genomicsdb-<VER>.jar bundles native libtiledbgenomicsdb-<VER> shared libaries for Linux and OSX. This native library should not have dynamic dependencies with other shared libraries and is statically linked with all other dependencies like C/C++ runtime libraries, ssl, protobuf, curl, etc. The only dynamic dependency is with backward compatible glibc and zlib. See https://github.com/GenomicsDB/GenomicsDB/wiki/Compiling-GenomicsDB#building-a-distributable-jar.
To build and test gatk with GenomicsDB using Docker, specify the following optional build arguments
| Build Argument | Default |
|---|---|
| os=ubuntu:trusty|centos:7|<linux_base:ver> | centos:7 |
| user=<user_name> | gatk |
| branch=master|develop|<any_gatk_branch> | master |
Examples:
git clone https://github.com/nalinigans/TestGenomicsDB-gatk.git
cd TestGenomicsDB-gatk
docker build --build-arg os=ubuntu --build-arg branch=nalini_test -t gatk:ubuntu .
To run and enter the bash shell:
docker run -it gatk:ubuntu
To delete docker images:
docker image rm -f gatk:ubuntu
docker system prune #optional