From ian.clark at rothamsted.ac.uk  Fri May  4 12:41:12 2012
From: ian.clark at rothamsted.ac.uk (Ian Clark (RRes-Roth))
Date: Fri, 4 May 2012 16:41:12 +0000
Subject: [Bio-Linux] TaxInspector
Message-ID: <20120504164118.880259370@ixe-mta-29.emailfiltering.com>

Hi Tim etc

Just tried TaxInspector for the first time and was unable to obtain the relevant database. Tried several other sources to obtain taxdmp.zip but each time was unsuccessful, either time out or failed. Any ideas

http://darwin.nerc-oxford.ac.uk/databases/taxonomy/taxdmp.zip

Thanks

Ian

-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
Sent: 30 April 2012 14:15
To: Bio-Linux mailing list
Subject: [Bio-Linux] Fwd: Introductory Bio-Linux course to be held at the University of Manchester, 3rd July.

Dear Bio-Linux users,

Here is an announcement for another of our upcoming courses.  As ever, please forward to people you think may be interested, especially students and postdocs in the north of England.

Cheers,

TIM

===

The NBAF node at CEH Wallingford provides a range of  bioinformatics services for NERC researchers as part of the Environmental Bioinformatics Centre (http://nebc.nerc.ac.uk).  NBAF staff will deliver a 1-day introductory Bio-Linux course at the University of Manchester on the 3rd July 2012.  We particularly encourage PhD students to attend.
See our NBAF courses page (http://nebc.nerc.ac.uk/support/training/) for information on all our courses and freely available course materials.

There is a small ?25 registration fee to cover costs and lunch.  For any queries regarding the course arrangements, please contact the local host Norman Morrison (morrison at cs.man.ac.uk).  For queries on the course content please contact NBAF-W (helpdesk at nebc.nerc.ac.uk.)

Sign-up:
http://estore.manchester.ac.uk/browse/extra_info.asp?compid=1&modid=5&prodid=396&deptid=111&catid=140&CourseDate=856

Schedule:
https://docs.google.com/document/d/1BrhYOtO9NNjgF1saLVTXK5T43iWAVggIHEwxtKVLBpM/edit




--
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

--
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 mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

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This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning.


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This message has been scanned for viruses and
dangerous content by MailScanner, and we believe 
but do not warrant that this e-mail and any attachments
thereto do not contain any viruses. However, you are fully
responsible for performing any virus scanning.


From tbooth at ceh.ac.uk  Tue May  8 09:40:58 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Tue, 08 May 2012 14:40:58 +0100
Subject: [Bio-Linux] TaxInspector
In-Reply-To: <20120504164118.880259370@ixe-mta-29.emailfiltering.com>
References: <20120504164118.880259370@ixe-mta-29.emailfiltering.com>
Message-ID: <1336484458.3975.4.camel@barsukas.nwl.ac.uk>

Hi Ian,

I've not looked at TaxInspector in a long while.  It really should be
modified to run off the official web services but this requires adding
some fairly substantial caching code.

Anyway, I digress.  That link no longer exists (it points to a server in
CEH Oxford and CEH Oxford closed 2 years ago!) but the file you want
should be this one:

ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip

Does that work for you?  It may be that there are firewall issues with
using FTP, which is why I used an HTTP link in the first place.

Cheers,

TIM

On Fri, 2012-05-04 at 17:41 +0100, Ian Clark (RRes-Roth) wrote:
> Hi Tim etc
> 
> Just tried TaxInspector for the first time and was unable to obtain
> the relevant database. Tried several other sources to obtain
> taxdmp.zip but each time was unsuccessful, either time out or failed.
> Any ideas
> 
> http://darwin.nerc-oxford.ac.uk/databases/taxonomy/taxdmp.zip
> 
> Thanks
> 
> Ian
> 
> -----Original Message-----
> From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth
> Sent: 30 April 2012 14:15
> To: Bio-Linux mailing list
> Subject: [Bio-Linux] Fwd: Introductory Bio-Linux course to be held at the University of Manchester, 3rd July.
> 
> Dear Bio-Linux users,
> 
> Here is an announcement for another of our upcoming courses.  As ever, please forward to people you think may be interested, especially students and postdocs in the north of England.
> 
> Cheers,
> 
> TIM
> 
> ===
> 
> The NBAF node at CEH Wallingford provides a range of  bioinformatics services for NERC researchers as part of the Environmental Bioinformatics Centre (http://nebc.nerc.ac.uk).  NBAF staff will deliver a 1-day introductory Bio-Linux course at the University of Manchester on the 3rd July 2012.  We particularly encourage PhD students to attend.
> See our NBAF courses page (http://nebc.nerc.ac.uk/support/training/) for information on all our courses and freely available course materials.
> 
> There is a small ?25 registration fee to cover costs and lunch.  For any queries regarding the course arrangements, please contact the local host Norman Morrison (morrison at cs.man.ac.uk).  For queries on the course content please contact NBAF-W (helpdesk at nebc.nerc.ac.uk.)
> 
> Sign-up:
> http://estore.manchester.ac.uk/browse/extra_info.asp?compid=1&modid=5&prodid=396&deptid=111&catid=140&CourseDate=856
> 
> Schedule:
> https://docs.google.com/document/d/1BrhYOtO9NNjgF1saLVTXK5T43iWAVggIHEwxtKVLBpM/edit
> 
> 
> 
> 
> --
> 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
> 
> --
> 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 mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 
> --
> This message has been scanned for viruses and dangerous content by MailScanner, and we believe but do not warrant that this e-mail and any attachments thereto do not contain any viruses. However, you are fully responsible for performing any virus scanning.
> 
> 

-- 
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

-- 
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 kissaj at muohio.edu  Sun May 13 07:25:08 2012
From: kissaj at muohio.edu (Andor J Kiss)
Date: Sun, 13 May 2012 07:25:08 -0400
Subject: [Bio-Linux] Mothur on Ubuntu 10.10
Message-ID: <1336908308.3663.5.camel@methy1>

Hello,

  I'm running Ubuntu 10.10 (not vanilla BioLinux 6) and I'd like to
install Mothur.  I've added the BioLinux Repositories and can install
most software.  When I try to install the Mothur package
(bio-linux-mothur) I get an error that states "can't install mothur;
can't install bio-linux-catchall"

Any suggestions would be appreciated.

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



From tbooth at ceh.ac.uk  Mon May 14 06:02:20 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 14 May 2012 11:02:20 +0100
Subject: [Bio-Linux] Mothur on Ubuntu 10.10
In-Reply-To: <1336908308.3663.5.camel@methy1>
References: <1336908308.3663.5.camel@methy1>
Message-ID: <1336989740.3975.6900.camel@barsukas.nwl.ac.uk>

Hi,

There is a dependency on Catchall but it's only a "Recommends"
dependency so it shouldn't be strictly enforced.  How are you trying to
install the package?  Can you please try 
'apt-get install bio-linux-mothur'
and send me the full output?  Maybe I've messed something up in the
control file.

Cheers,

TIM

On Sun, 2012-05-13 at 12:25 +0100, Andor J Kiss wrote:
> Hello,
> 
>   I'm running Ubuntu 10.10 (not vanilla BioLinux 6) and I'd like to
> install Mothur.  I've added the BioLinux Repositories and can install
> most software.  When I try to install the Mothur package
> (bio-linux-mothur) I get an error that states "can't install mothur;
> can't install bio-linux-catchall"
> 
> Any suggestions would be appreciated.
> 
> 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

-- 
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 kissaj at muohio.edu  Mon May 14 07:42:47 2012
From: kissaj at muohio.edu (Andor J Kiss)
Date: Mon, 14 May 2012 07:42:47 -0400
Subject: [Bio-Linux] Mothur on Ubuntu 10.10
In-Reply-To: <1336989740.3975.6900.camel@barsukas.nwl.ac.uk>
References: <1336908308.3663.5.camel@methy1>
	<1336989740.3975.6900.camel@barsukas.nwl.ac.uk>
Message-ID: <1336995767.3663.11.camel@methy1>

$sudo apt-get install bio-linux-mothur
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
bio-linux-mothur : Depends: mothur (>= 1.22.0) but it is not installable
                    Recommends: bio-linux-catchall but it is not
installable
E: Broken packages




On Mon, 2012-05-14 at 06:02 -0400, Tim Booth wrote: 
> Hi,
> 
> There is a dependency on Catchall but it's only a "Recommends"
> dependency so it shouldn't be strictly enforced.  How are you trying to
> install the package?  Can you please try 
> 'apt-get install bio-linux-mothur'
> and send me the full output?  Maybe I've messed something up in the
> control file.
> 
> Cheers,
> 
> TIM
> 
> On Sun, 2012-05-13 at 12:25 +0100, Andor J Kiss wrote:
> > Hello,
> > 
> >   I'm running Ubuntu 10.10 (not vanilla BioLinux 6) and I'd like to
> > install Mothur.  I've added the BioLinux Repositories and can install
> > most software.  When I try to install the Mothur package
> > (bio-linux-mothur) I get an error that states "can't install mothur;
> > can't install bio-linux-catchall"
> > 
> > Any suggestions would be appreciated.
> > 
> > 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 tbooth at ceh.ac.uk  Mon May 14 08:44:58 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 14 May 2012 13:44:58 +0100
Subject: [Bio-Linux] Mothur on Ubuntu 10.10
In-Reply-To: <1336995767.3663.11.camel@methy1>
References: <1336908308.3663.5.camel@methy1>
	<1336989740.3975.6900.camel@barsukas.nwl.ac.uk>
	<1336995767.3663.11.camel@methy1>
Message-ID: <1336999498.3975.6958.camel@barsukas.nwl.ac.uk>

Hi,

OK, so what if you just try:

apt-get install mothur

Cheers,

TIM

On Mon, 2012-05-14 at 12:42 +0100, Andor J Kiss wrote:
> $sudo apt-get install bio-linux-mothur
> Reading package lists... Done
> Building dependency tree       
> Reading state information... Done
> Some packages could not be installed. This may mean that you have
> requested an impossible situation or if you are using the unstable
> distribution that some required packages have not yet been created
> or been moved out of Incoming.
> The following information may help to resolve the situation:
> 
> The following packages have unmet dependencies:
> bio-linux-mothur : Depends: mothur (>= 1.22.0) but it is not installable
>                     Recommends: bio-linux-catchall but it is not
> installable
> E: Broken packages
> 


-- 
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 kissaj at muohio.edu  Mon May 14 09:19:33 2012
From: kissaj at muohio.edu (Andor J Kiss)
Date: Mon, 14 May 2012 09:19:33 -0400
Subject: [Bio-Linux] Mothur on Ubuntu 10.10
In-Reply-To: <1336999498.3975.6958.camel@barsukas.nwl.ac.uk>
References: <1336908308.3663.5.camel@methy1>
	<1336989740.3975.6900.camel@barsukas.nwl.ac.uk>
	<1336995767.3663.11.camel@methy1>
	<1336999498.3975.6958.camel@barsukas.nwl.ac.uk>
Message-ID: <1337001573.3445.28.camel@methy1>

okay, so maverick has been dropped by the repos, so maybe that's the
problem....



$sudo apt-get install mothur
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Package mothur is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'mothur' has no installation candidate





On Mon, 2012-05-14 at 08:44 -0400, Tim Booth wrote: 
> Hi,
> 
> OK, so what if you just try:
> 
> apt-get install mothur
> 
> Cheers,
> 
> TIM
> 
> On Mon, 2012-05-14 at 12:42 +0100, Andor J Kiss wrote:
> > $sudo apt-get install bio-linux-mothur
> > Reading package lists... Done
> > Building dependency tree       
> > Reading state information... Done
> > Some packages could not be installed. This may mean that you have
> > requested an impossible situation or if you are using the unstable
> > distribution that some required packages have not yet been created
> > or been moved out of Incoming.
> > The following information may help to resolve the situation:
> > 
> > The following packages have unmet dependencies:
> > bio-linux-mothur : Depends: mothur (>= 1.22.0) but it is not installable
> >                     Recommends: bio-linux-catchall but it is not
> > installable
> > E: Broken packages
> > 
> 
> 




From A.J.Pemberton at bham.ac.uk  Mon May 14 11:15:12 2012
From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton)
Date: Mon, 14 May 2012 16:15:12 +0100
Subject: [Bio-Linux] Mothur on Ubuntu 10.10
In-Reply-To: <1337001573.3445.28.camel@methy1>
References: <1336908308.3663.5.camel@methy1>
	<1336989740.3975.6900.camel@barsukas.nwl.ac.uk>
	<1336995767.3663.11.camel@methy1>
	<1336999498.3975.6958.camel@barsukas.nwl.ac.uk>
	<1337001573.3445.28.camel@methy1>
Message-ID: <5FAE4EF51F20774D9C21A133494A3FE019EDC51353@LESMBX1.adf.bham.ac.uk>

Guys,

Yes, I was on the Ubuntu site on Friday. Ubuntu 10.10 is no longer supported. That may be the problem. Andor, you may need to bite the bullet and update your version. I am reliably told Ubuntu 11.10 is good at the moment, if you do not want to move to the latest LTS 12.04. I know Tim has warned us about 12.04 breaking some bio-linux packages. Not sure if 11.10 is in the same category since that is the first Unity release. You can install gnome 3 if you do not like Unity. Tim?

Regards,

Tony Pemberton


-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Andor J Kiss
Sent: 14 May 2012 14:20
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] Mothur on Ubuntu 10.10

okay, so maverick has been dropped by the repos, so maybe that's the
problem....



$sudo apt-get install mothur
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Package mothur is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'mothur' has no installation candidate





On Mon, 2012-05-14 at 08:44 -0400, Tim Booth wrote: 
> Hi,
> 
> OK, so what if you just try:
> 
> apt-get install mothur
> 
> Cheers,
> 
> TIM
> 
> On Mon, 2012-05-14 at 12:42 +0100, Andor J Kiss wrote:
> > $sudo apt-get install bio-linux-mothur
> > Reading package lists... Done
> > Building dependency tree       
> > Reading state information... Done
> > Some packages could not be installed. This may mean that you have
> > requested an impossible situation or if you are using the unstable
> > distribution that some required packages have not yet been created
> > or been moved out of Incoming.
> > The following information may help to resolve the situation:
> > 
> > The following packages have unmet dependencies:
> > bio-linux-mothur : Depends: mothur (>= 1.22.0) but it is not installable
> >                     Recommends: bio-linux-catchall but it is not
> > installable
> > E: Broken packages
> > 
> 
> 


_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


From pjotr.public15 at thebird.nl  Mon May 14 11:28:02 2012
From: pjotr.public15 at thebird.nl (pjotr.public15 at thebird.nl)
Date: Mon, 14 May 2012 17:28:02 +0200
Subject: [Bio-Linux] Mothur on Ubuntu 10.10
In-Reply-To: <5FAE4EF51F20774D9C21A133494A3FE019EDC51353@LESMBX1.adf.bham.ac.uk>
References: <1336908308.3663.5.camel@methy1>
	<1336989740.3975.6900.camel@barsukas.nwl.ac.uk>
	<1336995767.3663.11.camel@methy1>
	<1336999498.3975.6958.camel@barsukas.nwl.ac.uk>
	<1337001573.3445.28.camel@methy1>
	<5FAE4EF51F20774D9C21A133494A3FE019EDC51353@LESMBX1.adf.bham.ac.uk>
Message-ID: <20120514152802.GA8028@thebird.nl>

I know some people swear by Ubuntu, but the Debian release management
does better when it comes to consistency and robustness. Things you
should aim for in a server style environment. BioLinux is great on
Debian too: not that big a step. I have been on Debian the last seven
years. I see no reason to use Ubuntu for bioinformatics. Debian is
what I recommend.

Pj.

On Mon, May 14, 2012 at 04:15:12PM +0100, Anthony Pemberton wrote:
> Guys,
> 
> Yes, I was on the Ubuntu site on Friday. Ubuntu 10.10 is no longer supported. That may be the problem. Andor, you may need to bite the bullet and update your version. I am reliably told Ubuntu 11.10 is good at the moment, if you do not want to move to the latest LTS 12.04. I know Tim has warned us about 12.04 breaking some bio-linux packages. Not sure if 11.10 is in the same category since that is the first Unity release. You can install gnome 3 if you do not like Unity. Tim?
> 
> Regards,
> 
> Tony Pemberton
> 
> 
> -----Original Message-----
> From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Andor J Kiss
> Sent: 14 May 2012 14:20
> To: Bio-Linux help and discussion
> Subject: Re: [Bio-Linux] Mothur on Ubuntu 10.10
> 
> okay, so maverick has been dropped by the repos, so maybe that's the
> problem....
> 
> 
> 
> $sudo apt-get install mothur
> Reading package lists... Done
> Building dependency tree       
> Reading state information... Done
> Package mothur is not available, but is referred to by another package.
> This may mean that the package is missing, has been obsoleted, or
> is only available from another source
> 
> E: Package 'mothur' has no installation candidate
> 
> 
> 
> 
> 
> On Mon, 2012-05-14 at 08:44 -0400, Tim Booth wrote: 
> > Hi,
> > 
> > OK, so what if you just try:
> > 
> > apt-get install mothur
> > 
> > Cheers,
> > 
> > TIM
> > 
> > On Mon, 2012-05-14 at 12:42 +0100, Andor J Kiss wrote:
> > > $sudo apt-get install bio-linux-mothur
> > > Reading package lists... Done
> > > Building dependency tree       
> > > Reading state information... Done
> > > Some packages could not be installed. This may mean that you have
> > > requested an impossible situation or if you are using the unstable
> > > distribution that some required packages have not yet been created
> > > or been moved out of Incoming.
> > > The following information may help to resolve the situation:
> > > 
> > > The following packages have unmet dependencies:
> > > bio-linux-mothur : Depends: mothur (>= 1.22.0) but it is not installable
> > >                     Recommends: bio-linux-catchall but it is not
> > > installable
> > > E: Broken packages
> > > 
> > 
> > 
> 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 


From kissaj at muohio.edu  Mon May 14 12:53:20 2012
From: kissaj at muohio.edu (Andor J Kiss)
Date: Mon, 14 May 2012 12:53:20 -0400
Subject: [Bio-Linux] Mothur on Ubuntu 10.10
In-Reply-To: <5FAE4EF51F20774D9C21A133494A3FE019EDC51353@LESMBX1.adf.bham.ac.uk>
References: <1336908308.3663.5.camel@methy1>
	<1336989740.3975.6900.camel@barsukas.nwl.ac.uk>
	<1336995767.3663.11.camel@methy1>
	<1336999498.3975.6958.camel@barsukas.nwl.ac.uk>
	<1337001573.3445.28.camel@methy1>
	<5FAE4EF51F20774D9C21A133494A3FE019EDC51353@LESMBX1.adf.bham.ac.uk>
Message-ID: <1337014400.3445.37.camel@methy1>

Yep, I'll jump to 12.04 when BioLinux 7 (?) is ready.  I'm right in the
middle of manuscripts, etc so I can't risk an upgrade.  Will partition
and install biolinux6.

Thanks!


On Mon, 2012-05-14 at 11:15 -0400, Anthony Pemberton wrote: 
> Guys,
> 
> Yes, I was on the Ubuntu site on Friday. Ubuntu 10.10 is no longer supported. That may be the problem. Andor, you may need to bite the bullet and update your version. I am reliably told Ubuntu 11.10 is good at the moment, if you do not want to move to the latest LTS 12.04. I know Tim has warned us about 12.04 breaking some bio-linux packages. Not sure if 11.10 is in the same category since that is the first Unity release. You can install gnome 3 if you do not like Unity. Tim?
> 
> Regards,
> 
> Tony Pemberton
> 
> 
> -----Original Message-----
> From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Andor J Kiss
> Sent: 14 May 2012 14:20
> To: Bio-Linux help and discussion
> Subject: Re: [Bio-Linux] Mothur on Ubuntu 10.10
> 
> okay, so maverick has been dropped by the repos, so maybe that's the
> problem....
> 
> 
> 
> $sudo apt-get install mothur
> Reading package lists... Done
> Building dependency tree       
> Reading state information... Done
> Package mothur is not available, but is referred to by another package.
> This may mean that the package is missing, has been obsoleted, or
> is only available from another source
> 
> E: Package 'mothur' has no installation candidate
> 
> 
> 
> 
> 
> On Mon, 2012-05-14 at 08:44 -0400, Tim Booth wrote: 
> > Hi,
> > 
> > OK, so what if you just try:
> > 
> > apt-get install mothur
> > 
> > Cheers,
> > 
> > TIM
> > 
> > On Mon, 2012-05-14 at 12:42 +0100, Andor J Kiss wrote:
> > > $sudo apt-get install bio-linux-mothur
> > > Reading package lists... Done
> > > Building dependency tree       
> > > Reading state information... Done
> > > Some packages could not be installed. This may mean that you have
> > > requested an impossible situation or if you are using the unstable
> > > distribution that some required packages have not yet been created
> > > or been moved out of Incoming.
> > > The following information may help to resolve the situation:
> > > 
> > > The following packages have unmet dependencies:
> > > bio-linux-mothur : Depends: mothur (>= 1.22.0) but it is not installable
> > >                     Recommends: bio-linux-catchall but it is not
> > > installable
> > > E: Broken packages
> > > 
> > 
> > 
> 
> 
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From kissaj at muohio.edu  Thu May 31 13:27:22 2012
From: kissaj at muohio.edu (Andor J Kiss)
Date: Thu, 31 May 2012 13:27:22 -0400
Subject: [Bio-Linux] BioLinux 7.0 & TESLA GPU
Message-ID: <1338485242.4672.112.camel@methy1>

Hello,

Will the upcoming release of Biolinux (7) support GPU (nVIDIA TESLA)
computing?

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