build difficulties, docker error

[jpdna]

Hi,

We are excited about the potential to use GenomicsDB for some large cohort projects at NIH, both with GATK and for other purposes, but I am having trouble getting the build of GenomicsDB to succeed on any of my Mac, Ubuntu, or Centos7 - various dependencies and env paths not found on each despite try to add them.

Could it be the case that the documentation here:
https://github.com/Intel-HLS/GenomicsDB/wiki/Building-GenomicsDB-Version-0.4.0
is out of date? With first issue being need to use cmake ?

I was hoping to be able to use Docker, at least to see a working example by studying the docker file, but I find that:

docker run -it -v myoutput:/output/ intelhlsgenomicsdb/genomicsdb_builder build_genomicsdb

as suggested here: https://hub.docker.com/r/intelhlsgenomicsdb/genomicsdb_builder/
https://github.com/Intel-HLS/GenomicsDB/tree/geno-build-docker_ming/docker/GenomicsDB_builder

fails with

docker run -it -v myoutput:/output/ intelhlsgenomicsdb/genomicsdb_builder build_genomicsdb
....
   Called from: [3]	/home/default/build_src/GenomicsDB/cmake/Modules/Findlibuuid.cmake
                [2]	/home/default/build_src/GenomicsDB/cmake/Modules/FindTileDB.cmake
                [1]	/home/default/build_src/GenomicsDB/CMakeLists.txt
CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:108 (message):
  Could not find libuuid headers and/or libraries (missing:
  LIBUUID_INCLUDE_DIR LIBUUID_LIBRARY)
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:315 (_FPHSA_FAILURE_MESSAGE)
  cmake/Modules/Findlibuuid.cmake:14 (find_package_handle_standard_args)
  cmake/Modules/FindTileDB.cmake:37 (find_package)
  CMakeLists.txt:110 (find_package)


   Called from: [3]	/home/default/build_src/GenomicsDB/cmake/Modules/Findlibuuid.cmake
                [2]	/home/default/build_src/GenomicsDB/cmake/Modules/FindTileDB.cmake
                [1]	/home/default/build_src/GenomicsDB/CMakeLists.txt
-- Configuring incomplete, errors occurred!
See also "/home/default/build_src/GenomicsDB/build/CMakeFiles/CMakeOutput.log".
ERROR: build_gdb not find Makefile
/usr/bin/build_genomicsdb: line 78: return: -1: invalid option
return: usage: return [n]
FAIL: cannot build GenomicsDB
/usr/bin/build_genomicsdb: line 95: return: can only `return' from a function or sourced script

I'm happy to use any flavor of Linux you recommend.
Any suggestions, or especially recipe to follow on a fresh install of whatever OS you suggest, would be much appreciated.

For our projects we are likely to use the Java wrappers and Spark, so possibly we could use the maven artifact you publish at:
https://mvnrepository.com/artifact/com.intel/genomicsdb
and not have to worry about doing the build, does this seem viable?

However - I would very much like to get the build to succeed locally in any case.

Thanks.
Justin Paschall
Bioinformatics Scientist
National Human Genome Research Institute (NHGRI)
National Institutes of Health

[kgururaj]

Hello Justin, we hope that you will find GenomicsDB useful in your work.

• For general compilation: I would clone the master branch from Github and follow the instructions on https://github.com/Intel-HLS/GenomicsDB/wiki/Compiling-GenomicsDB. We develop on CentOS-7 machines.
• Unfortunately, the Docker parts of GenomicsDB are outdated and not maintained. If a GenomicsDB Docker container would be useful to you, we can create a new container.
• If you use the jar file from Maven central, the Java/Spark API can be used directly.
• The compilation error in your message shows missing libuuid headers. Search for libuuid-devel in the compilation page