Re: canu

[Andreas Tille <tille@debian.org>]

Am Wed, Nov 01, 2023 at 10:02:24AM +0000 schrieb Tony Travis:
> I didn't say that you gave advice "to use bioconda": I said that I had
> followed your advice 'about installing "canu" under "bioconda3"'.
> 
> I needed to fix the problem we encountered with "canu" installed from the
> Debian-Med package quickly and adopted a pragmatic solution. This is what I
> read in your notes about packaging "canu" for Debian-Med:
> 
> > Installing with a 'package manager' is not encouraged, but if you have no other choice:
> > 
> > Conda: conda install -c conda-forge -c bioconda -c defaults canu
> > 
> > Homebrew: brew install brewsci/bio/canu

I keep on insisting that these are *not* my notes.  Its Upstream
README.md what you are quoting.  I'm pretty sure I will not write such
advise since I'm literally uneducated about conda and have no idea about
such command lines.
 
> At the time, I believed that had no other choice...
> 
> > > However, I would be interested to know if you have any plans to package it
> > > again for Debian-Med?
> > 
> > Canu is and remains packaged for Debian Med.  Since you are using Ubuntu
> > which derives from Unstable you will not even miss it even if the package
> > might be removed from testing (which the bug you read is about).
> > 
> > In short: Please be more verbose about your problem.
> 
> Upon further investigation, it seems that the problems were caused by a
> broken "Slurm" instance on the system in question due to an upgrade (the
> saved state of the job queue was inconsistent with the new version of
> "Slurm"). I didn't know that "canu" automatically detects the presence of a
> job scheduler and will try to use it by default.

In any case I'd recommend to add command line and output to give some
context for your readers.
 
> I keep forgetting that this is a Debian forum and you prefer me to send bug
> reports to the Ubuntu Bug-Tracker. I will refrain from posting about
> Debian-Med issues that I encounter under Ubuntu here in future.

Please understand me correctly:  I'd love to help you - but you need to
provide context.  Writing something in the sense of "canu is broken
under Debian thus I had to use conda" is neither sufficient information
to help you nor helpful for our project.
 
Our bug tracker gathers some context (installed packages) and asks you
for details which is helpful.  If you can't use `reportbug` for whatever
reason using this mailing list is a fallback we like to provide since
Debian Med people like to care about their users. 

BTW, should we take the message that it makes sense to suggest
slurm-client for canu from your observation?

Kind regards
   Andreas.

-- 
http://fam-tille.de