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Old 09-28-2017, 07:00 PM   #1
neokao
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Location: USA

Join Date: Mar 2015
Posts: 30
Default rnacocktail basic questions

My lab typically does RNA-seq ~once a year and I do the bioinformatic analysis myself. So the annoying part for me being not the expert in routine NGS analysis from raw data, every time I get new RNA-seq raw data I almost have to redo the setup and software installation with some new (and maybe better) analysis tools developed and my working computer (MacOS) being upgraded.

I have some basic concept of using Unix but yet I feel the most challenging part
to me to to get these new softwares running correctly.

This time, I decided to try out RNACocktail based on a Nature Communications paper.

After some trial and error, I managed to get it installed on my Mac (MacOS 10.13).

"pip install rnacocktail-0.2.1.tar.gz --user
Processing ./rnacocktail-0.2.1.tar.gz
Collecting pysam (from RNACocktail-Pipeline==0.2.1)
Using cached pysam-0.12.0.1.tar.gz
Collecting pybedtools (from RNACocktail-Pipeline==0.2.1)
Using cached pybedtools-0.7.10.tar.gz
Requirement already satisfied: six in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from pybedtools->RNACocktail-Pipeline==0.2.1)
Installing collected packages: pysam, pybedtools, RNACocktail-Pipeline
Running setup.py install for pysam ... done
Running setup.py install for pybedtools ... done
Running setup.py install for RNACocktail-Pipeline ... done
Successfully installed RNACocktail-Pipeline-0.2.1 pybedtools-0.7.10 pysam-0.12.0.1"

However, after I tried this:
run_rnacocktail.py -h

I got this error message:

-bash: run_rnacocktail.py: command not found

Any suggestions? Thanks.

Last edited by neokao; 09-28-2017 at 08:10 PM.
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