I saw this same problem with our upload1 set to run on the cluster (it had worked properly a few months prior). I found out that the cluster sysadmins had set the nodes for local access only (no web access), direct file uploads and FTP to local disk worked but URL-based uploads did not. The job indicated success, however the file was empty. Interestingly the 'info' box had the error: Unable to fetch ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Agrobacterium_tumefaciens_C58_uid57865/NC_003063.fna [Errno ftp error] [Errno 113] No route to host Switching it back to the local job runner fixed it. chris On Aug 31, 2012, at 9:27 AM, Nate Coraor <nate@bx.psu.edu> wrote:
On Aug 31, 2012, at 8:33 AM, Geert Vandeweyer wrote:
Hi Nate,
The datafile is really empty on the disk (size 0, checked at the "full path" etnry from the dataset info).
Best regards,
Geert Vandeweyer
Although it should generate an error rather than an empty file, can you ensure that new_file_path in Galaxy's config is pointed at a filesystem that is shared between the cluster and the Galaxy server? If it is, you may need to add some debugging to the upload tool to figure out exactly where the problem is.
--nate
On 08/29/2012 06:05 PM, Nate Coraor wrote:
On Jul 16, 2012, at 6:14 AM, Geert Vandeweyer wrote:
Hi,
We have set up a local instance of galaxy-dist, using pbs-python to communicate with our HPC. Everything is working great, except for the upload functionality.
When I assign the upload1 to local:/// , uploading of small files through the web-site works, and upload of large files by ftp works as well. When I let upload1 to be handled by the default_cluster_job_runner ( = pbs:///), I get empty data sets. Galaxy does not report any errors however and the data state is ok.
Has anybody seen this issue and solved it? Using the local:/// job handler causes a massive performance hit on the galaxy process.
Best regards,
Geert Vandeweyer Hi Geert,
Sorry for the delayed response. If you're still having this issue, if you view the empty dataset, can you see the data it's supposed to contain? i.e. does the underlying output file for the upload tool actually contain the data, or is it really empty on disk?
--nate
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--
Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
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