Re: [galaxy-dev] History is not up-to-date
Hi Carl, it looks like the time is not correct. System Time: 2016-06-20T09:30:00.038328386Z EventsListeners: 0 Init SHA1: Init Path: /usr/local/bin/docker Docker Root Dir: /mnt/sda1/var/lib/docker Labels: provider=virtualbox the clock on my mac says 11:25 Is there an easy way to fix this or do I need to run galaxy in a new container? I run the container with -privileged=true, so it should be possible but so far I didn't find how... Thanks for your help. Cheers, Philipp -----Original message----- From: Philipp Rathert <philipp.rathert@ibc.uni-stuttgart.de> Sent: Wednesday 15th June 2016 9:07 To: 'Carl Eberhard' <carlfeberhard@gmail.com> Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date HI Carl, I am travelling these days but will check on Monday. Thanks in advance. Cheers, Philipp From: Carl Eberhard [mailto:carlfeberhard@gmail.com] Sent: Tuesday, June 14, 2016 6:24 PM To: Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de> Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] History is not up-to-date Hi, Phillip Quick questions: - is the time properly set on the computer where you've got Galaxy running in the browser? - is the time in the docker container also correct? From you terminal output it looks like the update time might be the issue and we can then take it from there. Thanks On Tue, Jun 14, 2016 at 11:28 AM, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de <mailto:philipp.rathert@ibc.uni-stuttgart.de> > wrote: Dear All, I have a problem with my histories. We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all. however, something is running in the back 129.69.102.30 - - [14/Jun/2016:12:57:21 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:21 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2) 129.69.102.30 - - [14/Jun/2016:12:57:25 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:25 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 1) 129.69.102.30 - - [14/Jun/2016:12:57:29 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:29 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:33 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:33 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0) 129.69.102.30 - - [14/Jun/2016:12:57:37 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z HTTP/1.1" 200 - "http://129.69.102.42/ <http://129.69.102.42/> " "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4" [pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:37 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3) I am not sure how to fix this and I am happy for any suggestion. Cheers, Philipp ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
Hi Philipp, this has been fixed in the mean time on the release_16.04 branch of Galaxy, see https://github.com/galaxyproject/galaxy/pull/2506 Can you try to update your Galaxy server in the container and check if it's working? Cheers, Nicola On 20/06/16 10:31, Rathert, Philipp, Dr. wrote:
RE: [galaxy-dev] History is not up-to-date
Hi Carl,
it looks like the time is not correct.
System Time: 2016-06-20T09:30:00.038328386Z
EventsListeners: 0
Init SHA1:
Init Path: /usr/local/bin/docker
Docker Root Dir: /mnt/sda1/var/lib/docker
Labels:
provider=virtualbox
the clock on my mac says 11:25
Is there an easy way to fix this or do I need to run galaxy in a new container? I run the container with -privileged=true, so it should be possible but so far I didn't find how...
Thanks for your help.
Cheers,
Philipp
-----Original message----- *From:* Philipp Rathert <philipp.rathert@ibc.uni-stuttgart.de> *Sent:* Wednesday 15th June 2016 9:07 *To:* 'Carl Eberhard' <carlfeberhard@gmail.com> *Cc:* galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] History is not up-to-date
HI Carl,
I am travelling these days but will check on Monday.
Thanks in advance.
Cheers,
Philipp
*From:*Carl Eberhard [mailto:carlfeberhard@gmail.com] *Sent:* Tuesday, June 14, 2016 6:24 PM *To:* Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de> *Cc:* galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] History is not up-to-date
Hi, Phillip
Quick questions:
- is the time properly set on the computer where you've got Galaxy running in the browser?
- is the time in the docker container also correct?
From you terminal output it looks like the update time might be the issue and we can then take it from there. Thanks
On Tue, Jun 14, 2016 at 11:28 AM, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de <mailto:philipp.rathert@ibc.uni-stuttgart.de>> wrote:
Dear All,
I have a problem with my histories.
We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all.
however, something is running in the back
129.69.102.30 - - [14/Jun/2016:12:57:21 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"
[pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:21 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2)
129.69.102.30 - - [14/Jun/2016:12:57:25 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"
[pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:25 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 1)
129.69.102.30 - - [14/Jun/2016:12:57:29 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"
[pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:29 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0)
129.69.102.30 - - [14/Jun/2016:12:57:33 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"
[pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:33 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0)
129.69.102.30 - - [14/Jun/2016:12:57:37 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"
[pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:37 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3)
I am not sure how to fix this and I am happy for any suggestion.
Cheers,
Philipp
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi, the image has the latest version, so you should be able to just repull the image. Cheers, Bjoern Am 20.06.2016 um 12:16 schrieb Nicola Soranzo:
Hi Philipp, this has been fixed in the mean time on the release_16.04 branch of Galaxy, see
https://github.com/galaxyproject/galaxy/pull/2506
Can you try to update your Galaxy server in the container and check if it's working?
Cheers, Nicola
On 20/06/16 10:31, Rathert, Philipp, Dr. wrote:
RE: [galaxy-dev] History is not up-to-date
Hi Carl,
it looks like the time is not correct.
System Time: 2016-06-20T09:30:00.038328386Z
EventsListeners: 0
Init SHA1:
Init Path: /usr/local/bin/docker
Docker Root Dir: /mnt/sda1/var/lib/docker
Labels:
provider=virtualbox
the clock on my mac says 11:25
Is there an easy way to fix this or do I need to run galaxy in a new container? I run the container with -privileged=true, so it should be possible but so far I didn't find how...
Thanks for your help.
Cheers,
Philipp
-----Original message----- *From:* Philipp Rathert <philipp.rathert@ibc.uni-stuttgart.de> *Sent:* Wednesday 15th June 2016 9:07 *To:* 'Carl Eberhard' <carlfeberhard@gmail.com> *Cc:* galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] History is not up-to-date
HI Carl,
I am travelling these days but will check on Monday.
Thanks in advance.
Cheers,
Philipp
*From:*Carl Eberhard [mailto:carlfeberhard@gmail.com] *Sent:* Tuesday, June 14, 2016 6:24 PM *To:* Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de> *Cc:* galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] History is not up-to-date
Hi, Phillip
Quick questions:
- is the time properly set on the computer where you've got Galaxy running in the browser?
- is the time in the docker container also correct?
From you terminal output it looks like the update time might be the issue and we can then take it from there. Thanks
On Tue, Jun 14, 2016 at 11:28 AM, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de <mailto:philipp.rathert@ibc.uni-stuttgart.de>> wrote:
Dear All,
I have a problem with my histories.
We are running the Docker galaxy stable version 16.04 and when I start a tool the history does not show that it is running. it is not specific for any tool but for all.
however, something is running in the back
129.69.102.30 - - [14/Jun/2016:12:57:21 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"
[pid: 271|app: 0|req: 74/163] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:21 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A16.601Z => generated 2511 bytes in 33 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 2)
129.69.102.30 - - [14/Jun/2016:12:57:25 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"
[pid: 271|app: 0|req: 75/164] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:25 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A20.635Z => generated 2511 bytes in 29 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 1)
129.69.102.30 - - [14/Jun/2016:12:57:29 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"
[pid: 271|app: 0|req: 76/165] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:29 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A24.673Z => generated 2112 bytes in 30 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0)
129.69.102.30 - - [14/Jun/2016:12:57:33 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"
[pid: 272|app: 0|req: 90/166] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:33 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A28.711Z => generated 2112 bytes in 32 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 0)
129.69.102.30 - - [14/Jun/2016:12:57:37 +0000] "GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z HTTP/1.1" 200 - "http://129.69.102.42/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_3) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"
[pid: 271|app: 0|req: 77/167] 129.69.102.30 () {44 vars in 964 bytes} [Tue Jun 14 12:57:37 2016] GET /api/histories/5114a2a207b7caff/contents?v=dev&q=update_time-ge&qv=2016-06-14T12%3A49%3A32.749Z => generated 2112 bytes in 27 msecs (HTTP/1.1 200) 3 headers in 124 bytes (1 switches on core 3)
I am not sure how to fix this and I am happy for any suggestion.
Cheers,
Philipp
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Björn Grüning -
Nicola Soranzo -
Rathert, Philipp, Dr.