Hello everyone! I'm new to bioinformatics, and I'm having a really hard time trying to make this work. What I'm trying to set up is this https://github.com/NYU-BFX/lncRNA-screen
So I'm working with Long non-coding RNAs, and this pipeline created by Applied Bioinformatics Laboratories (New York, NY), does exactly what I need. However, I'm finding quite hard to set it up, could anyone help me?
*It says it uses SGE which I only got it to work with docker, is SGE really necessary? I only have 1 machine.
*Needs to install and set to path r/3.3.0, python/2.7.3, java/1.8 and samtools/1.3
*It has a linked folder for my RNA-seq and Chip-seq but I don't know how that works.
*Also says I need https://github.com/NYU-BFX/RNA-Seq_Standard even if I have my own RNA-seq (which I do have).
*The documentation says sratoolkit is included, but, my lack of experience makes me not understand how that works. *Here's a requirement file https://github.com/NYU-BFX/lncRNA-screen/blob/master/inputs/system_requirement.txt
This is my first post here, so I may do something wrong or post this question in the wrong place.