Hello! After almost a week of troubleshooting, I finally got it working and I now have a local installation of galaxy that uses 9/10 cores and 32 GB of memory on my macbook pro 
. I left one for the OS so it doesn’t crash. If anyone else has this problem, please use these job_conf.xml settings in your file, and change the number of cores
( 9). It will make all tools default to using the number of cores specified.
<?xml version="1.0"?>
<job_conf>
<plugins>
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
</plugins>
<handlers>
<handler id="main"/>
</handlers>
<destinations default="multicore_destination">
<destination id="multicore_destination" runner="local">
<param id="local_slots">9</param>
</destination>
<tools>
<tool id="*" destination="local"/>
</tools>
</destinations>
</job_conf>
Below is proof :). Trimmomatic using 46 threads running on multiple cores. I confirmed it works with BWA-mem as well.
