[Gmod-ajax] gmod initial configuration issues

[Sridhar A. M. <sma...@wv...>]

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 <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 bytes 0-262143


With Kind Regards,

Sridhar