Merge pull request #1844 from ComparativeGenomicsToolkit/docker-fixes

prep release 3.1.0

Author: glennhickey

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-v3.0.1.tar.gz
-cd cactus-bin-v3.0.1
+tar -xzf cactus-bin-v3.1.0.tar.gz
+cd cactus-bin-v3.1.0
 ```
 
 ## Setup
 
 To build a python virtualenv and activate, do the following steps. This requires Python version >= 3.9 (so Ubuntu 18.04 users should use `-p python3.9` below):
 ```
-virtualenv -p python3 venv-cactus-v3.0.1
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\nexport LD_LIBRARY_PATH=$(pwd)/lib:\$LD_LIBRARY_PATH\n" >> venv-cactus-v3.0.1/bin/activate
-source venv-cactus-v3.0.1/bin/activate
+virtualenv -p python3 venv-cactus-v3.1.0
+printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\nexport LD_LIBRARY_PATH=$(pwd)/lib:\$LD_LIBRARY_PATH\n" >> venv-cactus-v3.1.0/bin/activate
+source venv-cactus-v3.1.0/bin/activate
 python3 -m pip install -U setuptools pip wheel
 python3 -m pip install -U .
 python3 -m pip install -U -r ./toil-requirement.txt

ReleaseNotes.md

@@ -1,3 +1,22 @@
+# Release 3.1.0 2025-11-27
+
+This release contains several changes to address sensitivity problems with Progressive Cactus.
+
+- Fix bug where `docker run --user $(id -u):$(id -g)` did not work with the cactus release docker images
+- `cactus-update-prepare` regressions fixed (thanks @gwct)
+- Update `vcfwave` to bring in important patch that fixes a genotype-dropping issue
+- Update to vg 1.70.0.  Note that `giraffe` indexes from this vg won't be compatible with older versions
+- Use reference paths to guide snarl-tree construction (this could lead to better VCFs in very complex graphs)
+- Don't bother writing VCF variants with `AC=0`, which can arise in some weird cases.
+- Add `--lrGiraffe` option to produce long-read giraffe indexes
+- Use `jemalloc`, which significantly improves performance when `--consCores` is anything higher than about 20
+- Use nested parallelism in BAR stage (together with jemalloc, I've been getting more than a 2X speedup in `cactus_consolidated`)
+- Add `--maskMode` option that can toggle between `RED` and `FasTAN` for masking in the preprocessor.
+- Update to the latest versions of `KegAlign` and `FastGA`
+- More aggressive `lastz` default parameters.  Also reduce branch length thresholds at which more sensitive parameters kick in.
+- Option to re-mask fully-masked contigs with the preprocessor (`--remask`)
+- 
+
 # Release 3.0.1 2025-10-15
 
 This release patches some bugs in new functionality

doc/progressive.md

@@ -289,12 +289,12 @@ 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 --user $(id -u):$(id -g) -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v3.0.1 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+docker run --user $(id -u):$(id -g) -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v3.1.0 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:v3.0.1 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v3.1.0 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```
@@ -511,7 +511,7 @@ cp <CACTUS-INSTALLATION-DIR>/src/cactus_progressive_config.xml ./config.xml
 If you are running cactus directly from `docker run`, then do (making sure to use the same docker image that you will use to run cactus):
 
 ```
-docker run --user $(id -u):$(id -g) -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v3.0.1 cp /home/cactus/cactus_env/lib/python3.10/site-packages/cactus/cactus_progressive_config.xml /data/config.xml
+docker run --user $(id -u):$(id -g) -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v3.1.0 cp /home/cactus/cactus_env/lib/python3.10/site-packages/cactus/cactus_progressive_config.xml /data/config.xml
 ```
 
 You can then edit `config.xml` and use it to override cactus's defaults by adding `--configFile config.xml` to any cactus command.  If you are using `docker run -v $(pwd):/data` then you would add `--configFile /data/config.xml` to your command instead. 

setup.py

@@ -16,7 +16,7 @@
 
 setup(
     name = "Cactus",
-    version = "3.0.1",
+    version = "3.1.0",
     author = "Benedict Paten",
     package_dir = {'': 'src'},
     packages = find_packages(where='src'),

src/cactus/shared/common.py

@@ -320,7 +320,7 @@ def getDockerTag(gpu=False):
         return "latest"    
     else:
         # must be manually kept current with each release        
-        return 'v3.0.1' + ('-gpu' if gpu else '')
+        return 'v3.1.0' + ('-gpu' if gpu else '')
 
 def getDockerImage(gpu=False):
     """Get fully specified Docker image name."""