[Bioperl-l] Bug # 2908: ecoli.nt not available

Dave Messina David.Messina at sbc.su.se
Sun Apr 25 05:27:39 EDT 2010

On Apr 24, 2010, at 11:25 AM, Iftekharul Haque wrote:

> Hi All,
> Thinking I'll start small, just to get the hang of how this works.
> First, an administrative question: most of the discussions on the bug
> tracker look very brief and to the point. I imagine all initial
> discussion first happens on the mailing list, and then comments are
> put on the tracker, to reduce "noise"?

I don't think there's a hard and fast rule on this. Often discussion starts on the list because that's where the bug is first reported.

In my opinion all of the critical information relevant to the bug should be on the bug report, and often some of that info is simply a link to the relevant mailing list thread.

> Second: I've looked at bug # 2908
> http://bugzilla.open-bio.org/show_bug.cgi?id=2908 (ecoli.nt not
> available from ftp://ncbi.nlm.nih.gov, causes
> t/Tools/Run/StandaloneBlast.t to fail)
> Wondering aloud here: would it make sense to include a compressed
> reference file to test against rather than depend on a changing
> source? Then this problem could be solved once and for all.


Actually, we could make the database ourselves and have it contain only a handful of sequences. From my reading of the testfile, there's no need to use a downloaded database to test against here.


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