Update Snakefile to work from cluster

Snakefile

@@ -19,8 +19,9 @@ configfile: "config.yaml"
 R = config["R"]
 
 # Setup the required simulation and method parameters.
-shell("Rscript code/simulation-pars.R")
-shell("Rscript code/method-pars.R")
+# /dev/null is used to suppress the log files.
+shell("{R} CMD BATCH code/simulation-pars.R /dev/null")
+shell("{R} CMD BATCH code/method-pars.R /dev/null")
 
 # Retrieve the simulations and method paramters from file.
 sim_ids = json.loads(open(config["sim_ids_path"]).read())
@@ -51,6 +52,7 @@ rule run_method:
 			fun = lambda wc: config["code_folder"] + "run-" + wc.method_id.split('_')[0] + ".R"
 	output: res = config["results_folder"] + "{sim_id}-{method_id}.rds"
 	log:	config["logs_folder"] + "run_method-{sim_id}-{method_id}.Rout"
+	resources: mem_mb=lambda wildcards, attempt: attempt * 2000
 	shell:	'''{R} CMD BATCH --no-restore --no-save\
 		"--args sim={input.sim} fun={input.fun}\
 		meth_pars={input.method_pars} res={output.res}"\