Initial outline of installation

jeromekelleher · jeromekelleher · commit e6d12435a77f · 2025-11-20T14:04:23.000Z
diff --git a/docs/alignments_analysis.md b/docs/alignments_analysis.md
@@ -1 +1,2 @@
+(sec_alignments_analysis)=
 # Alignments analysis
diff --git a/docs/arg_analysis.md b/docs/arg_analysis.md
@@ -1 +1,2 @@
+(sec_arg_analysis)=
 # ARG analysis
diff --git a/docs/inference.md b/docs/inference.md
@@ -1,2 +1,4 @@
+(sec_inference)=
+
 # Inference
 
diff --git a/docs/installation.md b/docs/installation.md
@@ -1,3 +1,4 @@
+(sec_installation)=
 # Installation
 
 
@@ -8,4 +9,15 @@ python -m pip install sc2ts
 ```
 
 This installs the minimal version of sc2ts which provides the Python interfaces to
-analyse a
+perform
+{ref}`sec_arg_analysis`
+and
+{ref}`sec_alignments_analysis`.
+
+To perform {ref}`sec_inference` we require some additional dependencies which are
+installed as follows:
+
+```sh
+python -m pip install 'sc2ts[inference]'
+```
+
