[Debian-med-packaging] Bug#824402: #824402: sra-toolkit bug

[Andreas Tille]

Hi Jana,

On Tue, Sep 06, 2016 at 08:02:25AM +0200, Jana Kisková wrote:
> 
> many thanks for effort, but unfortunately, new version doesn't work well,
> because of another error:

Thanks to you for testing and reporting.  That's really valuable.
 
> $ latf-load -q PHRED_33 -o Desktop/test Desktop/test.fastq
> 2016-09-06T04:55:40 latf-load.2.7 warn: Deprecated argument '-q' may not be
> supported in future releases. Please use '--quality' instead.
> 2016-09-06T04:55:40 latf-load.2.7 err:
> libs/kdb/wdatabase.c:391:KDBManagerVCreateDBInt: path incorrect while
> creating manager within database module - accession="test" errors="0"
> status="failure"
> 2016-09-06T04:55:40 latf-load.2.7 err:
> libs/kdb/wdatabase.c:391:KDBManagerVCreateDBInt: path incorrect while
> creating manager within database module - load failed
> 
> I tried this on the two types of installation:
> - stable Debian upgraded to testing and then to unstable;
> - stable debian with just sra-toolkit (and deps) from the unstable
> installed.
> Result is the same.

I would definitely expect the same result.  Could you please check that
you are not affected by a non-standard confrom fasta file as it turned
out to be the case in the issue I reported to Github:

    https://github.com/ncbi/sra-tools/issues/40

> Maybe the problem is that there is sra-toolkit ver. 2.7.0-1 in unstable
> (only amd64), but there is just sra-toolkit-libs0 ver. 2.3.5-2+dfsg-1 (only
> i386) - when I tried to install sra-toolkit, it doesn't install
> sra-toolkit-libs0 as dependency.

This is wrong.  The package sra-toolkit-libs0 does not exist any more
for version 2.7.0-1.  The command to install would be something like

   sudo apt-get install -t unstable sra-toolkit

and it is not available for i386 - upstream explicitly stopped supporting
32 bit architectures.  See

   https://github.com/ncbi/ncbi-vdb/issues/8

> I can install older version manually, but
> the result is the same. I am sure that original bug is OK know, but this
> should be finalized properly - should I report another bug?

Its fine to open another bug.  Please make sure you attach the fastq
file in question.  Alternatively / in addition you could open an issue
in the sra-sdk bug tracker.  This would save me some time since I would
need to do this anyway.

Kind regards

      Andreas.

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