Update README.md with reqs and recs

README.md

@@ -8,6 +8,35 @@ A database of completed assemblies for metagenomics-related tasks
 Kalamari is a database of completed and public assemblies, backed by trusted institutions.
 These assemblies can be further used in formatted databases such as Kraken or Blast.
 
+### Prerequisites & Recommendations
+
+Requirements:
+- clone this repo locally `git clone https://github.com/lskatz/Kalamari.git`
+- NCBI entrez-utilities set of tools `edirect`, `esearch`, etc.
+  - install via your package manager
+  - debian/ubuntu: `apt install ncbi-entrez-direct` 
+
+Optional, but recommended:
+- `NCBI_API_KEY` environmental variable
+- `EMAIL` environmental variable
+
+Ensure that you have the [NCBI API key](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities).
+This key associates your edirect requests with your username.
+Without it, edirect requests might be buggy.
+After obtaining an NCBI API key, add it to your environment with
+
+    export NCBI_API_KEY=unique_api_key_goes_here
+
+where `unique_api_key_goes_here` is a unique hexadecimal number with characters from 0-9 and a-f.
+
+You should also set your email address in the 
+`EMAIL` environment variable as edirect tries to guess it, which is an error prone process.
+Add this variable to your environment with
+
+    export [email protected]
+
+using your own email address instead of `[email protected]`.
+
 ## Download instructions
 
 For usage, run `perl bin/downloadKalamari.pl --help`