From 5e324a3401a2b0d08ad58fb1db00c494e6c8b48c Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Wed, 25 Sep 2024 09:10:51 -0400
Subject: [PATCH] prep release 2.9.1

---
 BIN-INSTALL.md              | 10 +++++-----
 ReleaseNotes.md             | 10 ++++++++++
 doc/progressive.md          |  4 ++--
 setup.py                    |  2 +-
 src/cactus/shared/common.py |  2 +-
 5 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/BIN-INSTALL.md b/BIN-INSTALL.md
index 571bfb5d6..2007e6ecd 100644
--- a/BIN-INSTALL.md
+++ b/BIN-INSTALL.md
@@ -6,17 +6,17 @@ pre-compile binary, static linked distribution.
 ## Extracting
 If you have not already extract the distribution and cd into the cactus directory:
 ```
-tar -xzf cactus-bin-v2.9.0.tar.gz
-cd cactus-bin-v2.9.0
+tar -xzf cactus-bin-v2.9.1.tar.gz
+cd cactus-bin-v2.9.1
 ```
 
 ## Setup
 
 To build a python virtualenv and activate, do the following steps. This requires Python version >= 3.7 (so Ubuntu 18.04 users should use `-p python3.8` below):
 ```
-virtualenv -p python3 venv-cactus-v2.9.0
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.9.0/bin/activate
-source venv-cactus-v2.9.0/bin/activate
+virtualenv -p python3 venv-cactus-v2.9.1
+printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.9.1/bin/activate
+source venv-cactus-v2.9.1/bin/activate
 python3 -m pip install -U setuptools pip wheel
 python3 -m pip install -U .
 python3 -m pip install -U -r ./toil-requirement.txt
diff --git a/ReleaseNotes.md b/ReleaseNotes.md
index afbee9abd..282ef068a 100644
--- a/ReleaseNotes.md
+++ b/ReleaseNotes.md
@@ -1,3 +1,13 @@
+# Release 2.9.1 2024-09-25
+
+This release updates the pangenome pipeline, and adds `KegAlign` to progressive cactus. 
+
+- GPU lastz implementation changed from `SegAlign` to `KegAlign`, and should be more robust and better supported as a result. 
+- Path normalization added to pangenome pipeline to make sure no two equivalent alleles through any site have different paths. `AT` fields in VCF should now always be consistent with the graph as a result. 
+- Always chop nodes to 1024bp by default in pangenome pipeline. This ensures that all outputs (gfa, gbz, vcf etc) have compatible node ids.  Before, only GBZ and downstream graphs were chopped which was too confusing.  Old logic can be re-activated using the config XML though.  
+- Fix recent bug where using the `--mgMemory` option would crash `cactus-pangenome`
+- (Experimental) `--collapse` option added to pangenome pipeline to incorporate nearby self-alignments, including on the reference path. 
+
 # Release-2.9.0 2024-07-29
 
 This release addresses two important scaling issues in the pangenome pipeline.
diff --git a/doc/progressive.md b/doc/progressive.md
index c8b2e9327..ddfa1ce78 100644
--- a/doc/progressive.md
+++ b/doc/progressive.md
@@ -278,12 +278,12 @@ The Cactus Docker image contains everything you need to run Cactus (python envir
 
 ```
 wget -q https://raw.githubusercontent.com/ComparativeGenomicsToolkit/cactus/master/examples/evolverMammals.txt -O evolverMammals.txt
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.9.0 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.9.1 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 ```
 
 Or you can proceed interactively by running
 ```
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.9.0 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.9.1 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```
diff --git a/setup.py b/setup.py
index 360d1cc3e..24ab3f2fa 100644
--- a/setup.py
+++ b/setup.py
@@ -24,7 +24,7 @@ def run(self):
 
 setup(
     name = "Cactus",
-    version = "2.9.0",
+    version = "2.9.1",
     author = "Benedict Paten",
     package_dir = {'': 'src'},
     packages = find_packages(where='src'),
diff --git a/src/cactus/shared/common.py b/src/cactus/shared/common.py
index 4af78df69..a09412ddb 100644
--- a/src/cactus/shared/common.py
+++ b/src/cactus/shared/common.py
@@ -318,7 +318,7 @@ def getDockerTag(gpu=False):
         return "latest"    
     else:
         # must be manually kept current with each release        
-        return 'v2.9.0' + ('-gpu' if gpu else '')
+        return 'v2.9.1' + ('-gpu' if gpu else '')
 
 def getDockerImage(gpu=False):
     """Get fully specified Docker image name."""