Merge pull request #1340 from ComparativeGenomicsToolkit/toil-5.3

prep release v2.8.1

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-v2.8.0.tar.gz
-cd cactus-bin-v2.8.0
+tar -xzf cactus-bin-v2.8.1.tar.gz
+cd cactus-bin-v2.8.1
 ```
 
 ## 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-v2.8.0
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.8.0/bin/activate
-source venv-cactus-v2.8.0/bin/activate
+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
 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 2.8.1 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. 
+
+- Do not apply RED masker to contigs that are likely to crash it (tiny contigs and extremely low information contigs)
+- Add `--coverage` option to `cactus-hal2maf` to include table of coverage statistics in the output
+- Fix bug where `:start-end` contig suffixes caused the pangenome pipeline to crash.  They are now correctly handled as subranges
+- Turn off `abPOA` seeding by default, after finding (what must be a fairly rare) case where it doesn't work.
+- Improve `cactus-hal2chains` interface
+- Add range support to `cactus-hal2maf` via `--start/--length` or `--bedRanges`
+- Deprecate `cactus-maf2bigmaf --chromSizes` (use `--halFile` instead, as it handles "."s in genome names properly)
+- Fix bug where reference row could be lost in `cactus-hal2maf` MAF due to sorting error. 
+
 # Release 2.8.0 2024-03-13
 
 This release significantly changes the preprocessor step of Progressive Cactus in order to be more robust and efficient in the presence of unmasked repeats, something that seems more prevalent with newer, T2T assemblies. 

doc/progressive.md

@@ -279,12 +279,12 @@ 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:v2.8.0 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+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
 ```
 
 Or you can proceed interactively by running
 ```
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.8.0 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.8.1 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```

setup.py

@@ -24,7 +24,7 @@ def run(self):
 
 setup(
     name = "Cactus",
-    version = "2.8.0",
+    version = "2.8.1",
     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 'v2.8.0' + ('-gpu' if gpu else '')
+        return 'v2.8.1' + ('-gpu' if gpu else '')
 
 def getDockerImage(gpu=False):
     """Get fully specified Docker image name."""