Re: /usr/bin/picard Re: bcbio will need another while - needs gatk
Hi Steffen,
On Sun, Nov 15, 2020 at 02:39:03PM +0100, Steffen Möller wrote:
> >> I just checked what my installation has in this directory ... and it
> >> seems like I spotted a typo (or a creative fix of a typo elsewhere)
> > ?
> tranlate misses the "s"
Fixed in new upload. BTW, it would be perfectly fine if you simply
fix such things in a team upload.
> >> I presume you would be happy for me to put there a link from cnvkit.py
> >> (like bcbio expects it) to /usr/bin/cnvkit, right?
> > Well, I think its orthogonal to my own happyness. If it works for
> > you just do the same as in the given example package.
> I added that symlink and then patched bcbio to not expect the .py since
> bcbio ignored the $PATH on this one.
Fine for me. Regarding the .py extension I became quite relaxed. See
our package template:
https://salsa.debian.org/med-team/community/package_template/-/blob/master/debian/lintian-overrides
> > I think we are pretty close to snpEff due to Pierre's efforts.
>
> Nice!
>
> This may be worth a sidenote - bcbio to me is something metaphorical. We
> have it in the distribution already. And now we work to get all the
> runtime-dependencies in to make it functional. And snpEff is pretty high
> up (it interprets the importance of nucleotide variations, you need to
> have identified these variants for that, first). So, my comment on
> "snpeff" being invoked was to be interpreted as "see, here we are already".
Snpeff is wanted from several sided. I really hope we get it soon.
Kind regards
Andreas.
--
http://fam-tille.de
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