From: Mason Meyer <mmeyer20@uncc.edu>
To: Gwenivere Cackett <gwenivere.cackett.13@ucl.ac.uk>
CC: "Loraine, Ann" <Ann.Loraine@uncc.edu>
Date: Tue, Mar 13, 2018 at 2:47 PM
Subject: Re: IGB 'Problem Saving File'

Hello Gwenivere,

My name is Mason Meyer, Support Specialist for IGB. Thank you for contacting us so we can help resolve the issue you are currently experiencing.

I understand you are trying to save a track as either a bedgraph or graph file and are getting an error. We have recently noticed an issue relating to this feature and I think it may be the same one you are currently experiencing. We have fixed this issue and it will be incorporated into our next release once we test to determine that it is stable.

I have seen this problem when trying to save a graph file on a Windows computer, so I suspect that you are on Windows. Is this correct? Our goal is for IGB to function identically on all operating systems, but sometimes issues arise that are specific to one. This issue has been fixed on our development branch, but it won't be released until more testing has been performed to determine its stability.

What you can do, though, is install a copy of our development branch from this link:
https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/

To install, download the file for your operating system ( IGB-master-x64.exe if you are on Windows). Once the file has downloaded, install the program as you normally would, but since the program hasn't been officially released, your computer may ask if you want to trust this program. This is to be expected, but you shouldn't experience any problems as a result of installing this development version. However, since this version is still being developed, there is a chance that you may encounter some bugs in IGB that aren't in the released version of IGB. If you do notice anything unusual, please let me know, if you are able to, so we can fix these before the release.

You should be able to save your graph properly on this development version. If you run into any problems during the process, please let me know and I can help resolve the issue. I hope using the development version is able to suit your needs. If you have anymore questions or feedback for our team, please don't hesitate to contact me.

Thanks again,

Mason Meyer
IGB Support Specialist

From: Gwenivere Cackett <gwenivere.cackett.13@ucl.ac.uk>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Wed, Mar 14, 2018 at 10:38 AM
Subject: Re: IGB 'Problem Saving File'

Dear Mason Mayer,

Thanks for your help. I’ve tried downloading and installing the newer version from https://bitbucket.org/lorainelab/integrated-genome-browser/downloads/IGB-master-x64.exe.

However it won’t install. I do have a windows 64 machine (windows 10) and certainly have administrator privileges but when I try to run the .exe file it says I don’t have permission to access it (see below). Running as administrator doesn’t help.

Best wishes,

Gwenny Cackett

From: Mason Meyer <mmeyer20@uncc.edu>
To: Gwenivere Cackett <gwenivere.cackett.13@ucl.ac.uk>
Date: Sun, Mar 25, 2018 at 11:29 AM
Subject: Re: IGB 'Problem Saving File'

Hello again Gwenny,

I apologize for the delay in responding to you. I had an issue with my e-mail that was preventing me from receiving messages and I apologize for this inconvenience.

I am very curious to know more about the issue with the new version not installing for you. I suspect that it could be because you are on a 32-bit version of Windows, but I am really not sure about this as I have never seen this message myself. I will need to do some quick testing to see if this issue is caused by the 32-bit operating system, but you may be able to help me. If you are able, can you tell me what version of Windows you are running?

We are getting closer to releasing our development version to the public, but this still may not be ready for a little while, so I am hoping we can get this development version to work for you so you can save graph tracks as intended.

Thanks again,

Mason Meyer

From: Gwenivere Cackett <gwenivere.cackett.13@ucl.ac.uk>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Mon, Mar 26, 2018 at 5:29 AM
Subject: Re: IGB 'Problem Saving File'

Dear Mason,

Thanks for your help. Actually I’m running a 64-bit version, Windows 10. My laptop is pretty new and quite powerful, so it should be able to run anything. I am confused about the permission issue as I have admin permissions, since it’s my laptop.

Best wishes,

Gwenny

From: Mason Meyer <mmeyer20@uncc.edu>
To: Gwenivere Cackett <gwenivere.cackett.13@ucl.ac.uk>
Date: Mon, Mar 26, 2018 at 8:43 AM
Subject: Re: IGB 'Problem Saving File'

Hello again Gwenny,

Thanks for your quick response and for letting me know you’re running a 64-bit operating system.

As I continued to look into reasons why you saw the message you did, I realized that there could be some Antivirus software that’s preventing you from being able to run the IGB installer. My understanding of this is that our development branch does not have the same signed certificates that our publicly released branch has, so some antivirus software will flag the installer as coming from an unknown source. Letting the installer bypass any antivirus software before attempting to install would not cause any problems for you as our development branch does not contain any malicious software, so if you think this could be why you can’t open IGB, I would try to turn off your antivirus protection right before installing IGB and turn it back on when you’re done. I found this webpage that talks about the reasons you may be seeing the message you see, and antivirus software is listed as the second reason:
https://www.easeus.com/data-recovery/windows-cannot-access-the-specified-device-path-or-file.html

I actually have to do this on my computer when I am installing the development branch. Some antivirus programs will give you the option to trust the software, but others may prevent the software from opening without giving you a chance to trust the software, so the antivirus software may need to be turned off to get the IGB installer to open. Please let me know if you think this could be what is causing the issue for you, and if not, I will keep looking into it. If you need help figuring out how to turn off your antivirus software, please let me know and I can help with that.

Thanks again,

Mason Meyer
IGB Support Specialist

From: Gwenivere Cackett <gwenivere.cackett.13@ucl.ac.uk>
To: Mason Meyer <mmeyer20@uncc.edu>
Date: Mon, Mar 26, 2018 at 9:19 AM
Subject: Re: IGB 'Problem Saving File'

Hi Mason,

So I greenlit the software with my antivirus program (Avast), and it seems to have installed properly – I can open, load genomes etc. However, now there is a new issue: I can’t view .bam or .sam files of alignments. I can load them but the ‘Load Data’ button just makes everything in the track white, even though the data should be coloured blue. And these bam files can load in other programs so they’re fine…

This didn’t happen in the official IGB release so it’s something new.

Best wishes,

Gwenny

From: Mason Meyer <mmeyer20@uncc.edu>
To: Gwenivere Cackett <gwenivere.cackett.13@ucl.ac.uk>
Date: Mon, Mar 26, 2018 at 11:03 AM
Subject: Re: IGB 'Problem Saving File'

Hello again Gwenny,

Thanks for our your help in troubleshooting these issues. On my machines, I am able to load BAM files, so I am wondering if there is something minor going on that is causing you to experience the issue. Are you able to share any of your files with me, by chance, so I can use them to test this issue? If not, we may be able to figure out other ways to try to resolve the issue, but sharing the files will probably be the best way for me to troubleshoot.

Thanks again,

Mason Meyer
IGB Support Specialist