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Samtools path

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!

cnvs ngs sequencing samtools
• 1,766 views • link
updated by GenoMax GenoMax • written by ICfc97 • ICfc97

Can you paste the output of which samtools command??

• 0 views • link
written by Nitin Narwade Nitin Narwade

Yes, the output is:

/usr/local/bin/samtools
• 0 views • link
written by ICfc97 • ICfc97

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

• 0 views • link
written by Laura • Laura

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.

• 0 views • link
written by GenoMax GenoMax

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