Re: PIQUE packaging (Was: request for r-cran packages)

[Tony Travis <tony.travis@minke-informatics.co.uk>]

On 03/07/2019 09:18, Tony Travis wrote:
> On 02/07/2019 15:08, Andreas Tille wrote:
> > Hi Tony,
> >
> > On Wed, Mar 20, 2019 at 04:15:11PM +0100, Tony Travis wrote:
> > > >     2. Is there any description of PIQUE that could be used as long
> > > >        description for the package.  I've checked doc/pique_manual.odt
> > > >        but despite its filename it says it is the ParSNP manual
> > > >        (btw, parsnp is packaged) and doc/pique_tutorial.odt does
> > > >        also not contain anything that would enlighten me about PIQUE
> > > >        at first sight.
> > > >        Feel free to simply replace the FIXME in
> > > >         
> > > > https://salsa.debian.org/med-team/pique/blob/master/debian/control
> > >
> > > Yes, I'll sort that out: We called it "ParSNP" at first, but I 
> > > subsequently
> > > discovered that someone has already used that name!
> >
> > I've stumbled upon old mails.  Emmax is in new queue since some time but
> > final PIQUE packaging is just blocked due to missing long description.
>
> Hi, Andreas.
>
> OK, I'll sort that out.

Hi, Andreas.

Sorry, I really must apologise for taking so long to do this:

PIQUE is a software pipeline for performing genome wide association 
studies (GWAS). The main function of PIQUE is to provide ‘convenience’ 
wrappers that allow users to perform GWAS using the popular program 
EMMAX (Kang et al., 2010) without the need to be familiar with all of 
the software tools used to generate the required EMMAX input files. 
PIQUE will also perform a number of of quality control steps prior to 
running EMMAX, ensuring that the various input data files are in the 
correct format. PIQUE proceeds in two main stages although there are 
multiple entry and exit points from which the pipeline can be run. The 
first stage consists of running the “emmax-input” program, which can 
read genotype and phenotype information in several different formats and 
generates all the necessary input files required to run EMMAX. The 
second step in the pipeline uses the “emmax-run” program to actually run 
EMMAX using the files generated by “emmax-input” (or pre-existing 
user-supplied input files) to perform the GWAS and output the analysis 
summary files.

I'll update my PIQUE GitHub repository with the new documents ASAP:

> https://github.com/tony-travis/PIQUE.git

Thanks again,

  Tony.

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