Hi again,
The problem with the analysis results happens when using the web-start
version, but not the standalone local version -- see my email from a few
minutes ago for the details on my setup.
When I select one annotation, right click and select "analyze region" on
the standalone version, it works perfectly (at least for the NCBI-BLAST
analysis, which is all I've tried so far).
When I do the same using the web-start one, some problems occur:
- first, the range is wrong in the genomic region start an end fields,
it seems to get only the stop codon coordinates (e.g. 33347 to 33349,
instead of the correct 33347 and 36331).
Obnoxious, but not show stopping -- the users can always correct that
manually if I warn them beforehand of the problem. But unfortunately it
does not stop there.
After correcting the coordinates, I click on run, and Apollo tells me it
will take about X seconds to finish.
A while later, it give the following error message:
"Error running analysis: Relative URI "NCBI_BlastOutput.dtd"; can not be
resolved without a base URI"
The results do not get added to the analysis panel, I'm assuming they
don't even get parsed...
It appears to me that the file in question is sent by NCBI to Apollo, is
that right? I have used grep and find on all the Apollo directories I
could think of, and found nothing that seemed obvious to me.
Any idea how to solve this? Did I do anything wrong when I created my
web-start instance? To compile Apollo for the web-start, all I did was
copy my edited chado-adapter.xml, .style, and .tiers files to the conf
directory in the source Apollo distribution, and then run "ant jar" from
src/java. Did I miss anything?
Thanks
J
--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897
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