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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