> Da: Loraine, Ann [Ann.Loraine@uncc.edu]
> Inviato: venerdì 19 dicembre 2014 18.21
> A: Piero Montanari; Norris, David
> Cc: piero-mo@hotmail.com
> Oggetto: Re: Information about IGB
>
> Hello Piero,
>
> I’m forwarding your note to David Norris, the IGB lead developer.
>
> Question: Within IGB, a user can delete a track by operating the user interface. (See: https://wiki.transvar.org/display/igbman/Deleting+tracks) Is that enough or do you need us to add a “delete” command to the IGB command language?
>
> I’m not sure what you mean in #2. Maybe explain a little more detail?
>
> Best,
>
> Ann

> From: piero.montanari5@unibo.it
> To: Ann.Loraine@uncc.edu; dcnorris@uncc.edu
> CC: piero-mo@hotmail.com
> Subject: RE: Information about IGB
> Date: Fri, 19 Dec 2014 18:25:05 +0000
>
> Hello everyone,
>
> 1. I know that is possible to do it through the user interface, but i need to do it automaticaly within a Java application. It would be perfect if you are able to add a script command "delete" that does it. A sort of opposite of "load".
>
> 2. What I want to do is to export the information of the regions that are currently selected in IGB. In your browser it is already possible to select one or multiple regions clicking on it. What I need to do is to add a specific command to export the information that are selected. I will then use that information to run an algorithm. To recap what I want to do is to use the selected regions as input for another algorithm coded by us. Is it possible? which is the best way to do so?
>
> Thanks,
> Piero

From: Piero Montanari [piero-mo@hotmail.com]
Sent: Friday, March 06, 2015 7:32 AM
To: Loraine, Ann
Cc: Norris, David
Subject: RE: Information about IGB

Hello Ann,

I have not received any news from you regarding my questions.

To recap, what I want to do is to extract from IGB the information about the selected regions. Basically, I want to extract in some format (also a text format is enough) the information that are show in the "Selected Info" tab in the bottom part of IGB.

My question is: what is the best way to do so? Can I do it somehow or is it something that you have to do?

Thanks in advance,
Piero Montanari

From: Norris, David
Sent: Friday, March 06, 2015 9:25 AM
To: Piero Montanari; Loraine, Ann
Subject: RE: Information about IGB

Hi Piero,
I'm sorry for the delay in responding to your inquiry. We do not currently support an 'export selections' action as you have described. It would not be much trouble for us to allow selections to be dumped to a csv file, and we could also add a new scripting command for executing this feature. We are always interested in adding more analytical tooling into IGB, so if you believe this algorithm your team is developing would useful to the larger IGB community, I'd love to start a conversation with your developers about how they could build their analytics as a simple plugin to IGB instead of as a standalone piece of software. How soon would it be urgent for your team to have this functionality?

Best Regards,
-David

From: Piero Montanari <piero-mo@hotmail.com>
Date: Thursday, March 12, 2015 at 11:13 AM
To: "Norris, David" <dcnorris@uncc.edu>, "Loraine, Ann" <Ann.Loraine@uncc.edu>
Subject: RE: Information about IGB

Hello everyone,
I have developed the plugin but i don't know how to load it in IGB. I have created the <myplugin>.jar file but I do not understand how to load it in IGB. I am sure this is an easy task for you. If you could help me it would be really appreciated.

Thanks,
Piero

> From: Ann.Loraine@uncc.edu
> To: piero-mo@hotmail.com; dcnorris@uncc.edu
> Subject: Re: Information about IGB
> Date: Thu, 12 Mar 2015 15:23:15 +0000
>
> Hi Piero,
>
> David is at a conference this week but will be back on Monday. Do you need an answer before then or would it be OK to get back to you next week?
>
> Congrats on the new plugin - I hope we can help!
>
> Ann

> From: Piero Montanari [piero-mo@hotmail.com]
> Sent: Monday, March 16, 2015 11:30 AM
> To: Loraine, Ann; Norris, David
> Subject: RE: Information about IGB
>
> Hello everyone again,
>
> I was able to load and use my plugin. I am really glad for the help.
>
> I have now another question for you, evn though it is not urgent: is it possible to have a script command to remove a track currently loaded on IGB and one to remove all the tracks currently loaded. It would be really helpful for what we are doing. As soon as we have something that works fine, we will show you how our application functions.
>
> Finally, another general question on IGB. From what I got so far every time I want to use a genome version it is downloaded from an online repository. My question is: is it possible to download a specific genome version that we frequently use and keep it as local? If it was, it would be really helpful because we could use IGB without an internet connection and anyways we could avoid to donwload it every time it is needed.
>
> Thanks a lot for your collaboration. It is really appreciated.
>
> Piero Montanari

> From: dcnorris@uncc.edu
> To: piero-mo@hotmail.com; Ann.Loraine@uncc.edu
> CC: mmeyer20@uncc.edu
> Subject: RE: Information about IGB
> Date: Mon, 16 Mar 2015 16:03:20 +0000
>
> Hi Piero,
> I'm glad you were able to get your plugin to load. I'd be interested in seeing what you have created when and if you are ready to share your work. My team's focus currently is on some heavy architectural changes, but we hope to have much better plugin developer APIs and documentation by the end of the year. I'd be happy to add an additional scripting command to support a "delete all tracks" action, I will add this feature request to our issue tracker and can include it in the next minor release.
>
> Your question on the local caching of commonly used genomes is timely, we already have plans to implement a caching solution to prevent the need for IGB to require internet connectivity to access commonly referenced remote files. I hope to be able to include this feature in IGB 8.4.0 (i.e. the next major release). For now, if you want to achieve this behavior you can download the reference gene models and sequence locally and setup a custom genome which references these files. See https://wiki.transvar.org/pages/viewpage.action?pageId=23200542 for more details on how to load a custom genome. If you let me know which genome you are working with, I can tell you how to download the required files from our site http://igbquickload.org/. If you also have some frequently accessed data, leveraging a local "quickload" directory would be a great way to make those files easy to consume in IGB. I'd be happy to send over an example of how to do this for your reference if this sounds like it could be useful to you.
>
> Thank you for the feedback!
>
> Best Regards,
> -David

> From: Piero Montanari [piero-mo@hotmail.com]
> Sent: Mon 3/16/2015 12:27 PM
> To: Loraine, Ann; Norris, David
> Subject: RE: Information about IGB

Hi David,
when you have a working version of IGB with the "delete all tracks" script command, we will immediately use it.

Concerning the genome version, we are currently using H_sapiens_dec_2013. If it was possible to have it as local, it would be perfect. Let me know which is the best way to do so.

Thanks,
Piero

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