Putting bedtools in the path

[MaryGoAround]

Hello

I am trying to find mutational signature on your SV examples data and I am getting this error

> SV.vcf <- preprocessInput_sv(input_data =  sv_data,resdir = getwd())
[1] "Annotating mutation data:"
  |======================================================================| 100%
[1] "CHC018T"
sh: bedtools: command not found
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  no lines available in input
In addition: Warning message:
In system(paste("bedtools cluster -i tmp.bed -d 1000000", "> res.bed")) :
  error in running command
> 

I know bedtools has been installed on my MacBook

[fi1d18@cyan01 ~]$ which bedtools
/local/software/bedtools/2.21.0/bin/bedtools

How I can solve this error please?

Thank you

[MaryGoAround]

This worked

[fi1d18@cyan01 ~]$ module list
Currently Loaded Modulefiles:
  1) torque/current          8) python/2.7.5(default)
  2) moab/current            9) openmpi/1.6.4/gcc_of2
  3) null                   10) boost/1.54.0(default)
  4) jdk/1.8.0              11) Rstudio/0.98.495.R321
  5) gcc/8.2.0              12) bedtools/2.21.0
  6) R/3.6.1                13) bedops/2.4.26
  7) qt/4.8.5               14) samtools/1.3.2
[fi1d18@cyan01 ~]$ $PATH 
-bash: /local/software/samtools/1.3.2/bin:/local/software/bedops/2.4.26/bin:/local/software/bedtools/2.21.0/bin:/local/software/Rstudio/0.98.495/r321/bin:/local/software/boost/1.54.0/bin:/local/software/openmpi/1.6.4/gcc-ofed-2.0/bin:/local/software/python/2.7.5/bin/:/local/software/qt/4.8.5/bin:/local/software/libcurl/7.47.1/bin/:/local/software/R/3.6.1/bin:/local/software/gcc/8.2.0/bin:/local/software/jdk/jdk1.8.0_51/bin:/usr/lib64/qt-3.3/bin:/local/software/moab/default/sbin:/local/software/moab/default/bin:/local/software/torque/default/sbin:/local/software/torque/default/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lpp/mmfs/bin:/home/fi1d18/bin:/local/bin:.: No such file or directory
[fi1d18@cyan01 ~]$