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