diff --git a/python/farm_commands2.py b/python/farm_commands2.py
index 239828f5b..4da53adb3 100755
--- a/python/farm_commands2.py
+++ b/python/farm_commands2.py
@@ -17,12 +17,13 @@ def all(iterable):
 MAX_UNNAMED_DEPENDENCIES = 10
 
 class FarmJob:
-    def __init__( self, cmd_str_from_user, jobName = None, outputHead = None, outputFile = None, dependencies = [], dependencyNameString = None, dieOnFail = False):
+    def __init__( self, cmd_str_from_user, jobName = None, outputHead = None, outputFile = None, dependencies = [], dependencyNameString = None, dieOnFail = False, memlimit = None):
         self.cmd_str_from_user = cmd_str_from_user
         self.jobName = jobName
         self.outputHead = outputHead
         self.outputFile = outputFile
         self.dieOnFail = dieOnFail
+        self.memlimit = memlimit
 
         self.dependencies = dependencies
         if self.dependencies == None:
@@ -136,6 +137,9 @@ def buildExecutionString(job, farm_queue = None, debug = True):
         cmd_str = "bsub -r -q " + farm_queue 
         if farm_stdout != None:
             cmd_str += " -o " + farm_stdout
+
+        if ( job.memlimit != None ):
+            cmd_str += " -R \"rusage[mem=" + job.memlimit[0:-1] + "]\""
         
         # fixme
         if job.dependencies != []:
diff --git a/python/madPipelineUtils.py b/python/madPipelineUtils.py
index 3db856bd2..2fc78d41e 100755
--- a/python/madPipelineUtils.py
+++ b/python/madPipelineUtils.py
@@ -45,7 +45,7 @@ def appendExtension(path, newExt, addExtension = True):
 #    return os.path.join(OPTIONS.dir, s)
 
 class PipelineArgs:
-    def __init__( self, GATK_JAR = GATK_JAR, ref = 'hg18', name = None, memory = '3g', excludeChrs = [] ):
+    def __init__( self, GATK_JAR = GATK_JAR, ref = 'hg18', name = None, memory = '2g', excludeChrs = [] ):
         self.GATK = 'java -Xmx%s -Djava.io.tmpdir=/broad/shptmp/depristo/tmp/ -jar ' + GATK_JAR + ' -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -l INFO '
         self.ref = ref
         self.name = name
@@ -81,7 +81,7 @@ class PipelineArgs:
 #
 def simpleGATKCommand( pargs, name, args, lastJobs ):
     cmd = pargs.finalizedGATKCommand(args)
-    return [FarmJob(cmd, jobName = pargs.getCommandName(name), dependencies = lastJobs)]
+    return [FarmJob(cmd, jobName = pargs.getCommandName(name), dependencies = lastJobs, memlimit = pargs.memory)]
 
 # 
 # Takes a simpleGATKCommand and splits it by chromosome, merging output
@@ -99,7 +99,7 @@ def splitGATKCommandByChr( myPipelineArgs, cmd, outputsToParallelize, mergeComma
         if myPipelineArgs.convertToB36():
             chr_cmd_str = hg18args_to_b36(chr_cmd_str)
             
-        chrCmd = FarmJob(chr_cmd_str, jobName = cmd.jobName + '.byChr' + chr, dependencies = cmd.dependencies)
+        chrCmd = FarmJob(chr_cmd_str, jobName = cmd.jobName + '.byChr' + chr, dependencies = cmd.dependencies, memlimit = myPipelineArgs.memory)
         return chrCmd, chrOutputMap
 
     #print '######################################### chrsToSplitBy', myPipelineArgs.chrsToSplitBy(hg18)
@@ -110,7 +110,7 @@ def splitGATKCommandByChr( myPipelineArgs, cmd, outputsToParallelize, mergeComma
         mergeCommand = mergeCommands[i]
         mergeFile = outputsToParallelize[i]
         splitFiles = map(lambda x: x[1][i], splits)
-        return FarmJob(mergeCommand(splitFiles, mergeFile), jobName = cmd.jobName + '.merge', dependencies = splitCommands)
+        return FarmJob(mergeCommand(splitFiles, mergeFile), jobName = cmd.jobName + '.merge', dependencies = splitCommands, memlimit = myPipelineArgs.memory)
         
     mergeCommands = map(mergeCommand1, range(len(outputsToParallelize)))
 
@@ -127,4 +127,4 @@ def mergeByCat(splitFiles, mergeFile):
 
 def indexBAMFile( name, bamFile, lastJobs ):
     cmd = 'samtools index ' + bamFile
-    return [FarmJob(cmd, jobName = 'samtools.index.' + name, dependencies = lastJobs)], None
+    return [FarmJob(cmd, jobName = 'samtools.index.' + name, dependencies = lastJobs, memlimit = "1g")], None