Off topic:Setting paths for programs in a Json file when you have installed everything with Conda.

Question

[new15b]

Hi! We are currently trying to navigate how to analyze Cut and Run data and are attempting to follow the pipeline protocol for the bioinformatical analysis available. This involves the manipulation of a Json file, which requires paths for all of the programs the pipeline needs to run. Unfortunately, we have installed everything with Conda, because we do not have admin access to our server and cannot do sudo installs. How would we direct this pipeline properly? This is what it looks like in the Json form:

"Rscriptbin": "/n/app/R/3.3.3/bin", 
"pythonbin": "/n/app/python/2.7.12/bin", 
"perlbin": "/n/app/perl/5.24.0/bin",
"javabin": "/n/app/java/jdk-1.8u112/bin",
"trimmomaticbin": "/n/app/trimmomatic/0.36/bin", 
"trimmomaticjarfile": "trimmomatic-0.36.jar",

Etc. etc. etc.

How do you tell it to look for Conda programs? We would appreciate help.

Thanks!