Clarify instructions

Author: prehensilecode

README.md

@@ -4,10 +4,11 @@ Singularity recipe for AlphaFold, with example Slurm job script.
 This splits off my pull request https://github.com/deepmind/alphafold/pull/166
 
 ## Installation Instructions
-Check out this repo into the top of the alphafold source tree:
+Check out this repo into the top of the alphafold source tree to a directory called `singularity`:
 ```
 $ cd alphafold-v2.x.x
-$ git clone https://github.com/prehensilecode/alphafold_singularity
+$ git clone https://github.com/prehensilecode/alphafold_singularity singularity
+
 ```
 
 To use, first install the Python requirements:
@@ -22,3 +23,9 @@ sudo singularity build alphafold.sif alphafold_singularity/Singularity.def
 
 If your `/tmp` directory is small, you may need to set the [`SINGULARITY_TMPDIR`
 environment variable](https://sylabs.io/guides/3.3/user-guide/build_env.html#temporary-folders) to a directory on a filesystem with more free space.
+
+To run, modify the `$ALPHAFOLD_SRC/singularity/run_singularity.py` and change the 
+section marked `USER CONFIGURATION`. At the least, you will need to modify the values
+of:
+- `DOWNLOAD_DIR` - location where AlphaFold databases are downloaded
+- `singularity_image` - absolute path to the `alphafold.sif` Singularity image