IGV screenshot WITHOUT internet connection

[skang6]

Hi, 

I've tried to run IGV screenshot with a python code that I downloaded from github.

(https://github.com/stevekm/IGV-snapshot-automator)

With this script, it runs IGV on the X virtual frame buffer and then makes PNG files eventually.

It's working in the present of internet connection, however, it's not without it. 

There's a hg19.genome file in the 'igv/genome' folder, as well as a FASTA file (with fai). 

I have to run this in the absence of internet connection, and use this automator only because there are so many regions that I would like to see. 

Please check attachments with error and without.

I'm using IGV 2.4.4 on CentOS Linux 7.2.1511 (Red Hat 4.8.3).

Thank you for your help in advance. 

Seongmin

[James Robinson]

You need to download and define your own genome on local files if you want to run without internet.

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[skang6]

I surely downloaded and defined my own genome on local, but still comes up the error messages which say "Error loading genome" and "Unexpected error: null". 

I think I am missing something else. 

Here is a new error log and a capture file of my preference section Advanced.

Thanks,

On Wednesday, December 20, 2017 at 4:05:23 AM UTC+9, Jim Robinson wrote:

You need to download and define your own genome on local files if you want to run without internet.

On Tue, Dec 19, 2017 at 2:18 AM, skang6 <ksmks...@gmail.com> wrote:

Hi, 

I've tried to run IGV screenshot with a python code that I downloaded from github.

(https://github.com/stevekm/IGV-snapshot-automator)

With this script, it runs IGV on the X virtual frame buffer and then makes PNG files eventually.

It's working in the present of internet connection, however, it's not without it. 

There's a hg19.genome file in the 'igv/genome' folder, as well as a FASTA file (with fai). 

I have to run this in the absence of internet connection, and use this automator only because there are so many regions that I would like to see. 

Please check attachments with error and without.

I'm using IGV 2.4.4 on CentOS Linux 7.2.1511 (Red Hat 4.8.3).

Thank you for your help in advance. 

Seongmin

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[James Robinson]

Ahh, o.k.,  on startup its trying to download the list of available genome IDs.    Click "Edit server properties" and change the genome server url to something local.   It can be a file path.   I think the path can be empty,  but you can also download the "Genome Server URL" file from the url listed, save it locally and edit as required (probably removing everything except you local genome). 

Running without an internet connection should be possible,  but it isn't something we designed for or test so might take some more trial and error.

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[skang6]

As I tried to use IGV_2.3.97 version, it was working without connection but some errors come up as reading a batch file. 

Again, I tried to use IGV_2.2.13 version. Finally, It's working without any errors. 

I don't get it why it's working at the previous version, but there might be some bugs errors as loading the batch file at the higher version. I hope that bugs would be fixed later. 

Anyways, thank you for your help!

Seongmin

[James Robinson]

Could you open a git issue about this  github.com/igvteam/igv/issues?   We should have an option to run without internet and not rely on it accidentally working,  but that will need to be added.

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