Fork Link: https://bitbucket.org/Inaylor01/integrated-genome-browser/src/IGBF-2596/

Quick request for clarification:

Please confirm:

• Does it build in bitbucket?

It fails to build, will examine what happened further.

It says that it cannot find a specific artifact in repo2. Should we remove repo2 along with 1 and 3 as well?

No, you need to retain repo2.

I've run into an issue. So, building the project with repos 1-3 works perfectly however, if I comment out repo1's reference in the pom.xml file (or comment out repo1 and 3's references), I end up having an issue where the project won't build due to repo2's dependencies not being resolved.

Just wanted to put that out there but will continue trying to figure out the problem

Curiously, I've found removing just Repo3 from the pom.xml file allows the project to compile without issue but removing both Repo1 and Repo3 causes this error to come up.

I made sure to run maven on a clean install, and use the -u command to make sure everything was updated and it still wouldn't budge. My thought is that it has something to do with the bioviz repository itself but I am curious to hear what you all think?

The error screenshot is attached to the issue.

[~aloraine], Me and Chester Dias just met about the maven error I was running into and we both observed how when Repo 1 and 2 are in the pom.xml file, IGB would build properly. According to the error, there was a certain jar file, jlfgr (more details are in the error) that was missing. We found that it was located in repo1 and that's why it wouldn't build unless 1 was there.

Chester suggested that we could potentially either move the required jars from repo1 to 2, then get rid of repo1 or we could keep the repository references in a separate maven setting.xml file. I currently have my issue branch where Repos 1 and 2 are in the XML file and wasn't sure if I should submit that for review.

I wanted to get your take about how we should move forward.

[~aloraine] Please let us know if there is any specific reason for having multiple repos? Can we move all the required artifacts into one repo?

Yes we can, but it's hard to do because there are a lot of details to consider.

Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/859/igbf-2596-remove-repo1-and-3-from-918

Commit where repo3 is removed, leaving only 1 and 2

Request for functional review prior to merging:

• Please recruit one person on Windows and another person on Mac.

Test on each platform as follows:

• Install IGB
• Review logging messages - look for any "class not found" errors
• Open Arabidopsis genome and load some data from "Reads" and "Graphs" folders, again observing the console for possible errors

Logan Weidenhammer] - Could you please test Irvin's branch installer as per the above procedure?

Functional Review on Windows:

Installed IGB from Irvin's Fork
Reviewed the Log and did not find any 'class not found' errors.
Opened Arabidopsis genome
Loaded data for a read alignment, and a scaled coverage graph
Reviewed the Log again and did not find a 'class not found' error.

It looks like we still need a MacOS functional review.

Thanks Logan Weidenhammer!
Probably a Mac review won't be needed. So would recommend moving ahead with a PR.

Change of plan:

• Do not remove these from the POM at this time.
• We will need to check that this is feasible after returning DAS1 support.
• Moving to Done.

Note for Irvin Naylor - leaving this assigned to you reflecting the work you have done on it.