From 116c9bdad282be48f4468e3be3b9b36cced99539 Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Wed, 28 Jun 2023 14:43:42 -0400
Subject: [PATCH] prep release 2.6.2

---
 ReleaseNotes.md             | 8 ++++++++
 doc/progressive.md          | 6 +++---
 setup.py                    | 2 +-
 src/cactus/shared/common.py | 2 +-
 4 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/ReleaseNotes.md b/ReleaseNotes.md
index 85d157cd1..a30c88e6f 100644
--- a/ReleaseNotes.md
+++ b/ReleaseNotes.md
@@ -1,3 +1,11 @@
+# Release 2.6.2 2023-06-28
+
+This release patches a few bugs introduced or found in v2.6.1
+
+- Docker container fixed to include runtime libatomic dependency for odgi
+- `--refContigs` option fixed in `cactus-graphmap-split`
+- `cactus-pangenome` fixed to properly output intermediate GAF and unfiltered PAF alignment files
+
 # Release 2.6.1 2023-06-27
 
 This Release adds SLURM cluster support for Cactus (both progressive and pangenome). It also adds some new visualization features to the pangenome pipeline, along with several bugfixes.
diff --git a/doc/progressive.md b/doc/progressive.md
index f78dab8b2..0add344f7 100644
--- a/doc/progressive.md
+++ b/doc/progressive.md
@@ -169,12 +169,12 @@ Conservation scores can be computed using [phast](http://compgen.cshl.edu/phast/
 The Cactus Docker image contains everything you need to run Cactus (python environment, all binaries, system dependencies). For example, to run the test data:
 
 ```
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.1 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.2 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:v2.6.1 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.2 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```
@@ -210,7 +210,7 @@ You cannot run `cactus --batchSystem slurm` from *inside* the Cactus docker cont
 To run Progressive Cactus with CPU (default) lastz, you should increase the chunk size.  This will divide the input assemblies into fewer pieces, resulting in fewer jobs on the cluster.
 
 ```
-cp cactus-bin-v2.6.1/src/cactus/cactus_progressive_config.xml ./config-slurm.xml
+cp cactus-bin-v2.6.2/src/cactus/cactus_progressive_config.xml ./config-slurm.xml
 sed -i config-slurm.xml -e 's/blast chunkSize="30000000"/blast chunkSize="90000000"/g'
 sed -i config-slurm.xml -e 's/dechunkBatchSize="1000"/dechunkBatchSize="200"/g'
 ```
diff --git a/setup.py b/setup.py
index 234aeb6f7..0058426c5 100644
--- a/setup.py
+++ b/setup.py
@@ -24,7 +24,7 @@ def run(self):
 
 setup(
     name = "Cactus",
-    version = "2.6.1",
+    version = "2.6.2",
     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 4110c4c0a..b23209e4c 100644
--- a/src/cactus/shared/common.py
+++ b/src/cactus/shared/common.py
@@ -305,7 +305,7 @@ def getDockerImage():
 
 def getDockerRelease(gpu=False):
     """Get the most recent docker release."""
-    r = "quay.io/comparative-genomics-toolkit/cactus:v2.6.1"
+    r = "quay.io/comparative-genomics-toolkit/cactus:v2.6.2"
     if gpu:
         r += "-gpu"
     return r