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cerebis / meta-sweeper

Parametric sweep of simulated microbial communities and metagenomic sequencing.
GNU General Public License v3.0
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JNI_LIB_PATH should not be an explicit absolute path #53

Closed cerebis closed 7 years ago

cerebis commented 7 years ago

nextflow.config

The current configuration should utilise a Java environmental variable etc, rather than assume an explicit system path.

cerebis commented 7 years ago

I have modified the setup to rely on an environment variable. As not all distributions can pull down the required beagle library via package management, some users will need to build beagle-lib from source. This is easy enough, but where the resulting shared library is stored will be dependent on the user and their permissions -- i.e. not necessarily a system folder.

Therefore, we now make use of a BEAGLE_LIB variable that must be set prior to running the workflow. This path should point to the containing directory of the shared library libhmsbeagle-jni.so. The value will be handled internally by dependent processes.

The setup script bash_configure will check for this variable and object if it is not set, or the library itself is not found within it.