Single user Galaxy instance : job running for an unusually long time

Question: Single user Galaxy instance : job running for an unusually long time

4.5 years ago by

France

kramdi.a • 40 wrote:

Hi,

I am testing a tool integration on my basic Galaxy instance. When I test the tool outside of Galaxy with relatively small set of data as inputs, it takes about 30min to complete. Now, after what I hope is a correct integrated into Galaxy (no errors), the job is running for several hours without completing (yellow-state in History). I have used the same set of data.

Is this an indication for some integration problem ? What could be wrong ?

Any ideas would be appreciated.

Thank you

yellow-state jobs galaxy • 867 views

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modified 4.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.5 years ago by kramdi.a • 40

4.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

By "basic install" you mean just the default "getgalaxy" stable distribution? And by tool integration, you are testing your own?

Running the latest stable distribution and then moving to a production instance, in particular the database, are the first steps. Although with so little information it is difficult to know whether this will help or not. It just gives a baseline. Instructions are here:

https://wiki.galaxyproject.org/Admin/GetGalaxy - default install
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer - generally necessary to run tools not packaged with the distribution (including many Tool Shed repos)

Then check your tool against the documentation available under here in our wiki (and examine how existing tools are written):

The galaxy-dev@bx.psu.edu mailing list is still very much active, but there has been some cross-over, so let's see if more advice is posted. Without seeing the tool, the logs, knowing more about your system - this may be difficult.

I am making the assumption that the job in question is not an upload job. Please correct me if that is wrong.

Best, Jen, Galaxy team

ADD COMMENT • link modified 4.5 years ago • written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k

Hello,

Thank you for your response.

Yes, by basic install I mean the default "getgalaxy" distribution, it is suitable for development by a single user which is what I need. I am writing tool wrappers and I am only using Galaxy to test the tool's integration by running test with small datasets, I guess I don't have to look further into the configuration, or should I ? - I am testing my own tool on Galaxy. My tool works fine outside of Galaxy and I am using local data present on my disk. - Your assumption is correct, the job in question is not an upload job.

At this moment I enabled the "DEBUG" feature which is very helpful, and I was able to correct a misunderstanding I had about how Galaxy works, especially when dealing with outputs. So my problem turned into another question which I will post in another appropriate topic, this one is no longer relevant to my current situation.

Thank you !

2014-05-14 0:50 GMT+02:00 Jennifer Hillman Jackson on Galaxy Biostar < notifications@biostars.org>:

ADD REPLY • link written 4.5 years ago by kramdi.a • 40

Great, glad it is running! I am fairly certain that some tools do need the database upgrade (as noted on the production install wiki), but it sounds like you have your config now worked out for most dev. Best wishes, Jen, Galaxy team

ADD REPLY • link written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k

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