[Debian-med-packaging] Please test sra-toolkit (Was: sra-sdk git repository totally screwed up - I start from scratch and leave sra-sdk_.git for some time if somebody really cares about the history)

[Charles Plessy]

Le Tue, Aug 13, 2013 at 09:30:43PM +0200, Andreas Tille a écrit :
> 
> I realised that updating sra-sdk is way more work than expected but I
> got some testable state into the new Git repository.  I wonder whether
> anybody could give it a try to make sure I will only have broken the
> repository and not even messed up with the whole package.  It needs to
> be a severy cleaning up of lintian issues and I might do this the day
> after tomorrow but if somebody meanwhile could do some testing that
> would be welcome.

Hi Andreas,

I tested it with the following commands:

    wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP%2FSRP010%2FSRP010815/SRR407172/SRR407172.sra
    fastq-dump SRR407172.sra 

fastq-dump crashed quickly, while with the current version in Debian, it outputs
FASTQ reads in a file called SRR407172.fastq.

Sorry that this test is very inconvenient as the file is 4 Gb, but that was the
only example I could find quickly.  There must be other SRA files that are smaller,
but SRR407172.fastq is the one for which I was sure that I succeeded before.

For the Git repository, I do not know if I can find time in the short term to
repare it.  I think that you made the right choice to continue the work even if
it means to lose history.

Cheers,

-- 
Charles