Fix: Bundle description not getting added to repository.xml for soft clips operator

GroupId is given as com.igb instead of org.lorainelab.igb
cc: [~aloraine] and Noor Zahara

Fork link: https://bitbucket.org/Inaylor01/softclip_track_operation/src/IGBF-2581/

Change is done according to Supreeth's suggestion above

Please submit a PR when ready.

Pull request: https://bitbucket.org/lorainelab/softclip_track_operation/pull-requests/1/igbf-2581-fix-bundle-description-not

Some observations -

I read through the pom.xml file in full again to try and narrow down where the issue could be and I settled in around the sourceEncoding variable (currently set to UTF-8).
I figured the issue potentially might be solved by changing this variable to base64 to switch the encoding so the description will work but I ran into a few Maven compiler errors when I did some local testing, so I don't think I've got that quite yet.

I've done a bit of googling about UTF-8 and base64 to see if I maybe had a syntactical issue and will continue to work at it.

Am I in the right ballpark, however?

Suggestion:

• To understand the wrong behavior & fix it, it's helpful to examine a similar system that is working as expected.

We have an app that is super simple that is working as expected - https://bitbucket.org/lorainelab/super-simple-igb-app/src/master/
Build the app either on your local machine or in a bitbucket repo (using the pipeline script). Review the output of the build process to observe the correct behavior. Then look at what happens when you build the (broken) soft clip app. This may give you some ideas.

Some background:
Our Loraine Lab maven plugin bundle-markdown-encoder is supposed to take the file indicated by parameter "markdownFile" and base64-encode it for inclusion in the "repository.xml" file bundled with the app jar file. This is the step that appears to not be working properly with the soft clip app. Something about how the soft-clip app is configured is preventing this from happening.

Also look at the implementation of the plugin. This may also give you some ideas on what to do: https://bitbucket.org/lorainelab/bundlemarkdownencoder/src/master/

Fork link: https://bitbucket.org/Inaylor01/softclip_track_operation/src/IGBF-2581/

Everything works fine. But I am not sure if this is how the soft-clip option should appear if I select operations for a BAM file.

Please submit PR when ready.

Pull request: https://bitbucket.org/lorainelab/softclip_track_operation/pull-requests/2/igbf-2581-fix-bundle-description-not

For testing, try loading the App from team repo downloads section:
https://bitbucket.org/lorainelab/softclip_track_operation/downloads/

To do this:

• Add the above link as a new App Repository (Tools > App Manager > Manage Repositories)
• The soft clip app should appear in the list of available apps within App Manager
• When you select the soft clip app, you should see the description of the app shown in the App manager

If the above occurs, move to Done.

The softclip app appears as `Graph Soft Clips` application in the list of available apps and shows the description in the app manager
The soft Clip app installs as expected... There are no errors in the logs.
Tested on Mac OS Catalina 10.15.7