upload file not functioning in local installation galaxy
Hi, I have installed galaxy on our local server, when I was trying to upload data from: Get Data -> Upload File -> choose file. It is not uploading at all; but it works fine when using the URL option. I wonder do you have any suggestions about this problem? The output from the command line is pasted below: ====> 128.118.200.158 - - [15/Aug/2013:14:15:41 -0400] "GET /api/histories/5969b1f7201f12ae/contents?ids=f09437b8822035f7 HTTP/1.1" 200 - "http://128.118.201.68:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/histories/5969b1f7201f12ae HTTP/1.1" 200 - " http://128.118.201.68:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/histories/5969b1f7201f12ae/contents?ids=f09437b8822035f7 HTTP/1.1" 200 - "http://128.118.201.68:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:16:49 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:03 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - " http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:04 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - " http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:08 -0400] "GET /history HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" ==============> Thanks, Yinan -- Yinan Wan, graduate student Bioinformatics and Genomics program Huck Institutes of Life Sciences the Pennsylvania State University
Hi Yinan It might be unrelated, but we had a similar issue. The problem was due to the proxy settings of our server. Regards, Hans-Rudolf On 08/16/2013 08:23 PM, Yinan Wan wrote:
Hi,
I have installed galaxy on our local server, when I was trying to upload data from: Get Data -> Upload File -> choose file. It is not uploading at all; but it works fine when using the URL option. I wonder do you have any suggestions about this problem?
The output from the command line is pasted below: ====> 128.118.200.158 - - [15/Aug/2013:14:15:41 -0400] "GET /api/histories/5969b1f7201f12ae/contents?ids=f09437b8822035f7 HTTP/1.1" 200 - "http://128.118.201.68:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/histories/5969b1f7201f12ae HTTP/1.1" 200 - "http://128.118.201.68:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/histories/5969b1f7201f12ae/contents?ids=f09437b8822035f7 HTTP/1.1" 200 - "http://128.118.201.68:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:16:49 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:03 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:04 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:08 -0400] "GET /history HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" ==============>
Thanks, Yinan
-- Yinan Wan, graduate student Bioinformatics and Genomics program Huck Institutes of Life Sciences the Pennsylvania State University
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Hi Hans-Rudolf, Thanks for your reply. But do you have any idea what might be related with this "proxy issue"? What is required to open/set for galaxy to run? Or do you might share your experience of how you solve the problem? Thanks, Yinan On Mon, Aug 19, 2013 at 3:16 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Yinan
It might be unrelated, but we had a similar issue. The problem was due to the proxy settings of our server.
Regards, Hans-Rudolf
On 08/16/2013 08:23 PM, Yinan Wan wrote:
Hi,
I have installed galaxy on our local server, when I was trying to upload data from: Get Data -> Upload File -> choose file. It is not uploading at all; but it works fine when using the URL option. I wonder do you have any suggestions about this problem?
The output from the command line is pasted below: ====> 128.118.200.158 - - [15/Aug/2013:14:15:41 -0400] "GET /api/histories/**5969b1f7201f12ae/contents?ids=**f09437b8822035f7 HTTP/1.1" 200 - "http://128.118.201.68:8080/**history<http://128.118.201.68:8080/history>" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/histories/**5969b1f7201f12ae HTTP/1.1" 200 - "http://128.118.201.68:8080/**history<http://128.118.201.68:8080/history>" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/histories/**5969b1f7201f12ae/contents?ids=**f09437b8822035f7 HTTP/1.1" 200 - "http://128.118.201.68:8080/**history<http://128.118.201.68:8080/history>" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:16:49 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:03 -0400] "POST /tool_runner/upload_async_**create HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:04 -0400] "GET /tool_runner/upload_async_**message HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:08 -0400] "GET /history HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" ==============>
Thanks, Yinan
-- Yinan Wan, graduate student Bioinformatics and Genomics program Huck Institutes of Life Sciences the Pennsylvania State University
______________________________**_____________________________ 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/<http://galaxyproject.org/search/mailinglists/>
-- Yinan Wan, graduate student Bioinformatics and Genomics program Huck Institutes of Life Sciences the Pennsylvania State University
Hi One of our development boxes is (unfortunately) behind a different firewall, compared to the the other servers. We fixed the problem (ie "Get Data -> Upload File -> choose file. It is not uploading at all") by setting a proxy server. This could be done eg. by adding the following lines to "run.sh": http_proxy=http://******.fmi.ch:<port number> export http_proxy Obviously, this solved other problems as well, like "Get Data -> UCSC" Regards, Hans-Rudolf On 08/19/2013 04:01 PM, Yinan Wan wrote:
Hi Hans-Rudolf,
Thanks for your reply. But do you have any idea what might be related with this "proxy issue"? What is required to open/set for galaxy to run? Or do you might share your experience of how you solve the problem?
Thanks, Yinan
On Mon, Aug 19, 2013 at 3:16 AM, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
Hi Yinan
It might be unrelated, but we had a similar issue. The problem was due to the proxy settings of our server.
Regards, Hans-Rudolf
On 08/16/2013 08:23 PM, Yinan Wan wrote:
Hi,
I have installed galaxy on our local server, when I was trying to upload data from: Get Data -> Upload File -> choose file. It is not uploading at all; but it works fine when using the URL option. I wonder do you have any suggestions about this problem?
The output from the command line is pasted below: ====> 128.118.200.158 - - [15/Aug/2013:14:15:41 -0400] "GET /api/histories/__5969b1f7201f12ae/contents?ids=__f09437b8822035f7 HTTP/1.1" 200 - "http://128.118.201.68:8080/__history <http://128.118.201.68:8080/history>" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/histories/__5969b1f7201f12ae HTTP/1.1" 200 - "http://128.118.201.68:8080/__history <http://128.118.201.68:8080/history>" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/histories/__5969b1f7201f12ae/contents?ids=__f09437b8822035f7 HTTP/1.1" 200 - "http://128.118.201.68:8080/__history <http://128.118.201.68:8080/history>" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:15:45 -0400] "GET /api/users/current HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:16:49 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:03 -0400] "POST /tool_runner/upload_async___create HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:04 -0400] "GET /tool_runner/upload_async___message HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" 128.118.200.158 - - [15/Aug/2013:14:17:08 -0400] "GET /history HTTP/1.1" 200 - "http://128.118.201.68:8080/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36" ==============>
Thanks, Yinan
-- Yinan Wan, graduate student Bioinformatics and Genomics program Huck Institutes of Life Sciences the Pennsylvania State University
_____________________________________________________________ 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/ <http://galaxyproject.org/search/mailinglists/>
-- Yinan Wan, graduate student Bioinformatics and Genomics program Huck Institutes of Life Sciences the Pennsylvania State University
participants (2)
-
Hans-Rudolf Hotz -
Yinan Wan