From tbooth at ceh.ac.uk  Thu Jun 16 12:11:05 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 16 Jun 2011 17:11:05 +0100
Subject: [Bio-Linux] New MrBayes-Multi uses OpenMPI
Message-ID: <1308240665.4584.8828.camel@barsukas>

Hi All,

At a suggestion from Tony Travis I've switched our MrBayes package from
using MPICH to OpenMPI.  This means that, after the update (version
3.1.2-4) you will no longer need to run mpd, but simply type:

mpirun.openmpi -np 4 mb-multi

Where "4" is the number of threads you actually want.  If you remove the
libmpich2-1.2 package then you'll just be able to type:

mpirun -np 4 mb-multi

As far as I know the decision as to which MPI implementation to use
before was essentially arbitrary, so I hope this won't cause a problem
for anyone, but let me know if it does.

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

-- 
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 Jun 16 12:23:42 2011
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 16 Jun 2011 17:23:42 +0100
Subject: [Bio-Linux] New MrBayes-Multi uses OpenMPI
In-Reply-To: <1308240665.4584.8828.camel@barsukas>
References: <1308240665.4584.8828.camel@barsukas>
Message-ID: <4DFA2E0E.3030508@abdn.ac.uk>

On 16/06/11 17:11, Tim Booth wrote:
> Hi All,
>
> At a suggestion from Tony Travis I've switched our MrBayes package from
> using MPICH to OpenMPI.  This means that, after the update (version
> 3.1.2-4) you will no longer need to run mpd, but simply type:
>
> mpirun.openmpi -np 4 mb-multi
>
> Where "4" is the number of threads you actually want.  If you remove the
> libmpich2-1.2 package then you'll just be able to type:
>
> mpirun -np 4 mb-multi
>
> As far as I know the decision as to which MPI implementation to use
> before was essentially arbitrary, so I hope this won't cause a problem
> for anyone, but let me know if it does.

Hi, Tim.

It might be a good idea to put a conflict with mpich2 into the control, 
because the MPI alternatives need to be set correctly to run OpenMPI 
versions if both MPICH2 and OpenMPI are installed. I've purged MPICH2 
from our Bio-Linux servers to avoid accidentally running the wrong 
version of "mpirun", "mpicc", etc.

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


From mashanovvlad at googlemail.com  Sat Jun 18 12:03:15 2011
From: mashanovvlad at googlemail.com (vladimir mashanov)
Date: Sat, 18 Jun 2011 12:03:15 -0400
Subject: [Bio-Linux] update bug
Message-ID: <BANLkTik=60q-YBQWuvZ5eXGD3RQwWCU_6Q@mail.gmail.com>

I noted yesterday, that I could not update the packages in my system.
The update manager gives me the following error:

E: Problem parsing dependency Depends
E: Error occurred while processing bio-linux-mira-3rd-party (NewVersion1)
E: Problem with MergeList
/var/lib/apt/lists/nebc.nerc.ac.uk_bio-linux_dists_unstable_bio-linux_binary-amd64_Packages
E: The package lists or status file could not be parsed or opened.
E: _cache->open() failed, please report.

I tried to remove the file
/var/lib/apt/lists/nebc.nerc.ac.uk_bio-linux_dists_unstable_bio-linux_binary-amd64_Packages,
but it did not help.

I would highly appreciate if someone could comment on this issue.

Thanks
Vladimir.


-- 
Vladimir Mashanov, PhD
Universidad de Puerto Rico
Faculdad de Ciencias Naturales
Departamento de Biologia
JGD Building, #220
PO Box 70377, UPR Station
Rio Piedras, PR 00936-8377
email: mashanovvlad at googlemail.com;
vladimir.mashanov at uprrp.edu


From mashanovvlad at googlemail.com  Sat Jun 18 12:25:23 2011
From: mashanovvlad at googlemail.com (vladimir mashanov)
Date: Sat, 18 Jun 2011 12:25:23 -0400
Subject: [Bio-Linux] update bug continued
Message-ID: <BANLkTinOrbmKeaszD+h7a7S9R+QzWzg9XQ@mail.gmail.com>

The problem is gone if I remove http://nebc.nerc.ac.uk/ bio-linux/
unstable bio-linux from my Software sources, but I would like to be
able to re-activate it as soon as the issue is resolved.

Thanks
Vladimir.


On 18 June 2011 12:03, vladimir mashanov <mashanovvlad at googlemail.com> wrote:
> I noted yesterday, that I could not update the packages in my system.
> The update manager gives me the following error:
>
> E: Problem parsing dependency Depends
> E: Error occurred while processing bio-linux-mira-3rd-party (NewVersion1)
> E: Problem with MergeList
> /var/lib/apt/lists/nebc.nerc.ac.uk_bio-linux_dists_unstable_bio-linux_binary-amd64_Packages
> E: The package lists or status file could not be parsed or opened.
> E: _cache->open() failed, please report.
>
> I tried to remove the file
> /var/lib/apt/lists/nebc.nerc.ac.uk_bio-linux_dists_unstable_bio-linux_binary-amd64_Packages,
> but it did not help.
>
> I would highly appreciate if someone could comment on this issue.
>
> Thanks
> Vladimir.
>
>
> --
> Vladimir Mashanov, PhD
> Universidad de Puerto Rico
> Faculdad de Ciencias Naturales
> Departamento de Biologia
> JGD Building, #220
> PO Box 70377, UPR Station
> Rio Piedras, PR 00936-8377
> email: mashanovvlad at googlemail.com;
> vladimir.mashanov at uprrp.edu
>



-- 
Vladimir Mashanov, PhD
Universidad de Puerto Rico
Faculdad de Ciencias Naturales
Departamento de Biologia
JGD Building, #220
PO Box 70377, UPR Station
Rio Piedras, PR 00936-8377
email: mashanovvlad at googlemail.com;
vladimir.mashanov at uprrp.edu


From tbooth at ceh.ac.uk  Thu Jun 30 06:06:02 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 30 Jun 2011 11:06:02 +0100
Subject: [Bio-Linux] Kegg now charging for FTP downloads
Message-ID: <1309428362.3690.4921.camel@barsukas>

Hi All,

This news may be of direct relevance to some Bio-Linux users, so I
thought I would draw your attention to it.  The announcement was made
over a month ago but I only just saw it this morning (thanks to Bela
from CLC Bio).

http://www.genome.jp/kegg/docs/plea.html

The executive summary is that due to loss of funding, the team that
produce the KEGG set of databases are no longer going to allow free FTP
downloads for academic groups (as of today).  On-line browsing and
searching of the databases will remain free.

I suspect that anyone who already downloads directly from KEGG will have
seen the message, but I wonder if this is going to have any impact on
other applications or websites that use the KEGG data.  I've not heard
any news to that effect myself, though - has anyone else?

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

-- 
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 Simon.Wagstaff at liverpool.ac.uk  Thu Jun 30 06:15:02 2011
From: Simon.Wagstaff at liverpool.ac.uk (Wagstaff, Simon)
Date: Thu, 30 Jun 2011 11:15:02 +0100
Subject: [Bio-Linux] Kegg now charging for FTP downloads
In-Reply-To: <1309428362.3690.4921.camel@barsukas>
References: <1309428362.3690.4921.camel@barsukas>
Message-ID: <DC62E1323AF0C24A99A7A3FE6019CD4D634D73C43A@STAFFMBX1.livad.liv.ac.uk>

Hi Tim,
Thanks for the email - I wasn't aware of this and I suspect many others that use pathway software will also be unaware. Much of the interaction of network modelling software with KEGG and other databases is via automated scripting - users (like me) will only know about this as scripts stop interacting with the KEGG database. This combined with the location change of the data presents is likely to lead to some painful debugging.

Thanks for the info,

Cheers,

Simon

-----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 June 2011 11:06
To: bio-linux at nebclists.nerc.ac.uk
Subject: [Bio-Linux] Kegg now charging for FTP downloads

Hi All,

This news may be of direct relevance to some Bio-Linux users, so I
thought I would draw your attention to it.  The announcement was made
over a month ago but I only just saw it this morning (thanks to Bela
from CLC Bio).

http://www.genome.jp/kegg/docs/plea.html

The executive summary is that due to loss of funding, the team that
produce the KEGG set of databases are no longer going to allow free FTP
downloads for academic groups (as of today).  On-line browsing and
searching of the databases will remain free.

I suspect that anyone who already downloads directly from KEGG will have
seen the message, but I wonder if this is going to have any impact on
other applications or websites that use the KEGG data.  I've not heard
any news to that effect myself, though - has anyone else?

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

-- 
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.

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