Re: PIQUE packaging (Was: request for r-cran packages) [correction]
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 ignore the
available user interface in /usr/bin.
Hi, Andreas.
The EIGENSOFT "smartpca.perl" wrapper creates a parameter file for input
to "/usr/lib/eigensoft/smartpca" in a similar way that I did using a
subroutine in my "pique-input" script. However, I've changed my script
to use the public wrapper "/usr/bin/smartpca" as you suggest.
[...]
For Debian we usually trust *released* version (if available) so
if you would please tag what should be packaged I could package
your tagged release.
OK, I want to make some further changes before tagging a new release but
I've already pushed my changes to: https://github.com/tony-travis/PIQUE
[...]
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
20.04 LTS and install "med-bio" and "med-bio-dev", but not just to run
PIQUE :-)
[...]
It's not possible to test PIQUE without a data-set large enough to use for
GWAS, which is why I use "wget" to download one and avoid storing large blob
in the GitHub repo. The data-sets we normally use contain millions of SNPS,
but this small data-set is what we used during the development of PIQUE and
what we use when teaching how to use it.
Not sure if that helps?
The information itself helps. As far as I know its permitted in autopkgtest
to download data - so if we know there is no better way than we can try
this.
Thanks,
Tony.
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