How to compile gbwtwrapper library

Clone the gbwtgraph repository recursively

This will clone all the dependencies (recursively), which will then have to compile manually. To achieve that, is essential to make some modifications to the Makefiles. both gbwt and gbwt graph depend on sdsl-lite, located (at the time of writing) in deps/gbwt/deps/sdsl-lite and is different than the path in Makefiles, the later being "SDSL_DIR=../sdsl-lite". The most convenient way to fix this is by creating symbolic links. From one level outside the cloned project run:

Next compile and install the sdsl-lite go to gbwtgraph/deps/gbwt/deps/sdsl-lite and edit CMakeLists.txt then add somewhere at the top of the file

This flag is required for a dynamic library build.

Next run cmake

Ignore sudo if for some reason you already have the necessary privileges.

For that project the -fPIC flag seems to be included so a simple make will suffice. Navigate to gbwtgraph/deps/gbwt and run

From gbwtgraph/deps/libhandlegraph run

Here the make file is well preconfigured. So from the top level of the gbwtgraph repository run

Now the folder /usr/local/lib must include the following files libhandlegraph.a libhandlegraph.so libgbwt.a libgbwtgraph.a

Clone the wrapper

Run

Or just run build.script. Eventually you will end up with libgbwtwrapper.so in /usr/local/lib

You can find the list of exposed functions here