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

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!

conda json
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updated by Biostar Biostar • written by new15b • new15b

I guess in anaconda3/envs/yourenvname/bin and anaconda3/envs/yourenvname/lib did you tried that already?

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written by gb gb

Thank you so much! I will try that as soon as I get in to the lab! I'll let you know if that works. I'm sorry these are such basic questions - most of us have no idea what we are doing (ZERO programming/computer science background) and are just winging it.

Cheers!!!

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written by new15b • new15b

I think you need to move this "answer" to a reply on my comment... I don't know how the script works and how the code looks like but I would almost assume that if you can execute python or trimmomatic in your conda envorinment the following will also work:

"Rscriptbin": "", 
"pythonbin": "", 
"perlbin": "",
"javabin": "",
"trimmomaticbin": "", 
"trimmomaticjarfile": "",
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written by gb gb

Hi new15b, I'm having the same problem. How did you resolve out? Thanks a lot!

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written by ecalabr • ecalabr

Hello new15b!

We believe that this post does not fit the main topic of this site.

OP never followed up.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

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