Entering edit mode
3.8 years ago
zizigolu
★
4.3k
Hi
I am trying to used bedr package which need bedtools, tabix, bedops,
I have load these modules from our cluster but likely R can not locate them
How I need tell R where these tools are?
This is my 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
Can you clarify if you use bedR on the cluster or on your macbook?
@Friederike I have insulated bedR locally
bedtools
installed on your local Mac has no connection to being able to use the program on your cluster. Should you not investigate why the programs don't work on cluster even whenmodules
for those are added?Sorry @genomax I meant bedtools loaded from cluster and not installed on my Mac
I assume you are also loading
R
via a module? If all modules are loaded at the same time thenbedtools
should be in your$PATH
(check by usingecho $PATH
). If you are runningR
in its own shell then you will need to add modules in that shell or edit your code to provide full path to thebedtools
executables.Yes R also comes by a module
Then loading all required module simultaneously should make sure that
bedtools
is available in$PATH
. Did you check the contents of$PATH
after adding all modules?Somtimes modules may be setup to remove a specific pre-loaded module if they conflict each other. So check after you load all modules that they are still loaded by doing a
module list
.Thank you @genomax
This is what I observed
Thank you @genomax finally worked by removing one R versions from loaded modules