JNI code for fermi lite.
This project builds dynamic libraries with a JNI API. It allows Java code to call Heng Li's fermi lite assembler.
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
commit your changes and push your branch to github
# might have to do these to be able to sign the tagged version
# git config --global commit.gpgsign true
# gpg --list-keys # to get your key ID
# git config --global user.signingkey <your key ID>
# export GPG_TTY=$(tty)
# git config --global gpg.program gpg2
git tag -a -s 1.x.x -m 'tag comment'
git push origin 1.x.x
scripts/build_both_dylib_and_so.sh # build on Linux and move lib to src/main/c
# source artifactory credentials
./gradlew uploadArchive -Drelease=true
# go to https://oss.sonatype.org/#stagingRepositories and close and release your artifact
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 -DLIBFML_PATH=<that permanent location> when you run GATK (or other Java program).