[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: SPAdes for Debian

Sorry for this email but I have unsuscribed my email address from this list many times following the recommended way and nothing happened. Andreas please could you assist to me in thr unsuscription protocol? Or delete my email address from this list. Thank you.

Sent using CloudMagic

On mié, abr 02, 2014 at 6:45 AM, Anton Korobeynikov <anton@korobeynikov.info> wrote:


>> 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

To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
Archive: https://lists.debian.org/[🔎] CA+Ov9+=qCbj4sDxdGZB4OiYoQupaWx1=RchkdM1gcNLR=HXLmQ@mail.gmail.com

Reply to: