On 26/05/2021 16:41, Tony Travis wrote:
[...]
I will also be giving due credit to Debian-Med for packaging all the
software I'm now using as "Bio-Linux" = Ubuntu-MATE 20.04 + med-bio.
Hi, Debian-Med Team.
I gave due credit for your hard work packaging bioinformatics software
today in my talk
On 23/07/2020 22:31, Tony Travis wrote:
[...]
I just want to make sure you will not create the false impression to
naive users that installing med-* is needed to just run pique (which
meanwhile was accepted in unstable).
I am encouraging former Bio-Linux 8.0.8 users to upgrade to Ubuntu-MATE
On 23/07/2020 13:37, Andreas Tille wrote:
[...]
The "pique-input" script should be running /usr/lib/eigensoft/smartpca, not
/usr/bin/smartpca and my version does:
I'll check this. However, in principle I do not consider it the best
idea to use some program that is private to eigensoft and ign
Hi Tony,
On Thu, Jul 23, 2020 at 11:41:40AM +0100, Tony Travis wrote:
> On 23/07/2020 07:56, Andreas Tille wrote:
> > > > 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.
> > > > piqu
On 23/07/2020 07:56, Andreas Tille wrote:
Hi Tony,
On Wed, Jul 22, 2020 at 11:46:03PM +0100, Tony Travis wrote:
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
Hi Tony,
On Wed, Jul 22, 2020 at 11:46:03PM +0100, Tony Travis wrote:
> > 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: erro
On 20/07/2020 13:03, Andreas Tille wrote:
[...]
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
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 perfor
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 nee
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