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.vandenbeek@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_... , 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.flati@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.vandenbeek@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_... 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_...
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.flati@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/