[GenABEL-dev] Introducing OmicABELnoMM

[L.C. Karssen]

Dear list,

Here's an update on my first steps with OmicABELnoMM after uploading it
to SVN:

1) I spent some time getting several files into better compliance with
our coding style guide.

2) I started implementing autoconf/automake. This is hampered by 3).

3) I tried using the openblas package that comes with Debian/Ubuntu, but
that doesn't seem to work. After digging a lot, I now think this is
because the Debian package is not compiled with the USE_OPENMP=1 flag
(which is needed according to Alvaro's instructions).
I'm going to investigate two ways to solve this:
- rebuild the Debian package with openMP support. If that helps I have a
stronger case to try and change the Debian package
- Include a copy of openblas 2.8.2 into the OmicABELnoMM package. I've
already verified that that works (basically following Alvaro's
instructions), but from a design point of view I don't like really it.
It would clutter SVN with components we're not interested in
maintaining. An alternative may be to have a
'download-and-compile-openblas' script.
Let me know if you have any suggestions or comments.

4) I've added OmicABELnoMM to Jenkins. It doesn't look good yet, given
that all the builds so far failed, but that will only improve in the
future :-)


Best,

Lennart.


On 16-12-13 15:05, L.C. Karssen wrote:
> Dear list,
> 
> As you may have noticed, I have committed a first version of
> OmicABELnoMM to SVN on R-forge this morning.
> OmicABELnoMM is the no-mixed-models version of OmicABEL, allowing rapid
> genome-wide association analysis (linear regression), especially for
> multiple traits ("omics" data).
> OmicABELnoMM was written from scratch by Alvaro Jesus Frank so that the
> algorithm is well tailored to the different mathematics. Alvaro works in
> the same team at RWTH Aachen as Diego Fabregat Traver of OmicABEL fame,
> under the supervision of Paolo Bientinesi, Yurii Aulchenko and,
> recently, myself.
> 
> Please note that OmicABELnoMM is still under development (thanks Yakov
> and Sodbo for your contributions!). Most notably, work is still being
> done on the exact output file format. At present the output is stored in
> a filevector-format file. This will probably remain the same, but the
> order in which the information (betas, standard errors) is stored may
> change.
> 
> These are the development plans we have for OmicABELnoMM in the near future:
> - Implement autotools configuration
> - Improve the output file format
> - Add documentation
> 
> 
> Best regards,
> 
> Lennart.
> 
> 
> 
> 
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 

-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-

-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 230 bytes
Desc: OpenPGP digital signature
URL: <http://lists.r-forge.r-project.org/pipermail/genabel-devel/attachments/20131218/ce58d9c7/attachment.sig>