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 am comfortable with using Unix but yet I feel the most challenging part to me to to get these new softwares installed and running correctly maybe due to my lack of solid knowledge of computer science.

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.