From jvollme1 at gwdg.de  Sun Jul  6 12:06:27 2014
From: jvollme1 at gwdg.de (john vollmers)
Date: Sun, 6 Jul 2014 18:06:27 +0200
Subject: [Bio-Linux] Problem with package catalogue. Nothing can be
	installed anymore
Message-ID: <53B97403.6030508@gwdg.de>

Hello,
Ever since I ran into java-dependency problems while trying to install 
an external python module (Twilio), I cannot install or remove anything 
in biolinux anymore.

every time I try to open the ubuntu software center i get the following 
message:
"biolinux Items cannot be installed or removed until the package 
catalogue is repaired. Do you want to repair it now?"

But wen I click "OK" it always aborts the repair process with the 
message "Package operation failed" (however It won't let me look into 
the details).

When I look into the Software-Center history it seems that each time it 
tries to "repair the catalogue" it is actually trying to install 
"Oracle-Java8-installer" but fails every time.

what can I do?



From tbooth at ceh.ac.uk  Mon Jul  7 05:09:31 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 7 Jul 2014 10:09:31 +0100
Subject: [Bio-Linux] Problem with package catalogue. Nothing can be
	installed anymore
In-Reply-To: <53B97403.6030508@gwdg.de>
References: <53B97403.6030508@gwdg.de>
Message-ID: <1404724171.8857.32.camel@balisaur>

Hi John,

Sorry to hear you are having these problems.  The package manager is
normally very good at keeping your system in a consistent state, but
sometimes it can get stuck and needs a bit of help.  The first thing to
do is to use the command-line tool "apt-get", as this will give you
better diagnostic information and also provides options you can't get
through the GUI.

Please open a shell terminal and give the command:

sudo apt-get -f install

This should be the same as the "repair the catalogue" option but will
give more diagnostic output.  I'm guessing that the
oracle-java8-installer package is stuck in a half-installed state so you
can tell the system to remove it:

sudo apt-get remove oracle-java8-installer

or if that fails, you can speak more firmly to it:

sudo dpkg -P --force-all oracle-java8-installer

Where does that get you?

My personal advice would be to download the regular Java 8 release from
Oracle and install it into /opt or /usr/local, as I've had similar
issues in the past with these installer-wrapper packages and you don't
really gain much by using them.

Cheers,

TIM

On Sun, 2014-07-06 at 17:06 +0100, john vollmers wrote:
> Hello,
> Ever since I ran into java-dependency problems while trying to install 
> an external python module (Twilio), I cannot install or remove anything 
> in biolinux anymore.
> 
> every time I try to open the ubuntu software center i get the following 
> message:
> "biolinux Items cannot be installed or removed until the package 
> catalogue is repaired. Do you want to repair it now?"
> 
> But wen I click "OK" it always aborts the repair process with the 
> message "Package operation failed" (however It won't let me look into 
> the details).
> 
> When I look into the Software-Center history it seems that each time it 
> tries to "repair the catalogue" it is actually trying to install 
> "Oracle-Java8-installer" but fails every time.
> 
> what can I do?
> 

-- 
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


From Krishnaveni.Venkidusamy at unisa.edu.au  Sun Jul 13 21:42:59 2014
From: Krishnaveni.Venkidusamy at unisa.edu.au (Krishnaveni Venkidusamy)
Date: Mon, 14 Jul 2014 11:12:59 +0930
Subject: [Bio-Linux] BIolinux 7 qiime
Message-ID: <7792C5A2294F10499E64F6DC3C78E81D06212B3E32@ITUPC-EX1MBOX.UniNet.unisa.edu.au>

Hi All,

This is Krishna, 

I am a brand  new to the analysis through Biolinux. I use  BioLinux  to work on QIIME platform. 
I do installed Biolinux & (powered by Ubuntu ) OS. I also have  installed greengens and landmask file. However no use of this because of the reason in the terminal box. 
The terminal box miss the  sign ""$" and it couldnt further proceed with this qiime.  So I end up with the following  comments,!!!
I find very much difficult as I am new to Biolinux based QIIME. Could you please assit me with this?

I have  attached few outputs of terminal box which does miss the $ signs,

Thank you.
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From gawbul at gmail.com  Thu Jul 17 12:54:50 2014
From: gawbul at gmail.com (Steve Moss)
Date: Thu, 17 Jul 2014 17:54:50 +0100
Subject: [Bio-Linux] BIolinux 7 qiime
Message-ID: <CALKAsdouUEiGtv0qFyaNWjK1yPU98yDwk0dXb5KCqU3SpQ+Rgg@mail.gmail.com>

Dear Krishnaveni,

The $ symbol signifies part of the shell prompt. This usually corresponds
to an environment variable called PS1 (see
https://en.wikibooks.org/wiki/Guide_to_Unix/Environment_Variables#PS1). You
can change the shell prompt to be whatever you like (see
http://www.linuxnix.com/2013/04/linuxunix-shell-ps1-prompt-explained-in-detail.html
).

It just so happens that running QIIME changes you into a new shell, setup
with all the necessary environment variables from running the QIIME
commands, along with a custom shell prompt so that you know you are running
within the QIIME environment. Hence the 'qiime >' instead of the '$'. You
can still run commands as usual from that shell. If you type exit, it
should return you back to your usual shell prompt with the $ instead.

Cheers,

Steve
-- 
Steve Moss
http://about.me/gawbul

On 17 July 2014 12:00, <bio-linux-request at nebclists.nerc.ac.uk> wrote:

> Hi All,
>
> This is Krishna,
>
> I am a brand  new to the analysis through Biolinux. I use  BioLinux  to
> work on QIIME platform.
> I do installed Biolinux & (powered by Ubuntu ) OS. I also have  installed
> greengens and landmask file. However no use of this because of the reason
> in the terminal box.
> The terminal box miss the  sign ""$" and it couldnt further proceed with
> this qiime.  So I end up with the following  comments,!!!
> I find very much difficult as I am new to Biolinux based QIIME. Could you
> please assit me with this?
>
> I have  attached few outputs of terminal box which does miss the $ signs,
>
> Thank you.
>



<http://about.me/gawbul>
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From brian at helix.biology.mcmaster.ca  Fri Jul 18 08:27:57 2014
From: brian at helix.biology.mcmaster.ca (Brian Golding)
Date: Fri, 18 Jul 2014 08:27:57 -0400
Subject: [Bio-Linux] HWE error with Biolinux
Message-ID: <20140718122757.GA9691@helix.mcmaster.ca>



Upon login, I have started to get the message listed below.

(1) Are you working on a new version of Biolinux and should I simply wait
for that or (2) should I try the HWE upgrade or (3) would a release
upgrade completely break the system?

Brian
 
-------------------------------------------------------------------


Welcome to Ubuntu 12.04.4 LTS (GNU/Linux 3.5.0-52-generic x86_64)

 * Documentation:  https://help.ubuntu.com/

12 packages can be updated.
11 updates are security updates.



Your current Hardware Enablement Stack (HWE) is going out of support
on 08/07/14.  After this date security updates for critical parts
(kernel
and graphics stack) of your system will no longer be available.

For more information, please see:
http://wiki.ubuntu.com/1204_HWE_EOL

To upgrade to a supported (or longer supported) configuration:

* Upgrade from Ubuntu 12.04 LTS to Ubuntu 14.04 LTS by running:
sudo do-release-upgrade 

OR

* Install a newer HWE version by running:
sudo apt-get install linux-image-generic-lts-trusty

and reboot your system.

Last login:


From tbooth at ceh.ac.uk  Fri Jul 18 08:53:59 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 18 Jul 2014 13:53:59 +0100
Subject: [Bio-Linux] HWE error with Biolinux
In-Reply-To: <20140718122757.GA9691@helix.mcmaster.ca>
References: <20140718122757.GA9691@helix.mcmaster.ca>
Message-ID: <1405688039.12409.197.camel@balisaur>

Hi Brian,

The updated version of Bio-Linux is basically finished, but I've been
waiting on final tester feedback and trying to finish the release
announcement and new website content before I send it out to this list.

If you want to see what is going on, the discussion is over on the
developers list, including my provisional upgrade instructions posted
here:

http://nebclists.nerc.ac.uk/pipermail/bio-linux-dev/2014-June/000246.html

Doing a release upgrade won't "completely break the system" but it will
probably complain about the APT-sources having custom entries, and the
default Ubuntu upgrader doesn't know about extra important packages that
should be added to BL8, or how to switch from FreeNX to X2GO.  Therefore
you should use my upgrade script.  I'm hoping to make some final minor
fixes and announce it officially next week.

Cheers,

TIM

On Fri, 2014-07-18 at 13:27 +0100, Brian Golding wrote:
> 
> Upon login, I have started to get the message listed below.
> 
> (1) Are you working on a new version of Biolinux and should I simply wait
> for that or (2) should I try the HWE upgrade or (3) would a release
> upgrade completely break the system?
> 
> Brian
>  
> -------------------------------------------------------------------
> 
> 
> Welcome to Ubuntu 12.04.4 LTS (GNU/Linux 3.5.0-52-generic x86_64)
> 
>  * Documentation:  https://help.ubuntu.com/
> 
> 12 packages can be updated.
> 11 updates are security updates.
> 
> 
> 
> Your current Hardware Enablement Stack (HWE) is going out of support
> on 08/07/14.  After this date security updates for critical parts
> (kernel
> and graphics stack) of your system will no longer be available.
> 
> For more information, please see:
> http://wiki.ubuntu.com/1204_HWE_EOL
> 
> To upgrade to a supported (or longer supported) configuration:
> 
> * Upgrade from Ubuntu 12.04 LTS to Ubuntu 14.04 LTS by running:
> sudo do-release-upgrade 
> 
> OR
> 
> * Install a newer HWE version by running:
> sudo apt-get install linux-image-generic-lts-trusty
> 
> and reboot your system.
> 
> Last login:
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

-- 
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


From brian at helix.biology.mcmaster.ca  Fri Jul 18 09:12:30 2014
From: brian at helix.biology.mcmaster.ca (Brian Golding)
Date: Fri, 18 Jul 2014 09:12:30 -0400
Subject: [Bio-Linux] HWE error with Biolinux
In-Reply-To: <6149_1405688078_s6ICsbn3006758_1405688039.12409.197.camel@balisaur>
References: <20140718122757.GA9691@helix.mcmaster.ca>
 <6149_1405688078_s6ICsbn3006758_1405688039.12409.197.camel@balisaur>
Message-ID: <20140718131230.GB4016@helix.mcmaster.ca>

Thanks very much, I am in no hurry and am happy to sait a week (or
few; no shortage of work to do ;-).

Brian



On Fri, Jul 18, 2014 at 01:53:59PM +0100, Tim Booth wrote:
> Hi Brian,
> 
> The updated version of Bio-Linux is basically finished, but I've been
> waiting on final tester feedback and trying to finish the release
> announcement and new website content before I send it out to this list.
> 
> If you want to see what is going on, the discussion is over on the
> developers list, including my provisional upgrade instructions posted
> here:
> 
> http://nebclists.nerc.ac.uk/pipermail/bio-linux-dev/2014-June/000246.html
> 
> Doing a release upgrade won't "completely break the system" but it will
> probably complain about the APT-sources having custom entries, and the
> default Ubuntu upgrader doesn't know about extra important packages that
> should be added to BL8, or how to switch from FreeNX to X2GO.  Therefore
> you should use my upgrade script.  I'm hoping to make some final minor
> fixes and announce it officially next week.
> 
> Cheers,
> 
> TIM
> 
> On Fri, 2014-07-18 at 13:27 +0100, Brian Golding wrote:
> > 
> > Upon login, I have started to get the message listed below.
> > 
> > (1) Are you working on a new version of Biolinux and should I simply wait
> > for that or (2) should I try the HWE upgrade or (3) would a release
> > upgrade completely break the system?
> > 
> > Brian
> >  
> > -------------------------------------------------------------------
> > 
> > 
> > Welcome to Ubuntu 12.04.4 LTS (GNU/Linux 3.5.0-52-generic x86_64)
> > 
> >  * Documentation:  https://help.ubuntu.com/
> > 
> > 12 packages can be updated.
> > 11 updates are security updates.
> > 
> > 
> > 
> > Your current Hardware Enablement Stack (HWE) is going out of support
> > on 08/07/14.  After this date security updates for critical parts
> > (kernel
> > and graphics stack) of your system will no longer be available.
> > 
> > For more information, please see:
> > http://wiki.ubuntu.com/1204_HWE_EOL
> > 
> > To upgrade to a supported (or longer supported) configuration:
> > 
> > * Upgrade from Ubuntu 12.04 LTS to Ubuntu 14.04 LTS by running:
> > sudo do-release-upgrade 
> > 
> > OR
> > 
> > * Install a newer HWE version by running:
> > sudo apt-get install linux-image-generic-lts-trusty
> > 
> > and reboot your system.
> > 
> > Last login:
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 
> -- 
> 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
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


From kissaj at miamioh.edu  Fri Jul 18 10:12:16 2014
From: kissaj at miamioh.edu (Andor J Kiss)
Date: Fri, 18 Jul 2014 10:12:16 -0400
Subject: [Bio-Linux] HWE error with Biolinux
In-Reply-To: <20140718122757.GA9691@helix.mcmaster.ca>
References: <20140718122757.GA9691@helix.mcmaster.ca>
Message-ID: <1405692736.3938.7.camel@methy1>

Hi,

    I've done just the HWE upgrade (to the Trusty Kernel) and didn't
have issues at all with that "upgrade/update" - even though I know a lot
of people did have some problems.

    Q:  Will there be any issues from 12.04.4 LTS (BioLinux 7) with the
HWE ==>  BioLinux 8 (14.04)?  Or will the script deal with this (these)
issues?

Thanks, 
-- 
__________________________________________________________________
Andor J Kiss, Supervisor
Center for Bioinformatics and Functional Genomics
086 Pearson Hall ~ Miami University
700 East High Street
Oxford, Ohio  45056
USA

eMAIL: kissaj at MiamiOH.edu 
Telephone: +1 (513) 529-4280
Fax: +1 (513) 529-2431
URL (CBFG): http://www.cas.miamioh.edu/cbfg/  
URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss 


On Fri, 2014-07-18 at 08:27 -0400, Brian Golding wrote:

> 
> Upon login, I have started to get the message listed below.
> 
> (1) Are you working on a new version of Biolinux and should I simply wait
> for that or (2) should I try the HWE upgrade or (3) would a release
> upgrade completely break the system?
> 
> Brian
>  
> -------------------------------------------------------------------
> 
> 
> Welcome to Ubuntu 12.04.4 LTS (GNU/Linux 3.5.0-52-generic x86_64)
> 
>  * Documentation:  https://help.ubuntu.com/
> 
> 12 packages can be updated.
> 11 updates are security updates.
> 
> 
> 
> Your current Hardware Enablement Stack (HWE) is going out of support
> on 08/07/14.  After this date security updates for critical parts
> (kernel
> and graphics stack) of your system will no longer be available.
> 
> For more information, please see:
> http://wiki.ubuntu.com/1204_HWE_EOL
> 
> To upgrade to a supported (or longer supported) configuration:
> 
> * Upgrade from Ubuntu 12.04 LTS to Ubuntu 14.04 LTS by running:
> sudo do-release-upgrade 
> 
> OR
> 
> * Install a newer HWE version by running:
> sudo apt-get install linux-image-generic-lts-trusty
> 
> and reboot your system.
> 
> Last login:
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
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From tbooth at ceh.ac.uk  Fri Jul 18 11:29:32 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 18 Jul 2014 16:29:32 +0100
Subject: [Bio-Linux] HWE error with Biolinux
In-Reply-To: <1405692736.3938.7.camel@methy1>
References: <20140718122757.GA9691@helix.mcmaster.ca>
 <1405692736.3938.7.camel@methy1>
Message-ID: <1405697372.12409.222.camel@balisaur>

Hi Andor,

I believe it should work fine, but of course as long as there are
computer systems, there will will be bugs, so I can't give a cast iron
promise your system will work.

I can say that the upgrade will have been tested on a variety of
machines here which were in a variety of different states, and also by
external Bio-Linux testers, and also that upgrading a machine with HWE
is fully supported by Ubuntu, so it should work.  Even if it doesn't,
I've never hit any upgrade issues (other than hardware failures) that
couldn't be resolved with some small amount of tinkering, and I'll
answer any queries reported to this list as soon as I can, and add any
relevant fixes to the upgrade script.

I hope that reassures you, but you might still want to hold off
upgrading critical machines until a week or two after the announcement
(which as I said previously should be in about a week).

Cheers,

TIM


On Fri, 2014-07-18 at 15:12 +0100, Andor J Kiss wrote:
> Hi,
> 
>     I've done just the HWE upgrade (to the Trusty Kernel) and didn't
> have issues at all with that "upgrade/update" - even though I know a
> lot of people did have some problems.
> 
>     Q:  Will there be any issues from 12.04.4 LTS (BioLinux 7) with
> the HWE ==>  BioLinux 8 (14.04)?  Or will the script deal with this
> (these) issues?
> 
> Thanks, 
> 
> 
-- 
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


From tony.travis at abdn.ac.uk  Fri Jul 18 12:36:26 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Fri, 18 Jul 2014 17:36:26 +0100
Subject: [Bio-Linux] HWE error with Biolinux
In-Reply-To: <1405697372.12409.222.camel@balisaur>
References: <20140718122757.GA9691@helix.mcmaster.ca>
 <1405692736.3938.7.camel@methy1> <1405697372.12409.222.camel@balisaur>
Message-ID: <53C94D0A.1000301@abdn.ac.uk>

On 18/07/14 16:29, Tim Booth wrote:
> [...]
> I can say that the upgrade will have been tested on a variety of
> machines here which were in a variety of different states, and also by
> external Bio-Linux testers, and also that upgrading a machine with HWE
> is fully supported by Ubuntu, so it should work.  Even if it doesn't,
> I've never hit any upgrade issues (other than hardware failures) that
> couldn't be resolved with some small amount of tinkering, and I'll
> answer any queries reported to this list as soon as I can, and add any
> relevant fixes to the upgrade script.

Hi, Tim.

I upgraded two 12.04.4 HWE installations of Bio-Linux 7 using your beta
upgrade8 script without any problems. However, I did have some problems
doing the actual HWE upgrades on these original BL7 instances, because
they break X11. Your script works OK if you have upgraded to a new HWE
stack. I was tracking the HWE versions of the release iso's on my BL7.

Bye,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.


From tbooth at ceh.ac.uk  Wed Jul 30 11:54:57 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 30 Jul 2014 16:54:57 +0100
Subject: [Bio-Linux] Bio-Linux 8 now available
Message-ID: <1406735697.11394.42.camel@balisaur>

Dear All,

The Bio-Linux system gets a major new release every two years following
the regular Ubuntu "LTS" releases.  Since Ubuntu 14.04 LTS came out in
April I've been working with help from the Bio-Linux community to make
Bio-Linux 8 and it is now ready and available via the new website.

  http://environmentalomics.org/bio-linux/

Upgrades from Bio-Linux 7 to 8 do not require re-installation. I
encourage you all to upgrade soon, as new bioinformatics packages will
no longer be provided for Bio-Linux 7.  See the "Installation" section
for instructions on upgrading your BL7 machine.

The new Ubuntu 14.04 base system brings many benefits such as increased
hardware compatibility and new office and multimedia software, but
Bio-Linux itself also has many improvements and new/updated packages.
Also for the first time there is a version in OVA format for
VirtualBox/VMWare users, and this version will be updated whenever new
ISO files are released.  See the "What's New" and "Software List" pages
on the website for details.

As ever, please report problems and feedback to
helpdesk at nebc.nerc.ac.uk.  I can't promise to fix everything but will
endeavour to provide help and squash bugs where I can.  Also, please let
me know if you use Bio-Linux for teaching or manage a large installation
on your departmental server or computing lab.  The more we can prove
that people find this stuff useful, the more likely we are to get future
funding!

I hope you enjoy using Bio-Linux 8.

TIM

-- 
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


From raonyguimaraes at gmail.com  Wed Jul 30 14:01:45 2014
From: raonyguimaraes at gmail.com (=?ISO-8859-1?Q?Raony_Guimaraes_Corr=EAa_Do_Carmo_Lisboa_Cardenas?=)
Date: Wed, 30 Jul 2014 15:01:45 -0300
Subject: [Bio-Linux] Bio-Linux 8 now available
In-Reply-To: <1406735697.11394.42.camel@balisaur>
References: <1406735697.11394.42.camel@balisaur>
Message-ID: <CALenahnum_WatGBx2fveCq5iuX+Gnc8RJX-Px_4w_XcjdRwqBw@mail.gmail.com>

Hello Tim,

I've just installed this new version from the ISO and I have to say that
it's working beautifully!

With gnome-session this system is consuming only 475 mb of ram. I tried to
upgrade it with "update-manager -d"and even galaxy was still working after
the upgrade!

Thank you so much for this good piece of software and let me know how i
could contribute more to this project.

Kind Regards



_____________________________________________

Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
PhD Student in Bioinformatics

email: raonyguimaraes at gmail.com
skype/gtalk: raonyguimaraes
phone: +55 31 93404152

Laboratory of Clinical Genomics
UFMG School of Medicine
Federal University of Minas Gerais - UFMG
Av. Prof. Alfredo Balena, 190, Sala 321
Belo Horizonte, Brazil 30130-100
_____________________________________________


On Wed, Jul 30, 2014 at 12:54 PM, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Dear All,
>
> The Bio-Linux system gets a major new release every two years following
> the regular Ubuntu "LTS" releases.  Since Ubuntu 14.04 LTS came out in
> April I've been working with help from the Bio-Linux community to make
> Bio-Linux 8 and it is now ready and available via the new website.
>
>   http://environmentalomics.org/bio-linux/
>
> Upgrades from Bio-Linux 7 to 8 do not require re-installation. I
> encourage you all to upgrade soon, as new bioinformatics packages will
> no longer be provided for Bio-Linux 7.  See the "Installation" section
> for instructions on upgrading your BL7 machine.
>
> The new Ubuntu 14.04 base system brings many benefits such as increased
> hardware compatibility and new office and multimedia software, but
> Bio-Linux itself also has many improvements and new/updated packages.
> Also for the first time there is a version in OVA format for
> VirtualBox/VMWare users, and this version will be updated whenever new
> ISO files are released.  See the "What's New" and "Software List" pages
> on the website for details.
>
> As ever, please report problems and feedback to
> helpdesk at nebc.nerc.ac.uk.  I can't promise to fix everything but will
> endeavour to provide help and squash bugs where I can.  Also, please let
> me know if you use Bio-Linux for teaching or manage a large installation
> on your departmental server or computing lab.  The more we can prove
> that people find this stuff useful, the more likely we are to get future
> funding!
>
> I hope you enjoy using Bio-Linux 8.
>
> TIM
>
> --
> 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
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
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From jm at iehinc.com  Wed Jul 30 14:16:57 2014
From: jm at iehinc.com (James Mategko)
Date: Wed, 30 Jul 2014 11:16:57 -0700
Subject: [Bio-Linux] Bio-Linux 8 now available
In-Reply-To: <1406735697.11394.42.camel@balisaur>
References: <1406735697.11394.42.camel@balisaur>
Message-ID: <53D93699.6020408@iehinc.com>

Tim,

   I've been running the Beta ISO within a VM for the past few days and 
everything is running perfectly.

Thank You for all the hard work you and your team put into this release.

- James

On 7/30/2014 8:54 AM, Tim Booth wrote:
> Dear All,
>
> The Bio-Linux system gets a major new release every two years following
> the regular Ubuntu "LTS" releases.  Since Ubuntu 14.04 LTS came out in
> April I've been working with help from the Bio-Linux community to make
> Bio-Linux 8 and it is now ready and available via the new website.
>
>    http://environmentalomics.org/bio-linux/
>
> Upgrades from Bio-Linux 7 to 8 do not require re-installation. I
> encourage you all to upgrade soon, as new bioinformatics packages will
> no longer be provided for Bio-Linux 7.  See the "Installation" section
> for instructions on upgrading your BL7 machine.
>
> The new Ubuntu 14.04 base system brings many benefits such as increased
> hardware compatibility and new office and multimedia software, but
> Bio-Linux itself also has many improvements and new/updated packages.
> Also for the first time there is a version in OVA format for
> VirtualBox/VMWare users, and this version will be updated whenever new
> ISO files are released.  See the "What's New" and "Software List" pages
> on the website for details.
>
> As ever, please report problems and feedback to
> helpdesk at nebc.nerc.ac.uk.  I can't promise to fix everything but will
> endeavour to provide help and squash bugs where I can.  Also, please let
> me know if you use Bio-Linux for teaching or manage a large installation
> on your departmental server or computing lab.  The more we can prove
> that people find this stuff useful, the more likely we are to get future
> funding!
>
> I hope you enjoy using Bio-Linux 8.
>
> TIM
>


From tbooth at ceh.ac.uk  Thu Jul 31 06:12:11 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 31 Jul 2014 11:12:11 +0100
Subject: [Bio-Linux] Bio-Linux 8 - Some questions and answers
Message-ID: <1406801531.11394.99.camel@balisaur>

Hi,

I've had several responses to the announcement of Bio-Linux 8 and
various questions asked.  Many thanks for all the positive feedback.
For the questions, rather than reply to each question personally I'm
putting the answers here for everyone to see.

Q1) After upgrading will I still retain my current applications/
settings/programs etc.?

Yes, the upgrade will keep your files and settings.

Q2) The "runurl" command gives a "syntax error" and the upgrade script
won't even start, or else freezes and then gives a "timeout error".
What might be the problem?

Obviously you need a working net connection to do the upgrade.

One reason the above might happen is if you need to connect to the web
through a proxy server and this is not configured to work in the command
shell.  You need to set the correct proxy under System Settings->Network
and select "Apply System Wide", then open a fresh shell.  If you already
have Firefox working then look in the Firefox proxy settings and copy
them to the System Settings.

Q3) Can I still submit new wallpaper images for Bio-Linux 8?

We had a fantastic response to this and I'm delighted that so many
people wanted to share their photos.  What I propose to do is to stick
with the ones we have for now but some time in the new year I'll put out
another call and add a batch of new photos.

Q4) I try to upgrade but I get the error "An unresolvable problem
occurred while calculating the upgrade." - what can I do?

There are various things that might cause this, and I'm working on a
fix.  Please keep an eye on the Bio-Linux mailing list and I'll let you
know when there is an updated updater script to try.

Cheers,

TIM

-- 
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


From kissaj at miamioh.edu  Thu Jul 31 09:47:41 2014
From: kissaj at miamioh.edu (Andor J Kiss)
Date: Thu, 31 Jul 2014 09:47:41 -0400
Subject: [Bio-Linux] Bio-Linux 8 now available
In-Reply-To: <1406735697.11394.42.camel@balisaur>
References: <1406735697.11394.42.camel@balisaur>
Message-ID: <1406814461.4582.21.camel@methy1>

Hi Tim,

    Thanks so much for this!

Regards,
Andor

On Wed, 2014-07-30 at 16:54 +0100, Tim Booth wrote:

> Dear All,
> 
> The Bio-Linux system gets a major new release every two years following
> the regular Ubuntu "LTS" releases.  Since Ubuntu 14.04 LTS came out in
> April I've been working with help from the Bio-Linux community to make
> Bio-Linux 8 and it is now ready and available via the new website.
> 
>   http://environmentalomics.org/bio-linux/
> 
> Upgrades from Bio-Linux 7 to 8 do not require re-installation. I
> encourage you all to upgrade soon, as new bioinformatics packages will
> no longer be provided for Bio-Linux 7.  See the "Installation" section
> for instructions on upgrading your BL7 machine.
> 
> The new Ubuntu 14.04 base system brings many benefits such as increased
> hardware compatibility and new office and multimedia software, but
> Bio-Linux itself also has many improvements and new/updated packages.
> Also for the first time there is a version in OVA format for
> VirtualBox/VMWare users, and this version will be updated whenever new
> ISO files are released.  See the "What's New" and "Software List" pages
> on the website for details.
> 
> As ever, please report problems and feedback to
> helpdesk at nebc.nerc.ac.uk.  I can't promise to fix everything but will
> endeavour to provide help and squash bugs where I can.  Also, please let
> me know if you use Bio-Linux for teaching or manage a large installation
> on your departmental server or computing lab.  The more we can prove
> that people find this stuff useful, the more likely we are to get future
> funding!
> 
> I hope you enjoy using Bio-Linux 8.
> 
> TIM
> 
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