I recently installed galaxy program on our Linux server and it is going to be used for analyzing high-throuput sequencing data. I tried to upload a dataset (a bed format file) from local computer to galaxy server, but no success. The message of "Dataset is uploading" stays forever. The uploaded dataset was shown on the /galaxy-dist/database/tmp directory, but it didn't get transferred to the job-working directory or files directory before it was deleted by the galaxy. The output of run_functional_tests shows that uploading file went successfully. The paster.log file doesn't show error message about the uploading. Any configuration did I miss? Your feedback is highly appreciated. Thank you! Weihong
Hi, I am having the same issue today. It was working a few days ago, but now never finish uploading. Luciano On Dec 15, 2011, at 3:05 PM, weihong yan wrote:
I recently installed galaxy program on our Linux server and it is going to be used for analyzing high-throuput sequencing data. I tried to upload a dataset (a bed format file) from local computer to galaxy server, but no success. The message of "Dataset is uploading" stays forever. The uploaded dataset was shown on the / galaxy-dist/database/tmp directory, but it didn't get transferred to the job-working directory or files directory before it was deleted by the galaxy.
The output of run_functional_tests shows that uploading file went successfully. The paster.log file doesn't show error message about the uploading.
Any configuration did I miss? Your feedback is highly appreciated.
Thank you!
Weihong
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Galaxy was configured with Apache as proxy server. The uploaded file size is very small. The message from paster.log related with it is "POST /False?nginx_redir=/tool_runner/index HTTP/1.1" 200 - "http://galaxy.mcdb.ucla.edu/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_2; en-us) AppleWebKit/531.9 (KHTML, like Gecko) Version/4.0.3 Safari/531.9" Weihong --- On Thu, 12/15/11, Luciano Cosme <cosme.simple@gmail.com> wrote: From: Luciano Cosme <cosme.simple@gmail.com> Subject: Re: [galaxy-dev] file upload issue To: "weihong yan" <weihongyan@yahoo.com> Cc: galaxy-dev@lists.bx.psu.edu Date: Thursday, December 15, 2011, 1:09 PM Hi, I am having the same issue today. It was working a few days ago, but now never finish uploading. Luciano On Dec 15, 2011, at 3:05 PM, weihong yan wrote: I recently installed galaxy program on our Linux server and it is going to be used for analyzing high-throuput sequencing data. I tried to upload a dataset (a bed format file) from local computer to galaxy server, but no success. The message of "Dataset is uploading" stays forever. The uploaded dataset was shown on the /galaxy-dist/database/tmp directory, but it didn't get transferred to the job-working directory or files directory before it was deleted by the galaxy. The output of run_functional_tests shows that uploading file went successfully. The paster.log file doesn't show error message about the uploading. Any configuration did I miss? Your feedback is highly appreciated. Thank you! Weihong ___________________________________________________________ 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/
On Dec 15, 2011, at 4:39 PM, weihong yan wrote:
Galaxy was configured with Apache as proxy server. The uploaded file size is very small. The message from paster.log related with it is
"POST /False?nginx_redir=/tool_runner/index HTTP/1.1" 200 - "http://galaxy.mcdb.ucla.edu/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_2; en-us) AppleWebKit/531.9 (KHTML, like Gecko) Version/4.0.3 Safari/531.9"
Hi, The message I just sent may be irrelevant as I missed this followup. It looks like you've configured the nginx upload options (or uncommented them) even though you are not using the nginx upload module? --nate
Weihong
--- On Thu, 12/15/11, Luciano Cosme <cosme.simple@gmail.com> wrote:
From: Luciano Cosme <cosme.simple@gmail.com> Subject: Re: [galaxy-dev] file upload issue To: "weihong yan" <weihongyan@yahoo.com> Cc: galaxy-dev@lists.bx.psu.edu Date: Thursday, December 15, 2011, 1:09 PM
Hi, I am having the same issue today. It was working a few days ago, but now never finish uploading.
Luciano
On Dec 15, 2011, at 3:05 PM, weihong yan wrote:
I recently installed galaxy program on our Linux server and it is going to be used for analyzing high-throuput sequencing data. I tried to upload a dataset (a bed format file) from local computer to galaxy server, but no success. The message of "Dataset is uploading" stays forever. The uploaded dataset was shown on the /galaxy-dist/database/tmp directory, but it didn't get transferred to the job-working directory or files directory before it was deleted by the galaxy.
The output of run_functional_tests shows that uploading file went successfully. The paster.log file doesn't show error message about the uploading.
Any configuration did I miss? Your feedback is highly appreciated.
Thank you!
Weihong
___________________________________________________________ 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:
___________________________________________________________ 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:
On Dec 15, 2011, at 4:05 PM, weihong yan wrote:
I recently installed galaxy program on our Linux server and it is going to be used for analyzing high-throuput sequencing data. I tried to upload a dataset (a bed format file) from local computer to galaxy server, but no success. The message of "Dataset is uploading" stays forever. The uploaded dataset was shown on the /galaxy-dist/database/tmp directory, but it didn't get transferred to the job-working directory or files directory before it was deleted by the galaxy.
The output of run_functional_tests shows that uploading file went successfully. The paster.log file doesn't show error message about the uploading.
Any configuration did I miss? Your feedback is highly appreciated.
Hi Weihong, Sorry for the delayed response. Can you verify that the upload was not interrupted? Was the file in the tmp/ directory the same as the file you uploaded? Uploading huge files via a browser is not the most efficient way to get data into Galaxy. You may want to explore one of the other options in the wiki: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP Note that the "Upload via FTP" method was designed for FTP but does not actually require that you use FTP. --nate
Thank you!
Weihong
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participants (3)
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Luciano Cosme -
Nate Coraor -
weihong yan