Greeting oh great and powerful collective hive mind,
The analysis I want to perform is very similar to the viral-ngs pipeline created at Broad for the ebola analysis (Park et al., 2015, Cell 161, 1516-1526, June 18) however I'm not working with ebola or illumina data so I would like to tweak the pipeline for what I am doing.
I'm working on building a pipeline for my viral-ngs analysis and I'm wanting to use snakemake. I'm working through the tutorial and the slides but I have a few question because I'm not a programer by training I'm having some trouble understanding some things.
It seems like snakemake works like or is a virtual python environment and I'm not sure how to get the programs I want to use into the virtual environment. I'm reading the docs on Python packaging for virtual environments and it says to use pip inside the virtual environment so would I use pip inside my snakemake environment?
I know that to create a new workflow it is,
conda -n myworkflow
I feel okay with the making a config file and a Snakefile, I'm just not sure how to set my workflow up to have all the programs and dependencies I need/want in order to run the pipeline.