[Bio-linux-dev] HMMER version on Biolinux

[Tim Booth]

Hi Noel,

I think your question belongs on Bio-Linux-Dev so I'm copying that list
in on this reply.

I think HMMER has not been updated simply because I've not got around to
it.  The easiest thing for me to do in this case would be to copy
the .deb file from the latest Ubuntu version onto our package server.
Sometimes this approach works, sometimes not.

Since you have an immediate need for the software, could you please try
installing the package manually and let me know if it works?  If it
does, I'll put it on the server so everyone gets the upgrade.

To install manually:

Download the file:
http://mirrors.us.kernel.org/ubuntu/pool/universe/h/hmmer/hmmer_3.0-3_amd64.deb

Install it:
sudo dpkg -i hmmer_3.0-3_amd64.deb

If there are any dependency issues reported:
sudo apt-get -f install

Cheers,

TIM

On Thu, 2012-03-08 at 11:38 +0000, Noel Magnin wrote:
> Hi Tim
> 
> I think my question does not really belong to either list  
> (Biolinux-users or Biolinux-dev) so I decided to send you this mail  
> directly, sorry for this direct contact.
> The HMMER version installed on Biolinux appears to be 2.3.2 (2003) and  
> several programs (ex : Metaxa) require version 3 (2010).
> Upon checking under "Ubuntu soft center", I saw on the image "version 3.0".
> Is the update to 3.0 planned or is there some manual update to perform ?
> Thanks in advance for any hint about it
> Sincerely
> Noel
> 

-- 
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.