From: Piero Montanari [piero-mo@hotmail.com]
Sent: Monday, March 23, 2015 8:04 AM
To: Norris, David; Loraine, Ann
Cc: Meyer, Mason
Subject: RE: Information about IGB

Hi David,

I have tried to download the files from http://igbquickload.org/<http://igbquickload.org/.> but I don't understand which are the useful files: for each genome version there are a lot of different files.
Then, when I have downloaded them, how can I generate a personalized genome version with the right name and how I add that to IGB?

Thanks in advance for your help.
Piero

> From: dcnorris@uncc.edu
> To: piero-mo@hotmail.com; Ann.Loraine@uncc.edu
> CC: mmeyer20@uncc.edu
> Subject: RE: Information about IGB
> Date: Mon 3/23/2015 10:58 AM

Hi Piero,
I have put together a quickload directory for your reference and use, which you can download from here (https://dl.dropboxusercontent.com/u/18695961/quickload.tar.gz). You will want to extract this directory somewhere on your local machine and then add it as a "Data Source" (see https://wiki.transvar.org/display/igbman/Adding+and+Managing+Data+Source+Servers). Once you have added this quickload directory, you will notice that on loading the latest human genome version data will load from both the remote igbquickload.org quickload and your new local quickload directory data source. I would suggest that you disable the igbquickload.org data source to avoid this duplication. If you have further questions please let me know.

As an update, we will be releasing IGB 8.3.2 by the end of the week, and it will include your requested feature of a "delete all tracks" scripting command.

Best Regards,
David

> From: Piero Montanari [piero-mo@hotmail.com]
> Sent: Wednesday, March 25, 2015 1:57 PM
> To: Norris, David
> Subject: RE: Information about IGB
>
> Hi David,
>
> I am sorry to bother you continuously, but I have another question. I had to modify the plugin I wrote for IGB to use some external jar libraries. Now when I install it in IGB, it gives me the following error: "error installing plugin... missing requirements".
>
> I don't understand where the problem is. All the dependencies are shows correctly in pom.xml of the plugin project and also in the repository.xml directory. Can you help me? Do you have any guess on which the problem is?
>
> Thanks,
> Piero

> From: dcnorris@uncc.edu
> To: piero-mo@hotmail.com
> Subject: RE: Information about IGB
> Date: Wed, 25 Mar 2015 18:33:26 +0000
>
> Hi Piero,
> No problem at all. What you are seeing is the result of what essentially amounts to a classloading problem. In the custom OSGi classloading model the dependencies specified in your plugins manifest (i.e. the package imports) must be exported by other installed bundles. If you loaded all of your dependencies into the runtime with the proper OSGi manifest information you would not see this error. OSGi is simply telling you that it cannot resolve the necessary classes from what is exported to satisfy your manifest imports.
>
> I recommend you not worry about wrapping all of your dependencies and deploying each one and instead simply embed your dependencies into your module.
>
> You can use the following in your pom.xml if you are using the bnd plugin.
>
> <plugin>
> <groupId>org.apache.felix</groupId>
> <artifactId>maven-bundle-plugin</artifactId>
> <extensions>true</extensions>
> <configuration>
> <instructions>
> <Bundle-SymbolicName>$

</Bundle-SymbolicName>
> <Embed-Dependency>*;scope=compile|runtime;inline=true</Embed-Dependenc
> y> <Embed-Transitive>true</Embed-Transitive>
> <Include-Resource>
>

> </Include-Resource>
> <Import-Package>*;resolution:=optional</Import-Package>
> <Export-Package>
> com.affymetrix.common
> </Export-Package>
> <Bundle-ActivationPolicy>lazy</Bundle-ActivationPolicy>
> </instructions>
> </configuration>
>
> Note these two line
> <Embed-Dependency>*;scope=compile|runtime;inline=true</Embed-Dependenc
> y> <Embed-Transitive>true</Embed-Transitive>
>
>
> This will actually "wrap" the dependencies and make them available to your plugin's classloader.
>
> Let me know how things work out and don't hesitate to reach out with more questions if they come up.
>
> Best Regards,
> David
>

From: Piero Montanari [piero-mo@hotmail.com]
Sent: Thursday, March 26, 2015 11:54 AM
To: Norris, David
Subject: RE: Information about IGB

Hi David,

that works perfectly. I was able to run my plugin and extract the information I wanted from IGB.
Now I am working on the GUI to use my application and I will be able to show you how it works (at least through snapshots) shortly.

I have a doubt: IGB seems to remember my preferences (datasource for quickloads, plugin repositories,...) even if I uninstall the current instance and re-install a new IGB version in a new directory. How is it possible? Where does it store the preferences in my machine? I don't know if I was clear....

I wanted also to point a minor bug. When you select a local source for the plugin repository and also for the data sources IGB gives the following problem:
if the address is "C:\Documents", it automatically turns it into "file:\C:\Documents" and it gives an error. The user has to manually delete "C:\" to get "file:\Documents" .
The same thing happens with the "SOURCE" attribute of regions belonging to a local .gtf file. The "SOURCE" attribute value is "file:\C:\Documents\etc" and it can gives problem if someone wants to use directly that attribute to do something.
Obviously this is not a big problem, but I thought you wanted to know about it.

By the way,I will stay tuned waiting for the minor update of this week.
Thanks again for your help,
Piero