Merge pull request #1134 from ComparativeGenomicsToolkit/oneshot

prep release 2.6.7

BIN-INSTALL.md

@@ -4,19 +4,19 @@ This describes the steps require to install the Cactus
 pre-compile binary, static linked distribution.
 
 ## Extracting
-If you have not already extract the distribution:
+If you have not already extract the distribution and cd into the cactus directory:
 ```
-tar -xzf "cactus-bin-${REL_TAG}.tar.gz"
-cd "cactus-bin-${REL_TAG}"
+tar -xzf cactus-bin-v2.6.7.tar.gz
+cd cactus-bin-v2.6.7
 ```
 
 ## 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-v2.6.6
-printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.6/bin/activate
-source venv-cactus-v2.6.6/bin/activate
+virtualenv -p python3 venv-cactus-v2.6.7
+printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.7/bin/activate
+source venv-cactus-v2.6.7/bin/activate
 python3 -m pip install -U setuptools pip
 python3 -m pip install -U .
 python3 -m pip install -U -r ./toil-requirement.txt

ReleaseNotes.md

@@ -1,3 +1,12 @@
+# Release 2.6.7 2023-08-16
+
+This release includes a patched vg and gfaffix
+
+- Update to `vg` version `1.50.1` which patches the path name incompatibility bug in `1.50.0`
+- Revert minigraph-cactus Reference path name convention introduced in v2.6.6 (ie haplotypes can be left unspecified)
+- Upgrade to GFAffix 0.1.5 which fixes a crash among other things (thanks @danydoerr!)
+- Fix bug where large input contig sizes (>2Gb) would break the pangenome pipeline with some versions of `awk`. 
+
 # Release 2.6.6 2023-08-03
 
 This release fixes a compatibility problem between Cactus and the newly released `vg` version `1.50.0`.

doc/progressive.md

@@ -169,12 +169,12 @@ Conservation scores can be computed using [phast](http://compgen.cshl.edu/phast/
 The Cactus Docker image contains everything you need to run Cactus (python environment, all binaries, system dependencies). For example, to run the test data:
 
 ```
-docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.6 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.7 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:v2.6.6 bash
+docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.7 bash
 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal
 
 ```
@@ -210,7 +210,7 @@ You cannot run `cactus --batchSystem slurm` from *inside* the Cactus docker cont
 To run Progressive Cactus with CPU (default) lastz, you should increase the chunk size.  This will divide the input assemblies into fewer pieces, resulting in fewer jobs on the cluster.
 
 ```
-cp cactus-bin-v2.6.6/src/cactus/cactus_progressive_config.xml ./config-slurm.xml
+cp cactus-bin-v2.6.7/src/cactus/cactus_progressive_config.xml ./config-slurm.xml
 sed -i config-slurm.xml -e 's/blast chunkSize="30000000"/blast chunkSize="90000000"/g'
 sed -i config-slurm.xml -e 's/dechunkBatchSize="1000"/dechunkBatchSize="200"/g'
 ```

setup.py

@@ -24,7 +24,7 @@ def run(self):
 
 setup(
     name = "Cactus",
-    version = "2.6.6",
+    version = "2.6.7",
     author = "Benedict Paten",
     package_dir = {'': 'src'},
     packages = find_packages(where='src'),

src/cactus/shared/common.py

@@ -305,7 +305,7 @@ def getDockerImage():
 
 def getDockerRelease(gpu=False):
     """Get the most recent docker release."""
-    r = "quay.io/comparative-genomics-toolkit/cactus:v2.6.6"
+    r = "quay.io/comparative-genomics-toolkit/cactus:v2.6.7"
     if gpu:
         r += "-gpu"
     return r