prep release 3.3.0

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-v3.2.1.tar.gz
-cd cactus-bin-v3.2.1
+tar -xzf cactus-bin-v3.3.0.tar.gz
+cd cactus-bin-v3.3.0
 ```
 
 ## 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-v3.2.1
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\nexport LD_LIBRARY_PATH=$(pwd)/lib:\$LD_LIBRARY_PATH\n" >> venv-cactus-v3.2.1/bin/activate
-source venv-cactus-v3.2.1/bin/activate
+virtualenv -p python3 venv-cactus-v3.3.0
+printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\nexport LD_LIBRARY_PATH=$(pwd)/lib:\$LD_LIBRARY_PATH\n" >> venv-cactus-v3.3.0/bin/activate
+source venv-cactus-v3.3.0/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 +1,27 @@
+# Release 3.3.0 2026-08-10
+
+This release a few general patches and  new pangenome functionality such as graph reference (gref), panacus and panpatch support.
+
+- Fix `--mgSplit` bug that could cause entire contigs to get erroneously filtered when single `--reference` provided.
+- Genome passed to `--includeRoot` treated as outgroup and not ingroup
+- `cactus-hal2seqfile` tool added to help with custom alignment updates
+- `cactus-phast` faster on fragmented genomes
+- Update to newer `FastGA`
+- `cactus-panpatch` tool added to do assembly patching with pangenome alignments of different assemblies of the same sample.
+- Increasing `--vcfwaveCores` now actually speeds up `vcfwave` (nearly linearly).
+- Update Toil to `v9.5.0`
+- `cactus-pangenome` now produces cleaner, more useful stats.  Including reports and bed files of everything that was clipped and where.
+- `maxMemory` automatically inferred on Slurm
+- `cactus-hal2maf` `single-ref` output type added to get single-copy reference for each block but multicopy everything else.
+- `--panacus` option added to `cactus-pangenome` to automatically generate a panacus report.
+- `--gref` option cleaned up and improved in terms of the computed cover and the output VCFs (still experimental).
+- `--vcfL` option added to cluster similar VCF alleles (experimental).
+- Update to new vg (a bit past v1.76.1)
+- Fix `--mgSplit` bug where reference contigs in chrOther could align together sometimes.
+- `hal2vg` now takes about 30% less memory
+- `--vcfReference` can select any genome, not just reference.
+- Long pause at the end of minigraph construct fixed, it was due to Python being very slow at zipping the file.
+
 # Release 3.2.1 2026-05-20
 
 This release patches a critical regression from 3.2.0 that broke gpu support in docker

doc/progressive.md

@@ -383,12 +383,12 @@ 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:v3.2.1 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:v3.3.0 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:v3.2.1 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v3.3.0 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```
@@ -605,7 +605,7 @@ 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:v3.2.1 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:v3.3.0 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 = "3.2.1",
+    version = "3.3.0",
     author = "Benedict Paten",
     package_dir = {'': 'src'},
     packages = find_packages(where='src'),

src/cactus/shared/common.py

@@ -404,7 +404,7 @@ def getDockerTag(gpu=False):
         return "latest"    
     else:
         # must be manually kept current with each release        
-        return 'v3.2.1' + ('-gpu' if gpu else '')
+        return 'v3.3.0' + ('-gpu' if gpu else '')
 
 def getDockerImage(gpu=False):
     """Get fully specified Docker image name."""