gatk-bwamem-jni

JNI code for bwa mem.

This project builds dynamic libraries with a JNI API. It allows Java code to call Heng Li's bwa mem aligner.

To build you'll need gmake, git, gcc, and Java 8.

To build and install a snapshot locally:

./gradlew install

This will work for testing but will only include a native library for your system.

To upload a snapshot from a Broad Institute OSX machine with both OSX and Linux binaries:

commit your changes and push your branch to github
scripts/build_both_dylib_and_so.sh
./gradlew uploadArchives printVersion

To upload to maven central

First follow the one-time setup instruction post on the Picard project Wiki page. You can ignore the last part about setting up sudo rights on picard02.

Then do the following:

commit your changes and push your branch to github
git tag -a -s <version>
./gradlew clean
scripts/build_both_dylib_and_so.sh
./gradlew uploadArchive -Drelease=true

Then you need to finalize the release to maven central:

• Go to https://oss.sonatype.org/#stagingRepositories, logging in if necessary. If you don't see anything, click "refresh".

• Find the release you just uploaded. It will probably be at the bottom with a name like comgithubbroadinstitute-1027, with your user ID listed as owner.

• Check the box next to your release, then select "close". Press the refresh button repeatedly until it updates and its status says "closed".

• Select your release again and click "release". Select the box to "automatically drop" in the pop-up confirmation dialog.

It may take ~30-180 minutes for the new release to show up on the maven central.

To use this JNI binding on another architecture for which we don't provide a binary:

Go into src/main/c. Modify the Makefile to produce a library name appropriate to your system. Type make (you'll need gmake, git, and gcc). Move the library you built somewhere permanent on your machine. Use -DLIBBWA_PATH=<that permanent location> when you run GATK (or other Java program).