README: Streamline, improve.

README.md

@@ -57,7 +57,12 @@ conda env create -n aviary -f aviary.yml
 conda activate aviary
 pip install -e .
 ```
+The `aviary` executable can then be run from any directory. Since the code in
+this directory is then used for running, any updates made there will be
+immediately available. We recommend this mode for developing and debugging
+aviary.
 
+## Checking installation
 Whatever option you choose, running `aviary --help` should return the following
 output:
 
@@ -86,22 +91,6 @@ Utility modules:
 
 ```
 
-Upon first running aviary you will be prompted to input the location for where you would like
-your conda environments to be stored, the GTDB release installed on your system, the location of your
-EnrichM database, and the location of your BUSCO database. These locations will be stored as environment
-variables, but for aviary to be able to use those environment variables you will have to either source your .bashrc
-or reactivate your conda environment depending on whether you installed aviary within a conda environment or not:
-
-```
-conda deactivate; conda activate aviary
-
-OR
-
-source ~/.bashrc
-```
-
-These environment variables can be reset using `aviary configure`
-
 ## Databases
 
 Aviary uses programs which require access to locally stored databases. 
@@ -111,7 +100,7 @@ The **required** databases are as follows:
 * [GTDB](https://gtdb.ecogenomic.org/downloads)
 * [EggNog](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#setup)
 * [CheckM2](https://github.com/chklovski/CheckM2)
-
+* [SingleM](https://wwood.github.io/singlem/)
 
 ### Installing databases