Document alphafold outputs.py

tools/alphafold/README.md

@@ -25,7 +25,13 @@ When you `planemo test` the wrapper should use the mock AlphaFold run, which cop
 
 ## Generating additional outputs
 
-The `./scripts/outputs.py` script is used to generate additional outputs from an AF2 run. This script is complex because it must handle all different output variations (monomer, multimer, N models, etc.). The test script `tests/test_outputs.sh` runs a basic end-to-end test with the sample outputs available in `test-data`. Each of these directories is a complete output directory for an AF2 run, for each of the three model presets:
+To run the outputs.py file you will need to install some dependencies (a virtual environment is highly recommended):
+
+```sh
+pip install -r scripts/requirements.txt
+```
+
+The `./scripts/outputs.py` script is used to generate additional outputs from an AF2 run. This script is complex because it must handle all different output variations (monomer, multimer, N models, etc.). The test script `tests/test_outputs.sh` runs a basic end-to-end test with the sample outputs available in `test-data/`. Each of these directories is a complete output directory for an AF2 run, for each of the three model presets:
 
 ```
 test-data

tools/alphafold/scripts/requirements.txt

@@ -0,0 +1,20 @@
+# tested on python3.8 + 3.10
+
+absl-py==1.0.0
+biopython==1.79
+chex==0.0.7
+dm-haiku==0.0.9
+dm-tree==0.1.6
+docker==5.0.0
+immutabledict==2.0.0
+jax==0.3.25
+ml-collections==0.1.0
+numpy==1.21.6
+pandas==1.3.4
+scipy==1.7.2
+tensorflow-cpu==2.11.0
+matplotlib==3.8.*
+
+-f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+jax==0.3.25
+jaxlib==0.3.25+cuda11.cudnn805