Merge pull request #1215 from ComparativeGenomicsToolkit/docker-fixes

prep release v2.6.11
ComparativeGenomicsToolkit · Oct 31, 2023 · fb04f4f · fb04f4f
2 parents ad6dfb7 + 71add96
commit fb04f4f
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diff --git 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-v2.6.10.tar.gz
-cd cactus-bin-v2.6.10
+tar -xzf cactus-bin-v2.6.11.tar.gz
+cd cactus-bin-v2.6.11
 ```
 
 ## 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-v2.6.10
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.10/bin/activate
-source venv-cactus-v2.6.10/bin/activate
+virtualenv -p python3 venv-cactus-v2.6.11
+printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.11/bin/activate
+source venv-cactus-v2.6.11/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
@@ -1,3 +1,9 @@
+# Release 2.6.11 2023-10-31
+
+This release fixes a bug introduced in v2.6.10 that prevents diploid samples from working with `cactus-pangenome`
+
+- Remove stray `assert False` from diploid mash distance that was accidentally included in previous release
+
 # Release 2.6.10 2023-10-30
 
 This release contains bug fixes for MAF export and the pangenome pipeline

diff --git a/doc/progressive.md b/doc/progressive.md
@@ -170,12 +170,12 @@ 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:v2.6.10 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.11 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:v2.6.10 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.11 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```
@@ -221,7 +221,7 @@ 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-v2.6.10/src/cactus/cactus_progressive_config.xml ./config-slurm.xml
+cp cactus-bin-v2.6.11/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
@@ -24,7 +24,7 @@ def run(self):
 
 setup(
     name = "Cactus",
-    version = "2.6.10",
+    version = "2.6.11",
     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
@@ -302,7 +302,7 @@ def getDockerTag(gpu=False):
         return "latest"    
     else:
         # must be manually kept current with each release        
-        return 'v2.6.10' + ('-gpu' if gpu else '')
+        return 'v2.6.11' + ('-gpu' if gpu else '')
 
 def getDockerImage(gpu=False):
     """Get fully specified Docker image name."""