Error loading genome hg19

[BFA PAG3]

Hello, 

Lately there has been an issue with my IGV app. Whenever I wanted to start it, it displayed an error message. At first it was something allong the line of  "warning : could not connect to the genome server".

So I thought there was an issue with one of my files and unnistalled IGV and downloaded it again from you webstie with the Java package inlcuded. 

Downloads | Integrative Genomics Viewer

But still, each time I try to start the app, it loads for a long time, and eventually display an error message saying "Error loading genome hg19" or the "warning : could not connet to the genome server" message if I try with another genome than hg19.

I downloaded the mm9 genome with this link https://s3.amazonaws.com/igv.org.genomes/mm39/mm39.genome and tried to open it on IGV 2.12.3, but annother error message appeared saying "connect timed out"

Is there anything you can do to help me ?

Best regards

Charles Le Ciclé

[igv-help]

Hi Charles,

I'm not sure why you cannot connect to the genome server. But a workaround would be to download your genome of interest and load it from a local file, thereby avoiding the connection to our genome server. Note that it is not sufficient to download the .genome file - you'll need to download all the data for the genome. There are instructions for how to do that here: https://github.com/igvteam/igv/wiki/Downloading-Hosted-Genomes-for-Offline-Use. The mm9 genome is one of the frequently used genomes referred to in the NOTE at the top of the page.

Helga

[BFA PAG3]

Hi Helga, 

Thank you for your help !

It worked great when I downloaded  the mm9 genome from the NOTE reference.

Then I tried to download the rn6 genome folowing the different steps. 

I tried to open it once everything was completed but I get a new error message saying "connect timed out". 

Even though nothing seem to be different between the mm9 folder and the rn6 forlder I created.

Charles

[igv-help]

Charles,

If you send us your updated local .json file for rn6, I can take a look.

Helga

[BFA PAG3]

Hello Helga, 

Here is my file. I belive the problem might be the part 3 of the procedure :  "Edit your local copy".

If this is the case could you explain what I should do to edit the file ?

Charles