Re: PIQUE packaging (Was: request for r-cran packages) [correction]
On Mon, Jul 20, 2020 at 11:33:18AM +0100, Tony Travis wrote:
> On 20/07/2020 10:46, Tony Travis wrote:
> > [...]
> > 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.
>
> Hi, Andreas.
>
> Please replace "emmax-input" and "emmax-run" with "pique-input" and
> "pique-run".
OK, just ITPed package. BTW, I was running make in the tests dir and
it ends with:
Analysis finished: Mon Jul 20 13:56:47 2020
Create sativas_GWAS.covar file...
smartpca -p sativas_GWAS.par > sativas_GWAS-smartpca.log
OOPS -i flag not specified at /usr/bin/smartpca line 21.
pique: error - Can't read sativas_GWAS.evec
make: *** [Makefile:29: input] Fehler 255
Kind regards
Andreas.
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http://fam-tille.de
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