Mavenization of HTSJDK and other useful additions

[nh13]

Please see pull-request #97. This differs as follows:

• Squash commits from the individual committers.
• LICENSE file is no longer present in the history.
• Rebased on top of master.

As an aside, we release HTSJDK and Picard at the same time. Therefore, I would be grateful to understand what I need to do to start publishing the HTSJDK release. The release script we use can be found in Picard: https://github.com/broadinstitute/picard/blob/master/src/scripts/release_picard.sh

[fnothaft]

+1, thanks for doing the cleanup @nh13!

As for pushing the releases, you are setup in Sonatype OSS and use Travis for CI, correct? Here's two thoughts:

• For pushing actual releases (e.g., via your script above) this is actually really easy. The build profile we've added in Maven should allow releases via a few targets. We keep our release scripts for ADAM here; you'd just need to add the one line that is in release.sh, which handles pushing the release to OSS Sonatype, tagging the repo as a release, and pushing to the git repo.
• You should also push snapshot releases. You can do that via "mvn deploy" when running in Travis. We don't use Travis CI for ADAM, but here's the config file that I use to push snapshots to Sonatype for a side project of mine.

[nh13]

@fnothaft thanks for the clear explanation. I will merge this in, and the start work on Picard's release script and travis.yml.

[fnothaft]

@nh13 no problem; I look forward to seeing the releases in Maven Central.

The one thing to add is that once you push the release to Sonatype, you need to log in and close/promote the release. This is pretty simple and is documented at Sonatype. You don't need to do anything for snapshot releases.

[cassiedoll]

Hey guys - just checking in to see if this awesome pom is going to make its way to maven central soon. Even just one static build (without any fancy auto updating) would be great!

[gdgib]

I'm wondering what the timeline on getting a copy of this into maven central might be. Any word on this? I know there's a lot of interest since the version there is quite old. I could happily handle the maven publishing, either directly or perhaps of a compatible fork if no one has time for this.

[holtgrewe]

I second @cassiedoll and @gdgib in that having a recent HTSJDK build on Maven central would be very useful. Currently, there is an inofficial release by the seqdoop people but that is built against an old version of cofoja which cannot be used in Java 8.

Is there a timeline for a (maybe static) upload to maven central?

[fnothaft]

+1, it'd be great to get this release on Maven Central since Cofoja blocks the use of Java 8. I'll echo @gdgib; specifically, I'd be glad to help with the release process.

[johnmu]

+1, I can also help with this!

[visze]

+1, need it!

[martenj]

+1, me too!

[tdanford]

+1

[antonkulaga]

+1

[julesjacobsen]

[laserson]

+1, please make this happen :)

[nh13]

Hello folks,

thanks to Frank, others, and yourselves we have a release to Maven central. We will distribute binaries to github as well as publishing them to maven central. My apologies for some duplicated effort here but it has really helped having all your help and the community call to action to get this one done.

Enjoy!

The Picard Team.

[gdgib]

Thank you so very much, I think I can safely say that we all really appreciate this effort.

[fnothaft]

Agreed! Thank you very much @nh13!

[julesjacobsen]

Awesome news! Many thanks, this is much appreciated and comes just in time.

[holtgrewe]

@nh13 I really appreciate your work, thank you!

The uploaded files do not play well with Java 6. Is this intentional? The seqdoop version was compatible with Java 6.

[jacarey]

@holtgrewe The htsjdk uploaded to sonatype was compiled for 1.7

It may take a little while for this to be uploaded to the repository. Please try again shortly and let me know if you are still having issues.

Thanks

[superbobry]

The release on Maven Central seems to carry Scala as dependency. I wonder was this intentional? The master version of htsjdk doesn't have any Scala code.

[jacarey]

Our sbt build file doesn't exclude the scala library

This will be fixed in the next build

[superbobry]

I see, thanks.

[heuermh]

It appears that picard 1.129 still has a compile-time dependency on testng

        <dependency>
            <groupId>org.testng</groupId>
            <artifactId>testng</artifactId>
            <version>6.8.8</version>
        </dependency>

Wasn't that resolved in #97?

[jacarey]

That was the case with htsjdk. There is still a dependency on testng at compile time because of a mis-placed test file.
src/java/picard/vcf/filter/TestFilterVcf.java

[heuermh]

I tried creating a pull request for that but the build fails

$ sbt
...
[info] downloading https://repo1.maven.org/maven2/org/apache/httpcomponents/httpcore/4.1.4/httpcore-4.1.4.jar ...
[info]  [SUCCESSFUL ] org.apache.httpcomponents#httpcore;4.1.4!httpcore.jar (164ms)
[info] Done updating.
picard/build.sbt:90: error: value assemblyMergeStrategy is not a member of scala.xml.NodeBuffer
possible cause: maybe a semicolon is missing before `value assemblyMergeStrategy'?
assemblyMergeStrategy in assembly := {
^
[error] Type error in expression
Project loading failed: (r)etry, (q)uit, (l)ast, or (i)gnore? i
[warn] Ignoring load failure: no project loaded.

Should I just create an issue instead?