Building and Installing from Source

Quick instructions for building and installing ncbi-vdb from source.

1. Dependencies:
   ncbi-vdb will attempt to utilize 3rd party libraries and development headers from your system if they can be located:
   libxml2 (needed for many loaders)
   libmagic (needed for copycat)
   libhdf5 (needed for pacbio-load)
   If any of these libraries cannot be located, their functionality will be missing from our library.

2. Create an ncbi source directory if needed.
   While this is not strictly required, our configuration scripts will benefit by being able to locate related projects without asking for explicit paths:
   $ mkdir ncbi

3. Check out the sources:
   $ cd ncbi
$ git clone https://github.com/ncbi/ncbi-vdb.git

4. If you have not yet installed ngs, please get the sources at this point. It is not necessary to build and install ngs yet, but since ncbi-vdb contains an ngs "engine", it needs some header files:
   $ git clone https://github.com/ncbi/ngs.git

5. Configure the build:
   $ cd ncbi-vdb
$ ./configure
   By default, configure will select a build-output directory under your $HOME and will install under /usr/local/ncbi-vdb on Linux. The default settings can be changed, of course. For all options, you can run:
   $ ./configure --help

6. Make the libraries:
   $ make

7. Install the libraries and includes (you may be asked for an admin password):
   $ sudo make install

At this point, the installation should be complete, although you will probably have to login again before all changes take place. If the installation is successful, you should find library code installed and an update to shell variables (only AFTER logging in again). To verify update of your environment:
$ echo $LD_LIBRARY_PATH # should now have the path to your installed ncbi-vdb libraries