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To Compile PluMA:

Install scons:
http://www.scons.org/

Once installed, the command to compile is:

"scons"

This will assume you have all compatible languages: C/C++, Python, CUDA, Perl, and R.

If you do not have some or all of the last three (CUDA, Perl, R) you can leave them out of the
compilation by passing "cuda=0", "perl=0" and/or "r=0" to scons, i.e.

scons cuda=0 r=0

Would run with Perl but not CUDA or R.
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To Run PluMA:

Upon successful compilation, the command to run PluMA is:

./pluma (config file) (optional restart point)

i.e.

./pluma config.txt

Would run the pipeline in the file config.txt

I can also run that pipeline from a specific stage by supplying an optional restart point, i.e.:

./pluma config.txt ATria

Would run starting from the "ATria" plugin in "config.txt".
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