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

Chris Fields cjfields at illinois.edu
Sun Apr 25 09:47:09 EDT 2010

On Apr 25, 2010, at 4:27 AM, Dave Messina wrote:

> 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.

Yes, and bug reports should be something 'closable'.  This (to me) means short and to the point.  Bug reports with a number of issues that need to be addressed should be broken into several reports, primarily b/c we can close each issue out as they are fixed, and if the bug needs to be reopened it doesn't require reopening a report containing other extraneous fixed bugs.

>> 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)
> [snip]
>> 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.
> Agreed.
> 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.
> Dave

How does this work cross-platform, cross-OS, 32 vs 64 bit, new vs old BLAST versions, etc?  That's my only concern with using a single database.

I don't think there is an issue, just can't recall.


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