bash loop to run tons of jobs but limit the background to a certain smaller number at a time. change the -gt 0 to be -gt _n_ to limit the number of background jobs to _n_

gistfile1.sh

# primate version
for f in ../packagePrimates/analysis/comparatorWrapper-primates.*/; do 
  for c in A B C D; do
    ##########
    # This block holds the background process count in check
    while [ $(jobs | wc -l) -gt 0 ]; do 
      sleep 2; 
    done; 
    ##########
    for partner in simChimp simGorilla simOrang; do 
      for m in prec recall fscore; do 
        b=$(basename $f); mkdir -p precRecallWiggles/primates/$b/; ./comparatorPlot.py --xml $f/comparatorMRCA.xml --mode $m --out precRecallWiggles/primates/$b/$b.simHuman.$c.$partner.$m.pdf --ref simHuman.chr$c --partner $partner & 
      done; 
    done; 
  done; 
done;

# mammal version
for f in ../packageMammals/analysis/comparatorWrapper-mammals.*/; do for c in D F H I J K; do while [ $(jobs | wc -l) -gt 0 ]; do sleep 2; done; for partner in simCow simDog simMouse simRat; do for m in prec recall fscore; do b=$(basename $f); mkdir -p precRecallWiggles/mammals/$b/; ./comparatorPlot.py --xml $f/comparatorMRCA.xml --mode $m --out precRecallWiggles/mammals/$b/$b.simHuman.$c.$partner.$m.pdf --ref simHuman.chr$c --partner $partner & done; done; done; done;