Hi Ivan,
I can provide an explanation about the first part at least. You are seeing
that "##failed" message due to a bug in Galaxy core code that I've previously
raised on this list. The path you see there is where the .pheno file should
(and does) end up after the tool is done. However, the code that generates the
"##failed" message is getting called before the .pheno file has been moved to
that path from its temporary location. Hence, it can't be found there at that
point in execution time.
While requiring a workaround is not ideal, a very simple one does exist. In
the history item for your uploaded dataset, click on the pencil ("Edit
attributes") and then click the button that says "Auto-detect".
Best,
Eric
________________________________________
From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
on behalf of Ivan Merelli [ivan.mere...@itb.cnr.it]
Sent: Wednesday, November 09, 2011 7:12 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] microarray & NGS
Hi Galaxy Users,
I'm interested in integrating microarray and NGS data.
My problem concerns the uploading of an affybatch object
in Galaxy (I have a local instance of galaxy, but exacly
the same problem is present in http://main.g2.bx.psu.edu)
After processing the upload, the only message in the
green output data box of the history is something like:
##failed to find
/galaxy/main_database/files/003/251/dataset_3251699_files/rexpression.pheno
Can you help me in understanding what's wrong?
In particular the data which I'm trying to upload are
created with rexpression (incidentally, is it still
supported or novel versions are attended?), because
this package gives my some problems and I'm trying
to upload manually some results (which seems ok on
the disk) to see what is happening.
Cheers,
Ivan
P.s.
Maybe some other packages exists to deal with microarray
data in Galaxy? e.g. retrieving data from GEO/ArrayExpress,
normalizing them, show in a matrix differential expressed
genes to join/confront them with novel NGS experiment...
I know it's a lot of stuff..
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