Merge pull request #1382 from ComparativeGenomicsToolkit/prepare

prepare release 2.8.2

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-v2.8.1.tar.gz
-cd cactus-bin-v2.8.1
+tar -xzf cactus-bin-v2.8.2.tar.gz
+cd cactus-bin-v2.8.2
 ```
 
 ## 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-v2.8.1
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.8.1/bin/activate
-source venv-cactus-v2.8.1/bin/activate
+virtualenv -p python3 venv-cactus-v2.8.2
+printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.8.2/bin/activate
+source venv-cactus-v2.8.2/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 +1,16 @@
+# Release 2.8.2 2024-05-09
+
+This release fixes some bugs and adds a (docker-only) `vcfwave` normalization option for pangenomes.
+
+- Use correct `bigChain.as` that allows chain scores to be huge (instead of capping them)
+- Update `odgi`, `vg`, `abPOA` and `taffy` to their latest releases
+- Fix `cactus-hal2maf` and `cactus-pangenome --odgi` to work with `--binariesMode docker`
+- `bcftools norm -f` now run by default on all non-raw VCF outputs (toggle off in the config)
+- Minigraph fasta file renamed from `.gfa.fa` to `.sv.gfa.fa` to be less confusing
+- Gap and empty MAF block filtering moved from `cactus-hal2maf` to `cactus-maf2bigmaf`.  So MAF output will now have a reference base for every position.
+- Fix `cactus-preprocess` to do only RED masking by default (there was previously a bug where it ran RED then lastz after).  The `--maskMode` option is also fixed to work properly.
+- Update to Toil 6.1.0
+
 # Release 2.8.1 2024-04-04
 
 This release patches some major recent bugs, including a major bug introduced in `cactus-hal2maf` in v2.7.2 that could produce negative-stranded (and out of order) reference rows. 

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:v2.8.1 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.8.2 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:v2.8.1 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.8.2 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```

setup.py

@@ -24,7 +24,7 @@ def run(self):
 
 setup(
     name = "Cactus",
-    version = "2.8.1",
+    version = "2.8.2",
     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 'v2.8.1' + ('-gpu' if gpu else '')
+        return 'v2.8.2' + ('-gpu' if gpu else '')
 
 def getDockerImage(gpu=False):
     """Get fully specified Docker image name."""