New to supporting Galaxy (local deployment) seeking help related to upload problem and log file locations

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New to supporting Galaxy (local deployment) seeking help related to upload problem and log file locations

zemay
I've recently been asked to support a local Galaxy deployment.  As I am new to the software, I'm having a hard time tracking down logs and honestly understanding how the system works.  

The actual problem is the scientist in question is not able to upload files.  The only upload feature I noticed running on the server was an sftp-server, so I restarted that, but it doesn't appear to have fixed anything.  Which lead me down the path of tracking down log files to help me troubleshoot, but I am unable to track those down.

I have looked through several of the previous discussions regarding uploading, and have not been able to find the answer to my question.

Any help would be appreciated.

thanks

Zack
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Re: New to supporting Galaxy (local deployment) seeking help related to upload problem and log file locations

Björn Grüning-3
Hi Zack,

can you provide us some more information of how you deploy your Galaxy?
Are you using nginx or another proxy? Can you share your job_conf.xml
file with us?

What means does not work? Jobs are turning grey? But never turn yellow?
Or do they turn red? Is any other tool working?

Cheers,
Bjoern

Am 20.06.19 um 16:37 schrieb [hidden email]:

> I've recently been asked to support a local Galaxy deployment.  As I
> am new to the software, I'm having a hard time tracking down logs and
> honestly understanding how the system works.
>
> The actual problem is the scientist in question is not able to upload
> files.  The only upload feature I noticed running on the server was
> an sftp-server, so I restarted that, but it doesn't appear to have
> fixed anything.  Which lead me down the path of tracking down log
> files to help me troubleshoot, but I am unable to track those down.
>
> I have looked through several of the previous discussions regarding
> uploading, and have not been able to find the answer to my question.
>
> Any help would be appreciated.
>
> thanks
>
> Zack ___________________________________________________________
> 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: %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/
>
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Re: New to supporting Galaxy (local deployment) seeking help related to upload problem and log file locations

zemay
PM, & Bjorn,
Thank you for the response.  I will get the job_conf.xml file and share it Monday.  Unfortunately I am unable to get into this system today.

From what I could tell when troubleshooting.
1. Nginx was not running, nor was it enabled in the config file I did find.  The current user accesses the galaxy program on port 8081
2. I am not sure, nor could I find where the galaxy logs were, however I wasn't aware of the job_conf.xml file either.  So I will check inside that file before sending it along to see if it provides log file location.
3. I did not actually deploy this Galaxy instance, I am extremely new (less than three logins to the system) to support of Galaxy
- I will be building a new system shortly, and have started reading best practices

Again Thank you for the response, and I will provide the job_conf.xml file Monday when I can access the system again.

Zack


On 6/22/19, 7:40 AM, "Björn Grüning" <[hidden email]> wrote:

    Hi Zack,

    can you provide us some more information of how you deploy your Galaxy?
    Are you using nginx or another proxy? Can you share your job_conf.xml
    file with us?

    What means does not work? Jobs are turning grey? But never turn yellow?
    Or do they turn red? Is any other tool working?

    Cheers,
    Bjoern

    Am 20.06.19 um 16:37 schrieb [hidden email]:
    > I've recently been asked to support a local Galaxy deployment.  As I
    > am new to the software, I'm having a hard time tracking down logs and
    > honestly understanding how the system works.
    >
    > The actual problem is the scientist in question is not able to upload
    > files.  The only upload feature I noticed running on the server was
    > an sftp-server, so I restarted that, but it doesn't appear to have
    > fixed anything.  Which lead me down the path of tracking down log
    > files to help me troubleshoot, but I am unable to track those down.
    >
    > I have looked through several of the previous discussions regarding
    > uploading, and have not been able to find the answer to my question.
    >
    > Any help would be appreciated.
    >
    > thanks
    >
    > Zack ___________________________________________________________
    > 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: %(web_page_url)s
    >
    > To search Galaxy mailing lists use the unified search at:
    > http://galaxyproject.org/search/
    >


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