Re: [galaxy-dev] another update problem
On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhar golha...@umdnj.edu wrote: I just updated my local galaxy instance using hg pull, and the history items are no longer expandable. What happened? Which browser(s) are affected? I recall reporting some issues with Internet Explorer only and the history peep view not working. Peter ___ 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/
Re: [galaxy-dev] another update problem
This is Safari on Mac OS X. I just reverted to my backup and the problem still exists so I don't know what is going on now. On 4/11/11 2:35 PM, Peter Cock wrote: On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhargolha...@umdnj.edu wrote: I just updated my local galaxy instance using hg pull, and the history items are no longer expandable. What happened? Which browser(s) are affected? I recall reporting some issues with Internet Explorer only and the history peep view not working. Peter -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. attachment: golharam.vcf___ 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/
Re: [galaxy-dev] another update problem
Couple of voodoo things to try: 1. Manually clean the cache of your web browser 2. Restart your apache/nginx Depending on your last update revision, it's possible that some of your javascripts were updated by the latest pull, but your webbrowser maintains a cached older version. Those are the two things I'd try first. Ryan Golhar wrote, On 04/11/2011 02:49 PM: Second problem...Galaxy no longer can determine when a job completes in PBS. I see it submit the job and the paster.log indicates the job ends, but the history display indicates the job hasn't been submitted. On 4/11/11 2:43 PM, Ryan Golhar wrote: This happens in Firefox on Mac as well. On 4/11/11 2:36 PM, Ryan Golhar wrote: This is Safari on Mac OS X. I just reverted to my backup and the problem still exists so I don't know what is going on now. On 4/11/11 2:35 PM, Peter Cock wrote: On Mon, Apr 11, 2011 at 7:26 PM, Ryan Golhargolha...@umdnj.edu wrote: I just updated my local galaxy instance using hg pull, and the history items are no longer expandable. What happened? Which browser(s) are affected? I recall reporting some issues with Internet Explorer only and the history peep view not working. Peter ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] another update problem
Hi Ryan, I still think it's a javascript problem (most of the fancy DHTML tricks in galaxy, like expanding/collapsing datasets, are done in javascript - so when something like that doesn't work, it's a good place to start). First indication: If you go to your galaxy server with Firefox and open the JavaScript error console, you'll see the following error: = Error: $.jStore is undefined Source File: http://X.X.edu/galaxy/static/scripts/galaxy.base.js?v=8 Line: 1 = Just to be sure, this is not a real galaxy bug, this is a mismatch between what should be the correct javascript and the actual javascript that you are using. So the next step is to see if there are real differences: compare the javascript you have with the one you're supposed to have (if you've updated to the latest galaxy-dist): ## Download your version: $ wget -O galaxy.base.js 'http://X.X.edu/galaxy/static/scripts/galaxy.base.js?v=8' ## Download galaxy's version: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist ## compare them: $ ls -l galaxy.base.js galaxy-dist/static/scripts/packed/galaxy.base.js -rw-r--r-- 1 gordon hannon 8787 Apr 11 16:11 galaxy-dist/static/scripts/packed/galaxy.base.js -rw-r--r-- 1 gordon hannon 9020 Feb 21 13:48 galaxy.base.js = # Obviously, they are not the same. # Assuming wget maintains the file's actual date (Yours is from Feb. 21st), then I can assume you're still using an older version of the javascript file. Perhaps you've pulled but didn't update ? Or merged and took the wrong version ? Check the actual file on your disk to continue and debug it, but IMHO it's definitely a javascript mismatch problem. Hope it helps, -gordon Ryan Golhar wrote, On 04/11/2011 03:13 PM: I restarted the galaxy daemon, apache, and cleared my cache. Still didn't help. I'd be happy to share the URL of my instance via private email if it'll help. On 4/11/11 3:05 PM, Assaf Gordon wrote: Couple of voodoo things to try: 1. Manually clean the cache of your web browser 2. Restart your apache/nginx Depending on your last update revision, it's possible that some of your javascripts were updated by the latest pull, but your webbrowser maintains a cached older version. Those are the two things I'd try first. ___ 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/
Re: [galaxy-dev] another update problem
Yeah, I pulled down a new version of galaxy-dist to a new directory and am comparing the differences using diff on my current instance. For some reason hg pull -u didn't work. It aborted because I installed a bam.xml for igv in display_applications/igv. Apparently one was added to galaxy-dist as well. I copied in the new one but now its complaining about some other file. I can't seem to force hg to update so I need to do some of the updating by hand. *** This is not fun *** On 4/11/11 4:19 PM, Assaf Gordon wrote: this is a mismatch between what should be the correct javascript and the actual javascript that you are using. So the next step is to see if there are real differences: compare the javascript you have with the one you're supposed to have (if you've updated to the latest galaxy-dist): -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. attachment: golharam.vcf___ 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/
Re: [galaxy-dev] another update problem
I screwed Galaxy. I will delete / reinstall it. At least I will delete it. I think I will revert back to the shell for awhile to get some work done. I've spent *way* too much time trying to get galaxy to work properly. Thanks for all the help everyone. On 4/11/11 4:32 PM, Ryan Golhar wrote: Yeah, I pulled down a new version of galaxy-dist to a new directory and am comparing the differences using diff on my current instance. For some reason hg pull -u didn't work. It aborted because I installed a bam.xml for igv in display_applications/igv. Apparently one was added to galaxy-dist as well. I copied in the new one but now its complaining about some other file. I can't seem to force hg to update so I need to do some of the updating by hand. *** This is not fun *** On 4/11/11 4:19 PM, Assaf Gordon wrote: this is a mismatch between what should be the correct javascript and the actual javascript that you are using. So the next step is to see if there are real differences: compare the javascript you have with the one you're supposed to have (if you've updated to the latest galaxy-dist): ___ 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/ -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information. attachment: golharam.vcf___ 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/
