Disclaimer! I feel like must put one in here. I am by no means an expert in anything that has to do with computational biology. I have found through my 2.5 years of teaching myself and getting advice, that more and more microbiologist are getting DNA sequencing datasets and have no idea how to analyze them. I am just going to be blogging handing out free tips and offer advice to pitfalls I fell into when I first started dipping my feet in the computational world.
I have been helping a fellow graduate student (microbial ecologist) with trying to run this program called pplacer. She, like me, has a strong background in microbiology and zero background in running anything from a terminal. After she spent about a week trying to get the program to run, she visited me. I sat there and listened to her problem and remembered something I learned in a computational phylogenetics course. The professor of that course told me about running executables and having to change the permissions. I dug through my notes (yes, I keep notes on everything that I do with a computer) and viola found the command:
chmod ugo+x scriptyouwanttorun
This will literally save you a lot of time! Just be sure to check that