Reed-CompBio · agitter · Oct 21, 2025 · Oct 14, 2025 · Oct 14, 2025 · Oct 14, 2025
diff --git a/docs/_static/config/beginner.yaml b/docs/_static/config/beginner.yaml
@@ -26,8 +26,9 @@ algorithms:
       include: true
       run1:
         k: 1
-        # run2: # uncomment for step 3.2
-        #   k: [10, 100] # uncomment for step 3.2
+
+      # run2: # uncomment for step 3.2
+      #   k: [10, 100] # uncomment for step 3.2
 
 # Here we specify which pathways to run and other file location information.
 # Assume that if a dataset label does not change, the lists of associated input files do not change
@@ -45,7 +46,7 @@ reconstruction_settings:
 
   # Set where everything is saved
   locations:
-    reconstruction_dir: "output/basic"
+    reconstruction_dir: "output/beginner"
 
 analysis:
   # Create one summary per pathway file and a single summary table for all pathways for each dataset

diff --git a/docs/_static/images/egf-interactome.png b/docs/_static/images/egf-interactome.png
diff --git a/docs/_static/images/egf-pathway.png b/docs/_static/images/egf-pathway.png
diff --git a/docs/tutorial/beginner.rst b/docs/tutorial/beginner.rst
diff --git a/docs/tutorial/docker_troubleshooting.rst b/docs/tutorial/docker_troubleshooting.rst
@@ -0,0 +1 @@
+TODO: add in the errors that people could possibly run into
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		TODO: add in the errors that people could possibly run into