Get Data - url upload (connection timed out)
Dear * I have a local galaxy instance installed on a cluster. I've been trying to upload data by URL but kept getting this error: *"unable to fetch <url of data> [Errno socket error] [Errno 110] connection timed out". *I've tried with and without file compression format and still gives me that error. Am I suppose to modify/edit any particular config file? Can't seem to find a similar thread or answer to this but perhaps I may have missed. Apologies if I have missed. Would appreciate if anyone can please advise. Thanks. Best regards liz
I doubt there is a config option somewhere that is going to fix this. Can your compute nodes download external data outside of Galaxy? (One could submit a test script to the cluster with a download and see if it succeeds.) If you give me the URL and let me know what kind of cluster you are running I could help you formulate that test. If we can confirm that the cluster nodes cannot download external files - it might be worth running `upload1` jobs with a local job runner instead of on the cluster - frequently login servers and web servers have more external access than compute nodes in cluster environments. Let me know if you need help configuring that. -John On Wed, Oct 1, 2014 at 3:41 AM, Elizabeth Chia <elchia@gmail.com> wrote:
Dear *
I have a local galaxy instance installed on a cluster.
I've been trying to upload data by URL but kept getting this error: "unable to fetch <url of data> [Errno socket error] [Errno 110] connection timed out". I've tried with and without file compression format and still gives me that error.
Am I suppose to modify/edit any particular config file?
Can't seem to find a similar thread or answer to this but perhaps I may have missed. Apologies if I have missed. Would appreciate if anyone can please advise.
Thanks.
Best regards liz
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Thanks for responding, John. Yes, you're right.. finally just struck me that the failure was due to my compute nodes not having internet connection. Unfortunately, we have to setup our cluster this way due to limited resources and galaxy would submit jobs to it. I guess the other option that works the same way is to use the Data Library option. Thanks anyway! liz On Thu, Oct 2, 2014 at 12:48 AM, John Chilton <jmchilton@gmail.com> wrote:
I doubt there is a config option somewhere that is going to fix this.
Can your compute nodes download external data outside of Galaxy? (One could submit a test script to the cluster with a download and see if it succeeds.) If you give me the URL and let me know what kind of cluster you are running I could help you formulate that test.
If we can confirm that the cluster nodes cannot download external files - it might be worth running `upload1` jobs with a local job runner instead of on the cluster - frequently login servers and web servers have more external access than compute nodes in cluster environments. Let me know if you need help configuring that.
-John
On Wed, Oct 1, 2014 at 3:41 AM, Elizabeth Chia <elchia@gmail.com> wrote:
Dear *
I have a local galaxy instance installed on a cluster.
I've been trying to upload data by URL but kept getting this error: "unable to fetch <url of data> [Errno socket error] [Errno 110] connection timed out". I've tried with and without file compression format and still gives me that error.
Am I suppose to modify/edit any particular config file?
Can't seem to find a similar thread or answer to this but perhaps I may have missed. Apologies if I have missed. Would appreciate if anyone can please advise.
Thanks.
Best regards liz
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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Elizabeth Chia -
John Chilton