Merge pull request #1452 from ComparativeGenomicsToolkit/docker-fixes

prep release 2.9.0

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-v2.8.4.tar.gz
-cd cactus-bin-v2.8.4
+tar -xzf cactus-bin-v2.9.0.tar.gz
+cd cactus-bin-v2.9.0
 ```
 
 ## 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-v2.8.4
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.8.4/bin/activate
-source venv-cactus-v2.8.4/bin/activate
+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
 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 +1,12 @@
+# Release-2.9.0 2024-07-29
+
+This release addresses two important scaling issues in the pangenome pipeline.
+
+- The haplotype sampling index (`--haplo`) can now be built without giraffe indexes (`--giraffe`).  This significantly reduces peak memory consumption when using `--haplo`, especially for big diverse pangenomes.
+- Previously, you could not align more than roughly 500 samples with Minigraph-Cactus, no matter how small the input genomes were. This bottleneck has been removed: you can now align as many genomes as your system resources allow. For very small genomes, this could be well into the tens of thousands.
+- Two bugs were recently found in `vcfwave`, which can be run with the `--vcfwave` option since v2.8.2. First the `AT` field is wrong in the output. Second, and more seriously, genotypes can be incorrect. The latter seems specific to multiallelic sites (but I'm not sure).  This release now strips `AT` fields (they are not relevant after re-alignment anyway). It also splits multiallelic sites before running `vcfwave` in an attempt to work around the genotyping bug.  
+
+
 # Release-2.8.4 2024-06-21
 
 This release updates `vcfbub` in order to fix a longstanding issue where this tool can produce invalid VCFs. 

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:v2.8.4 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+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
 ```
 
 Or you can proceed interactively by running
 ```
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.8.4 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.9.0 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```

setup.py

@@ -24,7 +24,7 @@ def run(self):
 
 setup(
     name = "Cactus",
-    version = "2.8.4",
+    version = "2.9.0",
     author = "Benedict Paten",
     package_dir = {'': 'src'},
     packages = find_packages(where='src'),

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 'v2.8.4' + ('-gpu' if gpu else '')
+        return 'v2.9.0' + ('-gpu' if gpu else '')
 
 def getDockerImage(gpu=False):
     """Get fully specified Docker image name."""