> 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 some
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_5
You'll need to make sure that bedtools is in your Galaxy user's path.
Best,
J.
On Jul 9, 2013, at 6:40 PM, Perez, Ricardo wrote:
> Dear all,
>
> As I was trying to do visualize my data set in trackster, I get the following
> error:
>
> /bin/sh: 1: bedtools: not found
> sort: fflush failed: st
