[Bio-Linux] Bio-Linux updated image and new packages

[Tim Booth]

Hi Andy,

Yes, abyss is compiled with default K-mer size 64, as this can only be
changed by recompilation of the binaries.  A quick look at the code
suggests that setting it to 96 would take a bit more memory for all jobs
while setting it over 96 will cause the software to handle memory
allocation in a completely different way (presumably resulting in a
significantly larger memory footprint and/or slowdown).  If you or other
people on this list think that I should change the default in the
package then let me know.

With Velvet, I was able to make a package that contained extra versions
of the executable compiled for different K-mer lengths but with the way
ABYSS is set up (30 separate compiled executables and various scripts)
this is not so easy.

You can get the source quickly by doing:

apt-get source abyss

Then you can either recompile as per the usual instructions or look in
debian/README.Debian for hints on how to recompile the DEB package with
a different configuration.

Thanks for the info on people who are using Bio-Linux.  I've just come
back from Berlin where a talk I gave seemed to go down pretty well and
at least two people want to start using it for their own teaching, which
is pretty cool.

Cheers,

TIM

On Mon, 2013-07-22 at 17:11 +0100, Andrew Millard wrote:
> Hi Tim,
> 
> Just a quick question on these updates. Is the abyss package complied as 
> it would be if downloaded directly from the source so a default kmer 
> size of 64 ? If so am correct in thinking to change this, the source 
> would have be downloaded and recompiled to increase the kmer size as 
> there will be no config file in the package ?
> 
> I am only asking, rather than testing myself as I am in the middle of 
> racking our new server that I will be installing biolinux on so dont 
> have anything to test it on
> 
> 
> 
> Hope you are well
> 
> cheers
> andy
> 
> 
> P.S I sent 2 visitors that I had spent a  week learning bio-informatics 
> with me back to Germany with bio-linux USBs. They were most impressed 
> with the ease of use and are keen to use in there own research groups.  
> The Division I am now part of in the Medical School, all PhD students 
> and PDRAs are using bio-linux ( ~20 people) . I know having info like 
> this helps with justification of bio-linux etc , so thought I would 
> mention it
> 
>