From 44aeddc8b6d722a16c1c1c4bb0d985144cbd6174 Mon Sep 17 00:00:00 2001
From: kcleal <clealk@cardiff.ac.uk>
Date: Fri, 26 Jul 2024 09:33:57 +0100
Subject: [PATCH] Updated docs

---
 docs/docs/guide/Genomes.md    | 46 ++++++++++++++++++++++++++++++-----
 docs/docs/guide/User_guide.md |  2 +-
 docs/docs/tutorial.md         |  6 ++---
 3 files changed, 44 insertions(+), 10 deletions(-)

diff --git a/docs/docs/guide/Genomes.md b/docs/docs/guide/Genomes.md
index f5abdd4..8796480 100644
--- a/docs/docs/guide/Genomes.md
+++ b/docs/docs/guide/Genomes.md
@@ -7,7 +7,19 @@ nav_order: 1
 
 # Genomes
 
+GW can load online reference genomes, although it is always best to 
+use a local file.
 
+To add or update a reference genome path and tag:
+
+1. Click on the Settings menu (click on cog)
+2. Goto Genomes menu
+3. Click on the "+" button at the top
+4. Type the name of the genome-tag you want e.g. `hg19`. If it exists already it will be updated. Hit ENTER
+5. Type the path to the local file. Hit ENTER.
+6. Optionally click the save button at the top. This will ensure that the genome-tag is saved to your config file.
+
+Once you have configured the path, the genome-tag will then point to your local file.
 
 
 # Ideograms
@@ -16,20 +28,42 @@ nav_order: 1
 Many of the reference genomes come with a preset ideogram and will be loaded automatically
 when a matching genome tag is used e.g. 'hg19' or 't2t' etc.
 
-To configure GW to use an ideogram for a genome tag add this to the 'tracks'
-section of settings (or your .gw.ini file)::
+You can also load ideograms easily by typing the command:
+
+    load ideogram hg19/t2t/hg38  # Choose the appropriate genome-tag
+
+To remove the ideogram use the remove command:
+
+    remove ideogram
+
+To configure GW to use a custom ideogram for a genome-tag add this to the 'tracks'
+section of settings (or your .gw.ini file):
 
     [tracks]
     hg38_ideogram=path_to_ideogram.bed
 
-This will set the ideogram path for the 'hg38' genome tag. Once this has been saved
-in the settings menu, the ideogram will be loaded whenever the hg38 genome tag is used.
-For example, using the load command::
+This will set the ideogram path for the 'hg38' genome-tag. Once this has been saved
+in the settings menu, the ideogram will be loaded whenever the hg38 genome-tag is used.
+For example, using the load command:
 
     load genome hg38
 
 Or when using 'hg38' tag from the command line.
 
-The CLI interface also has the `--ideogram` option
+The CLI interface also has the `--ideogram` option.
+
+---
+
+Any bed file can be used as an ideogram, and adding more than one ideogram will
+stack them on top of another. Idograms can be customised with different colours by
+adding in ARGB values into the header of your bed file. For example:
+
+    #gw LTR5 255,255,0,0
+    chr1    10000   20000
+
+The `#gw` header line will configure records with LTR5 in the name column to be a
+bright red colour on the ideogram.
+
+
 
 
diff --git a/docs/docs/guide/User_guide.md b/docs/docs/guide/User_guide.md
index 6f0cfe3..dca9b01 100644
--- a/docs/docs/guide/User_guide.md
+++ b/docs/docs/guide/User_guide.md
@@ -2,7 +2,7 @@
 title: User guide
 layout: default
 has_children: true
-nav_order: 4
+nav_order: 5
 ---
 
 # User guide
diff --git a/docs/docs/tutorial.md b/docs/docs/tutorial.md
index 30c9ab5..8393e39 100644
--- a/docs/docs/tutorial.md
+++ b/docs/docs/tutorial.md
@@ -13,11 +13,11 @@ quide for MacOS, but Linux or Windows is more or less the same.
 
 Firstly, here are some links for some test data:
 
-[Test bam file](https://kcleal.github.io/gw/docs/assets/data/demo1.bam) 
+[Test bam file](/assets/data/demo1.bam) 
 
-[Test bed file](https://kcleal.github.io/gw/docs/assets/data/demo1.bed) 
+[Test bed file](/assets/data/demo1.bed) 
 
-[Test vcf file](https://kcleal.github.io/gw/docs/assets/data/demo1.vcf)
+[Test vcf file](/assets/data/demo1.vcf)
 
 ## Launch GW