In a standard Linux environment with java installed, I can run the any java program using the command:
java -jar path/to/picard.jar
Where picard is an example of a java program. I can also specify how many CPU threads or RAM the JVM should use using this way:
java -XX:ParallelGCThreads=5 -Xms900m -jar path/to/program.jar
That JVM will get 5 threads and and 900 MB of RAM. All quite straight forward.
However, when I run java programs in an anaconda (conda) environment, which has it's own installation of java, I can run the software simply by typing it:
picard
How do I pass the resource parameters to anaconda? What are the default parameters?
My solution is to first, find where Conda installed Picard within your environment and then give a full path to picard.jar
while passing memory arguments to java
:
java -Xms4G -jar path_to/picard.jar [your_picard_command]