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

Iftekharul Haque iftekharul.haque at gmail.com
Sat Apr 24 05:25:42 EDT 2010

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"?

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)

Looks like ecoli.nt is no longer on the NCBI ftp server. This can be
adjusted to point to another file, and then the tests adjusted to
expect the correct results, but this bug would have to be reopened
when that other file disappears as well, which is conceivable.

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.


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