[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)

[Andreas Tille]

Hi Charles,

On Wed, Aug 14, 2013 at 01:34:47PM +0900, Charles Plessy wrote:
> 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.

Thanks for the test - I might try downloading the file and test it.
 
> 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.

OK, good to know - may be I might get it fixed.  At least it seems that
I should not upload the new version before it is fixed.

> 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.

Later I had the idea that if you had an old clone of the repository before I did
my dirty work you might push this to a freshly initialised repository on alioth.
Just do *not* git clone my stuff!!!  This way we might have some chance.

Many thanks for your comments and greetings from Le Camp after a great daytrip

    Andreas.

PS: Alioth admin is not here.

-- 
http://fam-tille.de