID: <1274718955.23154.32.camel@barsukas>

Hi Tony,

Oops - thanks for spotting that.  I've made the small fix for now.

I'm keen to get your ETOH patch into the final 6.0 release, but before
putting it into the package I need to try and work out:

1) What is the maximum space that this backup scheme might need?

2) What happens if the space runs out?

3) What do I need to change in our instructions?
(http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/backing-up-and-restoring#auto)

I'll look into this later in the week.  Does anyone else on this list
have comments on backups?  Do you rely on the internal backup system or
use something else?

Cheers,

TIM

On Wed, 2010-05-19 at 15:22 +0100, Tony Travis wrote:
> On 17/05/10 09:32, Tim Booth wrote:
> > Hi Tony,
> >
> > Yes, I changed the setup script to run 'mkfs.ext4' instead of
> > 'mkfs.ext3' as you suggested.
> >[...]
> 
> Hello, Tim.
> 
> Although /backups itself is now on an ext4 filesystem, your "backup" 
> script" does not detect or dump Bio-Linux on ext4 filesystems ;-)
> 
> Attached is a patch to show the differences between your backup script 
> and mine: I have a configuration file in /etc/default, and use ETOH.
> 
> Bye,
> 
>    Tony.
-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 
at CEH Wallingford
+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 a.travis at abdn.ac.uk  Mon May 24 20:33:04 2010
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Tue, 25 May 2010 01:33:04 +0100
Subject: [Bio-linux-dev] bio-linux-backups
In-Reply-To: <1274718955.23154.32.camel@barsukas>
References: <4BF010FD.2020208@abdn.ac.uk>	
	<1274085154.15465.224.camel@barsukas> <4BF3F431.7050101@abdn.ac.uk>
	<1274718955.23154.32.camel@barsukas>
Message-ID: <4BFB1AC0.8030608@abdn.ac.uk>

On 24/05/10 17:35, Tim Booth wrote:
> Hi Tony,
>
> Oops - thanks for spotting that.  I've made the small fix for now.
>
> I'm keen to get your ETOH patch into the final 6.0 release, but before
> putting it into the package I need to try and work out:

Hello, Tim.

Good news :-)

> 1) What is the maximum space that this backup scheme might need?

It depends how much filesystem activity there is. The ETOH schedule is a 
baseline incremental dump relative to quarterly level 0 dumps. In my 
experience, with 'typical' usage and ~2x compression, a backup disk the 
same size as the active disk is adequate for three months of ETOH dumps.

> 2) What happens if the space runs out?

The dump fails, and /var/lib/dumpdates is not updated. The previous dump 
at the current level is overwritten by an incomplete failed dump. We 
could use an Amanda-style estimate to decide if there is enough space to 
do the dump, but I don't think that is really necessary. The ETOH scheme 
provides some redundancy because the dump levels overlap.

> 3) What do I need to change in our instructions?
> (http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/backing-up-and-restoring#auto)

You still restore the level 0 dump, but instead of just restoring the 
level 9 incremental after that, you need to restore several incremental 
dumps. You don't need to restore them all because they overlap. This is 
only necessary for a bare-metal recovery. I sort the dumps by date and 
skip the redundant dump levels e.g. for the backups of '/' on "nbx1":

> root at nbx1:/backups# ls -rtlh sde*
> -rw-r--r-- 1 root root 120M 2010-04-18 07:39 sde1.bak.2
> -rw-r--r-- 1 root root 1.6G 2010-05-02 07:57 sde1.bak.1
> -rw-r--r-- 1 root root 179M 2010-05-09 07:38 sde1.bak.3
> -rw-r--r-- 1 root root 7.8G 2010-05-16 08:15 sde1.bak.0
> -rw-r--r-- 1 root root  90M 2010-05-18 07:55 sde1.bak.5
> -rw-r--r-- 1 root root  89M 2010-05-20 07:49 sde1.bak.7
> -rw-r--r-- 1 root root  81M 2010-05-21 07:40 sde1.bak.9
> -rw-r--r-- 1 root root  88M 2010-05-22 07:41 sde1.bak.8
> -rw-r--r-- 1 root root 107M 2010-05-23 07:38 sde1.bak.4
> -rw-r--r-- 1 root root  81M 2010-05-24 08:02 sde1.bak.6

Your "bio-linux-backups" overwrote my baseline level 0, so from this 
list, I would restore level 0, 4, 6. In practice, Most of the time, I 
usually just restore one or two files interactively but we had to put 
our disaster recovery plan into action and do a bare-metal recovery of a 
system in Florence from an off-site replica of the local backups in 
Aberdeen. The filesystems are still mounted during the dumps, so some 
errors are inevitable during an incremental restore but it does work.

> I'll look into this later in the week.  Does anyone else on this list
> have comments on backups?  Do you rely on the internal backup system or
> use something else?

I do rely on the internal backups, but I also keep off-site replicas of 
them so I can sleep at night...

Bye,

   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/~ajt