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Re: [Gmod-ajax] gmod initial configuration issues
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From: Sridhar A. M. <sma...@wv...> - 2018-08-30 18:39:05
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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...> 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://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> |
