Re: canu

[Tony Travis <tony.travis@minke-informatics.co.uk>]

On 01/11/2023 06:28, Andreas Tille wrote:
> [...]
> > @Andreas, I've now removed the "canu" package and followed your advice about
> > installing "canu" under "bioconda3":
>
> I *never ever* gave any advise to use bioconda.
>   
> > > https://salsa.debian.org/med-team/canu

Hi, Andreas.

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

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.

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.

Bye,

  Tony.

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