Ann Loraine

1. Changed osgi plugin to biz.aQute.bnd.builder.
2. Made the necessary changes to build.gradle file to stop importing htsjdk packages from the same library.

build.gradle file is attached to this ticket.

I have tested with my IGB with the jar with current changes, it is working fine in IGB.

(Note: IGBF-1767 (bundle resolution error) is also done. After this ticket, kindly review IGBF-1767 so that I can submit a pull request.

Review completed. Please proceed with pull request on github.

Ann Loraine

Branch: https://github.com/VallapuCharan/htsjdk/commit/506df2c2ad245aa779fd25462da80c2e76222bcb
Pull request submitted.

Merged pull request.

Uploaded newly built jar to nexus.

To test:

1. Download jar from nexus: https://nexus.bioviz.org/repository/maven-releases/htsjdk-igb/htsjdk-igb/2.16.2/htsjdk-igb-2.16.2.jar
2. Use bnd (see comment from linked issue) to inspect MANIFEST of jar.
3. Check that htsjdk does not import its own packages.
4. Check that the newly deployed artifact can support building IGB installer via bitbucket pipeline. For this, you can trigger a build on the master branch of your fork.

Confirmed items 2 and 3 above. Running:

• bnd print htsjdk-igb-2.16.2.jar

shows that the only packages being imported are:

[IMPEXP]
Import-Package
org.apache.commons.compress.compressors.bzip2

org.apache.commons.compress.utils

org.apache.commons.jexl2

Checking item 4 above:

• Triggered re-run of master branch pipeline on team repository. The newly deployed htsjdk-igb artifact should be used to build.
  Build is successful.

Based on above testing I am moving this to Closed.

To test:

1. Download biz.aQute.bnd-4.2.0.jar

2. execute this command
java -jar biz.aQute.bnd-4.2.0.jar print htsjdk-igb-2.16.2.jar

3. Check Import-Packages, it should not contain htsjdk packages. It should only contain below-mentioned packages.

Import-Package
org.apache.commons.compress.compressors.bzip2

org.apache.commons.compress.utils

org.apache.commons.jexl2