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-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Ivan Merelli [ivan.merelli@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.. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/