How to get jbrowse to read tracks from files outside of the root of the homepage?

Question

[kontra.levente]

Hello everyone!

I use apache (v2.4.18) on a GNU/linux (ubuntu) machine. /var/www/ is configure as the root for the homepage, jbrowse is installed in /var/www/html/summitdb/jbrowse, however the data is too big to store there.

My question is: how can I reach data with jbrowse outside /var/www/?

I have already tried using an alias without success:

I added the following to /etc/apache2/sites-available/000-default.conf

Alias "/data3" "/data/projects/summitdb/jbrowse/data3/"
       <Directory "/data/projects/summitdb/jbrowse/data3/">
                Require all granted
        </Directory>

Copied the trackList.json inside /var/www/html/summitdb/jbrowse/data and modified it like so:

"urlTemplate" : "/data3/tracks/100206/{refseq}/trackData.json",

The error massage is this: SyntaxError: missing : after property id when parsing fsl/trackList.json.

Actually this using an alias is recomanded at http://gmod.org/wiki/JBrowse_Configuration_Guide#Configuring_track_locations_with_Apache. What am I missing?

I also tried simply creating a symbolic link to my data and reach that by giving th link as atribute to the url www.myhompa.ge/summitdb/jbrowse/index.html?data=symlink but that does not seem to work either. Even though apache2 is set to allow symlinks.

In this case the error message is this: RequestError: Unable to load http://myhompa.ge/summitdb/jbrowse/symlink/trackList.json status: 403.

This is my first time with both with jbrowse and apache2 and I am very confused. Any help would be appreciated!

Thanks, Levi

[Matteo Schiavinato]

SyntaxError: missing : after property id when parsing fsl/trackList.json.

You're typing something wrong in the json file. Can you paste here the lines of such file?

[kontra.levente]

Here is the first 50 lines of the 1455260 lines, it's pretty much repetative after the first 25:

{ "tracks" : [ { "trackType" : null, "storeClass" : "JBrowse/Store/SeqFeature/NCList", "style" : { "className" : "feature" }, "compress" : 0, "label" : "100206", "metadata" : { "motif" : "Hnf4a", "cellLine" : "NB4", "antibody" : "CMYC", "totalTags" : "43803191", "totalPeaks" : "80236", "elementNumber" : "769", "stdDev" : "28.9426", "average" : "1.21196" }, "key" : "100206", "urlTemplate" : "/data3/tracks/100206/{refseq}/trackData.json", "type" : "FeatureTrack" }, { "metadata" : { "motif" : "Hnf4a", "cellLine" : "NB4", "antibody" : "MAX", "totalTags" : "46185428", "totalPeaks" : "111976", "elementNumber" : "857", "stdDev" : "29.0991", "average" : "1.30922" }, "key" : "100208", "type" : "FeatureTrack", "urlTemplate" : "/data3/tracks/100208/{refseq}/trackData.json", "label" : "100208", "compress" : 0, "trackType" : null, "style" : { "className" : "feature" }, "storeClass" : "JBrowse/Store/SeqFeature/NCList" }, { "trackType" : null, "style" : { "className" : "feature"

[kontra.levente]

oh, wow... sorry the lines are messed up... let me try that again

{
   "tracks" : [
      {
         "trackType" : null,
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "label" : "100206",
         "metadata" : {
            "motif" : "Hnf4a",
            "cellLine" : "NB4",
            "antibody" : "CMYC",
            "totalTags" : "43803191",
            "totalPeaks" : "80236",
            "elementNumber" : "769",
            "stdDev" : "28.9426",
            "average" : "1.21196"
         },
         "key" : "100206",
         "urlTemplate" : "/data3/tracks/100206/{refseq}/trackData.json",
         "type" : "FeatureTrack"
      },
      {
         "metadata" : {
            "motif" : "Hnf4a",
            "cellLine" : "NB4",
            "antibody" : "MAX",
            "totalTags" : "46185428",
            "totalPeaks" : "111976",
            "elementNumber" : "857",
            "stdDev" : "29.0991",
            "average" : "1.30922"
         },
         "key" : "100208",
         "type" : "FeatureTrack",
         "urlTemplate" : "/data3/tracks/100208/{refseq}/trackData.json",
         "label" : "100208",
         "compress" : 0,
         "trackType" : null,
         "style" : {
            "className" : "feature"
         },
         "storeClass" : "JBrowse/Store/SeqFeature/NCList"
      },
      {
         "trackType" : null,
         "style" : {
            "className" : "feature"

[Matteo Schiavinato]

My guess would be that you should put "null" and "0" between quotes.

[kontra.levente]

Hi Macspider,

Thanks for the tip. Unfortunately, that didn't work out, same error message.

Answer 1

[kontra.levente]

OK, it's working now. There were actually two tings. There was a line uncommented in the json file that caused syntax error (possibly my metadata adding script is not working perfectly). The other one was solved by moving the jbrowse out of /var/www/ to the folder where the data is, and making a symlink there. To me, it seams like apache2 actually follows the symlink but jbrowse not.

Thanks to anyone who gave it a thought!

Chears, Levi