Samtools path

Question

[ICfc97]

Hi!

I'm trying to use RDXplorer so as to detect CNVs in genome data but I'm having some problems setting the Samtools path in the shell script called globals.py.

#!/usr/bin/env python

###########################################
# EDIT PATHS ACCORDING THE LOCAL PATHS
# BEFORE RUNNING FIRST TIME
###########################################

SAMTOOLS_PATH="/usr/local/bin/samtools"
APP_HOME='/home/alumno04/TFM/rdxplorer'    

When I run the script the program says:

Samtools is essential. Please install it and/or configure globals.py
Doing this took 0 seconds 
DONE.

Can anybody tell me how to set SAMTOOLS_PATH to make it work? Thanks!

[Nitin Narwade]

Can you paste the output of which samtools command??

[ICfc97]

Yes, the output is:

/usr/local/bin/samtools

[Laura]

I am having this same issue, please could you advise how you resolved it? could it be a permissions restriction?

[GenoMax]

You can do export PATH=$PATH:/path_to_samtools_binary to fix this in general for bash shell.

If you are having the "same problem" as in original post the use the following setting

SAMTOOLS_PATH="/usr/local/bin/"

if the samtools binary is in that directory.