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Re: [Gmod-ajax] gmod initial configuration issues
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From: Sridhar A. M. <sma...@wv...> - 2018-08-30 19:39:03
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You are right that there is some issue about the subfolder. I checked all the folllowing urls https://localhost/jbrowse/data/json/pepperCM155/tracks.conf <https://localhost/jbrowse/data/json/pepperCM155/tracks.conf> https://localhost/jbrowse/data/json/pepperCM155 <https://localhost/jbrowse/data/json/pepperCM155/tracks.conf> https://localhost/jbrowse/data/json <https://localhost/jbrowse/data/json> https://localhost/jbrowse/data <https://localhost/jbrowse/data> All of them give “Forbidden You don’t have permission to access… “ on the webbrowser. And in apache logs I get, “client denied by server configuration /var/www/html/jbrowse/data/“, etc However, I can browse all the below, without any error. https://localhost/jbrowse/sample_data/json/v <https://localhost/jbrowse/sample_data/json/v>olvox/tracks.conf https://localhost/jbrowse/sample_data/json/v <https://localhost/jbrowse/sample_data/json/v>olvox https://localhost/jbrowse/sample_data/json <https://localhost/jbrowse/sample_data/json/v> https://localhost/jbrowse/sample_data <https://localhost/jbrowse/sample_data> If the issue is due to my global apache settings, I think I should not be able to browse even the sample_data subdirectories. Could it be due to the way the data directory is created by the reference_sequence/gff creation perl scripts and the corresponding permissions written to any config files read by jbrowse? I am also going to ask about this issue in an apache specific forum. With Kind Regards, Sridhar > On Aug 30, 2018, at 3:00 PM, Colin <col...@gm...> wrote: > > If you are able to access the jbrowse index.html (e.g. you see it on the web browser enough to get that error about tracks.conf) but you are not able to access the subfolder or files in that subfolder for your data then it seems to me that there is something about that subfolder that is causing the issue > > It is a little outside the realm of jbrowse to debug such an issue with apache but I think your configuration should work if you can get apache to cooperate. You can probably visit your url https://localhost/jbrowse/data/json/pepperCM155/tracks.conf <https://localhost/jbrowse/data/json/pepperCM155/tracks.conf> and see the error literally and then try and change config to make it work > > -Colin > > On Thu, Aug 30, 2018 at 2:38 PM Sridhar Acharya Malkaram <sma...@wv... <mailto:sma...@wv...>> wrote: > Thanks Colin, > > I’ll just tried newest 1.15.3 version. But I still get this error message. > Just to check, I tried to connect from localhost, but it still gives the error. > Some setting is probably preventing the web browser access. > Apache is running under username ‘apache’ and group ‘apache’, and the jbrowse directories and files are owned by 'apache’. So, it is puzzling why this happens. > > >> error] [client 10.1.1.254] client denied by server configuration: /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: https://10.1.1.2/jbrowse/?data=data/json/pepperCM155 <https://10.1.1.2/jbrowse/?data=data/json/pepperCM155> > >> error] [client 127.0.0.1] client denied by server configuration: /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: https://localhost/jbrowse/?data=data/json/pepperCM155 <https://localhost/jbrowse/?data=data/json/pepperCM155>With Kind Regards, > > Sridhar > > > >> On Aug 30, 2018, at 1:56 PM, Colin <col...@gm... <mailto:col...@gm...>> wrote: >> >> I think your config is probably fine, I have tested similar things. However, note that the latest JBrowse 1.15.3 release (available since yesterday) provides a possible fix for the 401 errors and I would upgrade (see http://jbrowse.org/blog/2018/08/29/jbrowse-1-15-3.html <http://jbrowse.org/blog/2018/08/29/jbrowse-1-15-3.html>) >> >> The 403 errors might suggest some actual permission problem on your data directory. You should try and view your apache error log to debug these >> >> >> -Colin >> >> >> On Thu, Aug 30, 2018 at 1:20 PM Sridhar Acharya Malkaram <sma...@wv... <mailto:sma...@wv...>> wrote: >> Hi I am trying to get Jbrowse configured with a genome and gene tracks, but am facing some problems that I couldn’t figureout after going through all guides/documentation. Any help is appreciated. >> >> I have installed jbrowse under the web_root directory (/var/www/html/jbrowse). The installation went fine without any errors. >> >> Then I used the script prepare-refseqs.pl <http://prepare-refseqs.pl/> to upload a fasta indexed genome sequence, under “data/json/pepperCM155" directory, relative to jbrowse installation. >> Also used the script flatfile-to-json.pl <http://flatfile-to-json.pl/> to upload a tabix indexed gff under the same directory. >> >> in the main jbrowse.conf the following was added >> >> [datasets.pepperCM155] >> url = ?data=data/json/pepperCM155 >> name = pepperCM155 >> >> Added the following in data/json/pepperCM155/tracks.conf >> >> [GENERAL] >> dataset_id=pepperCM155 >> refSeqs=seq/pepper.fa.fai >> >> [tracks.refseq] >> urlTemplate=seq/pepper.fa >> storeClass=JBrowse/Store/SeqFeature/IndexedFasta >> type=Sequence >> >> [tracks.genes] >> urlTemplate=pepper.gff3.gz >> storeClass=JBrowse/Store/SeqFeature/GFF3Tabix >> type=CanvasFeatures >> >> >> Upon viewing in browser I get the general “Congratulations, JBrowse is on the web!” page, with an error message, >> “RequestError: Unable to load https://10.1.1.2/jbrowse/data/json/pepperCM155/trackList.json?v=0.21140536806861931 <https://10.1.1.2/jbrowse/data/json/pepperCM155/trackList.json?v=0.21140536806861931> status:403 >> >> I see the following under apache ssl_error_log. >> [error] [client 10.1.1.254] client denied by server configuration: /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: https://10.1.1.2/jbrowse/?data=data/json/pepperCM155 <https://10.1.1.2/jbrowse/?data=data/json/pepperCM155> >> >> I am not sure what is the problem. >> >> I have proper ownership and permissions for the jbrowse directory and all underneath it. I have the following set in apache configurations files. >> >> Alias /jbrowse “/var/www/html/jbrowse” >> SetEnv JBROWSE_ROOT “/var/www/html/jbrowse" >> <Directory “/var/www/html/jbrowse”> >> SSLRequireSSL >> AllowOverride FileInfo Options AuthConfig >> Order deny, allow >> Deny from all >> Allow from 127.0.0.1 >> Allow from 10.1.1. >> AuthType Basic >> AuthName “Genome Browser” >> AuthBasicProvider external >> AuthExternal pwauth >> require valid-user >> </Directory> >> >> —— >> I could display the volvox test data. The reference sequence is displayed fine, but all the tracks are giving errors. For example, >> Error: HTTP 401 when fetching https:://10.1.1.2/jbrowse/sample_data/raw/volvox/volvox.subsubparts.gff3 <http://10.1.1.2/jbrowse/sample_data/raw/volvox/volvox.subsubparts.gff3> bytes 0-262143 >> >> >> With Kind Regards, >> >> Sridhar >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot <http://sdm.link/slashdot>_______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> > |
