Re: [Gmod-ajax] gmod initial configuration issues

[Colin <col...@gm...>]

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)

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...> 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 to upload a fasta indexed
> genome sequence, under “data/json/pepperCM155" directory, relative to
> jbrowse installation.
> Also used the script 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
>  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
>
> 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 bytes
> 0-262143
>
>
> With Kind Regards,
>
> Sridhar
>
>
>
>
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