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Re: SPAdes for Debian


>> What we'll certainly do - move the binaries besides spades.py into
>> /usr/share/spades/bin subdir.
> I guess you mean /usr/lib/spades/bin (since architecture dependant
> binaries belong to /usr/lib rather than /usr/share according to FHS

> It would be really great if you could provide such a suite which could
> be a simple script processing your test data youo are providing anyway
> and add a simple comparison mechanism to verify the result.  When I
> worked on the 3.0.0 package (which unfortunately is not finished yet ...
> exactly due to the reason that I stumbled upon some tests and wanted to
> do more comparisons) I realised that some output files are containing
> dates and time stamps and thus comparisons do not make any sense but
> other files need to match.  I guess it would be on one hand easy for you
> to define a valid test result and it would also be quite helpful for
> your users.
I believe that you need to run 3 cases:

1. spades.py --test
2. spades.py --iontorrent --test
3. dipspades.py --test

Probably you need only to look that it finishes w/o problems and the
final contigs file contains a single contig.

> In Debian we are maintaining libbam-dev (from samtools currently at
> version 0.1.19-1).
This looks like another package. I'm talking about
https://github.com/pezmaster31/bamtools (actually, we're using
IonTorrent fork which knows how to do multi-threaded processing).

> So if you would give me permission I would bounce this mail to the list
> and might do so in the future as well in case you might forget (you do
> not necessarily need to be subscribed but please ask for beeing CCed
> to receive direct answers to your mail).

With best regards, Anton Korobeynikov
Faculty of Mathematics and Mechanics, Saint Petersburg State University

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