Thank you for your quick response.  However, I have checked and bedtools are 
indeed in the galaxy path.  When reviewind the log, I get the following:

galaxy.jobs.runners.local DEBUG 2013-07-09 16:59:15,937 execution
finished: grep -v '^#'
/usr/local/galaxy/galaxy-dist/database/files/000/dataset_515.dat |
sort -k1,1 |           bedtools genomecov -bg -split -i stdin -g
/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len
       > temp.bg ; bedGraphToBigWig temp.bg
/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len
/usr/local/galaxy/galaxy-dist/database/files/000/dataset_519.dat

After reading the log, I ran the following command in my terminal:

bedtools genomecov -bg -split -i stdin -g 
/usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len

However this crashes.  After looking in my computer, I find that bedtools do 
not contain the file genomecov.  Is this an erroneous assumption of mine or 
have I installed something wrong?

Than you for your time,
--Ricardo Perez
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