Ah, and if you want to figure out the ID of a tool, you can click the small info button of a dataset produced by the tool, so in the case of the upload tool it reads: Galaxy Tool ID: upload1
On 9 May 2016 at 12:25, Marius van den Beek <m.vandenb...@gmail.com> wrote: > Puhh, you're right, and somewhere in the undepths of the wiki (I think) > this is documented, > but admittedly I didn't find it when searching for it. > If you want you could add a sample of your config to > https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced > , > I believe this is something that the galaxy devteam carefully keeps up to > date. > You would definitely have my +1 for a Pull Request. If you don't have the > time I can also do this for you. > > Marius > > On 9 May 2016 at 12:02, Tiziano Flati <tiziano.fl...@gmail.com> wrote: > >> Thank you very much, Marius, that worked! >> >> But how should I have known about the exact ID of the upload tool (i.e., >> upload1)? I think this is an extremely common pattern (upload data and >> execute jobs on a cluster) >> >> 2016-05-09 11:38 GMT+02:00 Marius van den Beek <m.vandenb...@gmail.com>: >> >>> Hi Tiziano, >>> >>> I think you are correct in your assumption. >>> If you do not need to have uploads run on pulsar, you should be able to >>> specify a local destination for uploads (the upload tool id is upload1) >>> in your job_conf.xml. >>> There are some examples described here: >>> >>> https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L496 >>> If you can place a copy of galaxy and a virtualenv on your pulsar >>> server, you could also set this up as in >>> >>> https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L379 >>> >>> Note that I haven't tried this yet, but I think this is a good start. >>> Let us know if that works. >>> >>> Cheers, >>> Marius >>> >>> >>> On 9 May 2016 at 10:42, Tiziano Flati <tiziano.fl...@gmail.com> wrote: >>> >>>> Hi all, >>>> >>>> I have succesfully setup a Galaxy-Pulsar architecture and I am able to >>>> run jobs over datasets* already uploaded on a history*. >>>> >>>> When I try to upload a new file to the history, though, the upload job >>>> fails with the following error: >>>> >>>> Traceback (most recent call last): >>>>> File "/home/flati/pulsar/files/staging/80/tool_files/upload.py", >>>>> line 18, in <module> >>>>> import galaxy.model # noqa >>>>> ImportError: No module named model >>>> >>>> >>>> Note: in job_conf.xml, Pulsar is the default destination: >>>> >>>> <destinations default="win_pulsar"> >>>> >>>> >>>> Does someone know what the problem is? >>>> I suspect that setting pulsar as the default destination causes the >>>> upload tool to run on Pulsar's side which, however, does not have access to >>>> Galaxy's lib directory (which contains the galaxy model module). >>>> >>>> Any help is very appreciated, >>>> Tiziano >>>> >>>> ___________________________________________________________ >>>> 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: >>>> https://lists.galaxyproject.org/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>> >>> >> >
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