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
[Errno ftp error] [Errno 113] No route to host
Switching it back to the local job runner fixed it.
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.
>> On 08/29/2012 06:05 PM, Nate Coraor wrote:
>>> On Jul 16, 2012, at 6:14 AM, Geert Vandeweyer wrote:
>>>> 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?
>>>> 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:
>> Geert Vandeweyer, Ph.D.
>> Department of Medical Genetics
>> University of Antwerp
>> Prins Boudewijnlaan 43
>> 2650 Edegem
>> Tel: +32 (0)3 275 97 56
>> E-mail: geert.vandewe...@ua.ac.be
> 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:
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: