Hi Eric,
sharing code for me is ok, so I can test it on my local instance
of galaxy. Let me know if I can help in debugging or so on.
As concerning rexpression, I think is a good package, although
some bugs (which I can summurize if useful, some of them were
easy to solve) and features can be improved (such as for example
the possibility to have exprSet in the history to work on differential
expressed genes and eventually join this information with NGS data)
Let me know how I can help...
Best
Ivan
Hi Ivan,
At the moment, my work is probably closer to "something new", but as I flesh it
out and if I add more tools, it could start coming back toward rexpression development.
I'd be glad to let you now when it is ready for testing, but can't promise exactly when
that will be. Also, I'd only be able to give you code, not access to a test server, as
our Galaxy instance is strictly internal. I do intend to try contributing anything that
will be generally useful back to galaxy-central though.
Best,
Eric
________________________________________
From: Ivan Merelli [ivan.mere...@itb.cnr.it]
Sent: Saturday, November 19, 2011 10:40 AM
To: Paniagua, Eric
Cc: ross.laza...@gmail.com; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] microarray& NGS
Hi Eric,
I'm using a local instance of galaxy, but I found an error also
in the main public server (no debug, I suppose the same error).
When I try do download the pheno file I recieve this error:
AttributeError: 'module' object has no attribute 'relpath'
Generally, I'm very interested in using galaxy for
microarray analysis (for this reason I was checking
the capability of rexpression) and if I can get
involved someway in the development of this part
(Eric, I did not understand if you are working on
something new or if you are reviewing rexpression)
I can help in testing/debug or giving suggestions
(maybe also in developing, but I'm quite new of galaxy).
Best,
I.
Hi Ivan,
That is correct, two files are uploaded. Both are stored in Galaxy's database (the
filesystem part "database/files", not the relational part), and many subsequent
operations on an affybatch or eset dataset will access the .affybatch or .eset file
directly. Lines from the .pheno file are simply what those datatypes make the history
item use for displaying info.
Having a single history item for both is normal for these datatypes. This is
because the affybatch and eset datatypes are *composite* datatypes representing
more than one file. This provides a mechanism for passing around a collection
of related files as a single unit. The details and the implementation of
composite datasets are a bit rough around the edges, but that's the concept.
For instance, try downloading one of the affybatch or eset objects you've
uploaded, by using the save button (ie the image of a tiny floppy disk in the
history item). I'd be interested to know what happens for you (are you running
a local instance or using the main public server?) and very interested to know
if it works; it fails for me, but I've only had time so far to partially debug
it.
Best,
Eric
________________________________________
From: Ivan Merelli [ivan.mere...@itb.cnr.it]
Sent: Friday, November 18, 2011 10:33 AM
To: Paniagua, Eric
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] microarray& NGS
Dear Eric, thank you for your answer.
Your workaround works for the pheno file.
A related question is: the affybatch and the
eset file formats require to upload two files
(rispectively the pheno and the eset/affybatch).
Is it normal to have finally only
the pheno one in the History?
I.
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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