Update install.rst

[RyloByte]

Made edits to this file to correct errors and add some content.
Here are some other suggestions about this doc:

1. A few sections from the documentation is missing: Fast, Taxonomic Reference, and Description of the Parameter file setting
2. A small section after the run command for MetaPathways describing the output directories and files and what to expect after run could help new users.
3. A line or two regarding setting right paths for all input and output directories.
4. At the beginning of the documentation a few lines indicating system requirements (RAM, dependencies, python version, storage space etc) would be good for new users.
5. Suggestion: Documentation can include both ways to run the pipeline- using the Virtual environment (for root users in case of individuals using personal computers) and conda environment ( for users working on servers and for those without root permissions)