Re: [Solexatools-users] solexatools

[Brian O'C. <boc...@uc...>]

Hi Robert & Nick,

Sorry to take so long to get back to you on this.  Things have been 
crazy in lab since your visit.  It was really nice meeting with you and 
I'm glad we got a chance to talk.  The SolexaLIMS web app is the best 
thing to start with since it's fairly self-contained and should be 
pretty easy to install.  In the solexa-lims directory, you'll find a 
.war file (under dist directory).  That's a pre-compiled version of the 
site.  You should be able to deploy it following the directions in the 
README.  This will let you track your samples being run on the solexa 
machine.  The next step is to install the SolexaPipeline component which 
integrates with the SolexaLIMS to display information about each of the 
pipeline steps being applied to the solexa datasets.  This project is 
much less mature and still contains some hard-coded assumptions about 
our setup in the Nelson lab.  The lab now has two developers working on 
this project to clean it up and get it ready for a 1.0 release.  I've 
cc'd them here along with the solexa-tools list where we post 
information about the project.  In the next couple weeks we're planning 
on doing a 1.0 release that should address the install issues.  If 
you're interested in hosting me I'm happy to come for a site visit to 
Yale and help you setup this pipeline after we do a release.  Just let 
me know.

Also, I wanted to follow up on our conversation about compressing the 
data. We really haven't had a chance to work on better compression for 
the images (or processed data).  If you're still interested in working 
on this I would love to help you out and send you the information on 
what we've tried so far.  I think we can get a 1:5 compression of the 
image data if we use the lzw compression algorithm from ImageMagick to 
create compressed tiff image files.  I just haven't had time to fully 
troubleshoot this and make sure the Solexa-provided pipeline produces 
the same results once the tiff files are compressed then decompressed.  
We also are thinking about converting text based sequence and intensity 
output from the solexa pipeline into more compact 2bit and NetCDF binary 
files respectively.  That's something we could explore together if 
you're interested and would make the exchange of large amounts of 
sequence data much more practical.

Hope that helps!!

--Brian

Robert Bjornson wrote:

> Hi Brian,
>
> I'm finally back at my desk in New Haven, and following up on my 
> discussion with you about the solexatools stuff.  Nick is very 
> interested in looking at your stuff, both the LIMS and the pipeline.  
> We poked around the sourceforge site, but didn't see any downloads, 
> just the source code repository.  From my recollection, I thought that 
> there was a package for the LIMS, but that the pipeline was a bit 
> harder to install.
>
> Can you help me point Nick in the most productive direction for 
> getting a look at both of these systems?  If giving him a login to 
> your copy of the pipeline is easiest, I think that would be fine 
> (he'll promise to be very careful and only make read access).
>
> Thanks,
>
> Rob