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Re: [Gmod-ajax] Multiple Jbrowse on same server issue
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From: Colin <col...@gm...> - 2021-10-16 20:06:16
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Seems like this is likely an apache config issue, hard to tell what exactly though. Note that even using Alias and Directory configs may be unneeded. For example, if you have a DocumentRoot e.g. <VirtualHost *:80> > DocumentRoot /var/www/html > </VirtualHost> > Then you can unzip the jbrowse folder to /var/www/html/jbrowse and visit http://yourserver/jbrowse/ -Colin On Sat, Oct 16, 2021 at 10:16 AM Justin Elser <jus...@or...> wrote: > Thanks for the reply. > > I haven't changed either of those files from the default. Like I said, it > seems to be getting the data before I have made *any* changes. All I have > done is: > unzip JBrowse-1.16.10.zip > mv JBrowse-1.16.10 jbrowse > cd jbrowse > ./setup.sh > > And then check it on the browser. And it's not like it is getting *all* > the data from the other instance, no tracks show up and it doesn't even say > a "Reference sequence" is available either. I should maybe also point out > that it looks the same even if I don't run "./setup.sh", which seems odd to > me as well. However, if I check before doing the "mv JBrowse-1.16.10 > jbrowse", I get a 404 error, so it seems to serving the correct directory. > > I also just moved things around, so now the directories are > /data/www/salvia/jbrowse and /data/www/panoryza/jbrowse, just because it > was confusing having the salvia one in /data/www/jbrowse/jbrowse, and I see > the same issue after reinstalling it in panoryza again. > > I'm attaching the conf files anyway, in case it helps, but they should be > identical to the ones in the zip file. > > Like I said, I'm confused why it is doing this, I don't see any way the 2 > instances are connected, other than the fact they are on the same server. > > Side note, nice to see you're still working with GMOD Scott! > > Please let me know what more info I can provide. > > Justin > > On 10/15/21 3:05 PM, Scott Cain wrote: > > [This email originated from outside of OSU. Use caution with links and > attachments.] > Hi Justin, > > I imagine it's a jbrowse configuration issue, like the config for the > panoryza jbrowse is looking in /data/www/jbrowse/jbrowse for a data > directory. I bet there is some place where you think it's using a relative > url when it's really using a file path. Can you post both of your > jbrowse.conf and/or jbrowse_conf.json files? > > Scott > > > > On Fri, Oct 15, 2021 at 3:00 PM Justin Elser <jus...@or...> > wrote: > > > > Hello, > > > > Hope this is the appropriate place to ask this, but I'm having an issue > with having multiple Jbrowse (1.16.10) instances running on the same apache > server. They are in separate vhosts though and being served from different > domains. > > > > I have had one setup for almost a year now and it works fine. However, I > am now trying to set up another one for a different species, and I thought > it would be easiest to just do a fresh install in a new directory. However, > after unzipping and running ./setup.sh, instead of seeing this screen: > > > > > > I see this: > > > > > > Like it is already loaded with some data, even though I haven't added > any yet. Also, the location in the dropdown "Sh6" appears to be from the > data loaded for the other species (Salvia hispanica - chia). > > > > I've tried to go ahead and load my reference data (this new one is for > rice), and I get the "Reference sequence" track but it always has "No > sequence available" and the "loc=" still references the "Sh6" instead of > "Chr1". > > > > I've also found that if I follow the exact same steps, but on a > different machine that doesn't already have a jbrowse instance installed, > it works exactly as I expect, so I'm pretty sure it is trying to read the > wrong data for some reason. > > > > For now, both sites are restricted to only be visible from some IP > addresses, but I can open it up temporarily if it would help. > > > > Also, just in case it helps, here are the relevant bits of the Apache > vhost entries for both: > > The one that works: > > /etc/httpd/conf.d/salvia.conf > > > > Alias /jbrowse "/data/www/jbrowse/jbrowse" > > > > <Directory "/data/www/jbrowse/jbrowse"> > > > > AllowOverride All > > > > Require all granted > > > > </Directory> > > > > > > The one that doesn't work: > > /etc/httpd/conf.d/panoryza-ssl.conf > > > > Alias /jbrowse "/data/www/panoryza/jbrowse" > > > > <Directory "/data/www/panoryza/jbrowse"> > > > > AllowOverride All > > > > Require all granted > > > > </Directory> > > > > > > > > I would appreciate any help in figuring out what I am doing wrong or how > to fix this. > > > > Thanks, > > Justin Elser > > > > -- > > ********************************************************** > > * * > > * Justin Elser * > > * Computational Biology Post Doc * > > * Dept. of Botany and Plant Pathology * > > * Oregon State University * > > * * > > * email: el...@sc... * > > * internet: www.science.oregonstate.edu/~elserj > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.science.oregonstate.edu%2F~elserj&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C550a37b3ec78421a66ed08d99027fc9d%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637699324131632320%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=QKpnruDgVGVi4knHL%2Feu8EgMcZ%2FimMJKFrWsm9aOebg%3D&reserved=0> > * > > * * > > ********************************************************** > > > > _______________________________________________ > > Gmod-ajax mailing list > > Gmo...@li... > > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C550a37b3ec78421a66ed08d99027fc9d%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637699324131642281%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=h0lYBFA8r1bcF60LPwRd9NoZVlAJulTbXIzia9u%2FMN4%3D&reserved=0> > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/ > <https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgmod.org%2F&data=04%7C01%7Cjustin.elser%40oregonstate.edu%7C550a37b3ec78421a66ed08d99027fc9d%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C637699324131652232%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=F%2BqWqomOgT%2Bu2k0sf1NzajeL8EuSuTU1JZLmUS9aehc%3D&reserved=0>) > 216-392-3087 > Ontario Institute for Cancer Research > > > -- > ********************************************************** > * * > * Justin Elser * > * Computational Biology Post Doc * > * Dept. of Botany and Plant Pathology * > * Oregon State University * > * * > * email: el...@sc... * > * internet: www.science.oregonstate.edu/~elserj * > * * > ********************************************************** > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
