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 <n...@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 >>> >>>> ___________________________________________________________ >>>> 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/ >> >> >> -- >> >> 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.vandewe...@ua.ac.be >> http://ua.ac.be/cognitivegenetics >> http://www.linkedin.com/pub/geert-vandeweyer/26/457/726 >> > > > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
