Re: Is bcbio good to go?
Hi Nilesh,
On 02.12.20 21:58, Nilesh Patra wrote:
> Is there any update on the status of bcbio?
>From some intial 4 it is now 9 tests that pass - of >80 and a manually
installed GATK.
> I do not see any missing remarks in the spreadsheet, but I admittedly
> do not know a way to parse the columns properly (specifically what do
> the colors mean?)
"green" - all fine
"yellow" - somehow stuck on salsa
"red" - nobody worked on this, yet
"blue" - we should not care
>
> If not, would you have a list of stuff left to be done?
>From a pre-spreadsheet time
https://salsa.debian.org/med-team/bcbio/-/blob/master/debian/TODO
It is not a complete catastrophe to tell our users to please install the
GATK themselves. Pyomo and adamjava (for qsignature) I think are the
next ones to go for. I had started with adamjava and ran into what
looked like circular dependencies in the subprojects of adamjava. Pyomo
is almost there, was in the archive before, we should have one of the
solvers in the distro that it wraps so we can help the testing a bit.
Thank you!
Best,
Steffen
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