diff --git a/BIN-INSTALL.md b/BIN-INSTALL.md index f9dee85bc..869e821e7 100644 --- a/BIN-INSTALL.md +++ b/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-v2.8.3.tar.gz -cd cactus-bin-v2.8.3 +tar -xzf cactus-bin-v2.8.4.tar.gz +cd cactus-bin-v2.8.4 ``` ## 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-v2.8.3 -printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.8.3/bin/activate -source venv-cactus-v2.8.3/bin/activate +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 python3 -m pip install -U setuptools pip wheel python3 -m pip install -U . python3 -m pip install -U -r ./toil-requirement.txt diff --git a/ReleaseNotes.md b/ReleaseNotes.md index c4a2ec43d..1907db7c2 100644 --- a/ReleaseNotes.md +++ b/ReleaseNotes.md @@ -1,3 +1,10 @@ +# 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. + +- `vcfbub` updated to `v0.1.1` which resolves a bub where records could be missing columns in the presence of `.` genotypes +- run `bcftools view` as sanity check on generated VCFs to prevent various normalization steps from ever silently producing invalid output. + # Release-2.8.3 2024-06-12 This release fixes some bugs and updates to the latest Toil. diff --git a/doc/progressive.md b/doc/progressive.md index bc7949373..4d32cd49f 100644 --- a/doc/progressive.md +++ b/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:v2.8.3 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal +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 ``` Or you can proceed interactively by running ``` -docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.8.3 bash +docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.8.4 bash cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal ``` diff --git a/setup.py b/setup.py index 1b5a01769..e35da5645 100644 --- a/setup.py +++ b/setup.py @@ -24,7 +24,7 @@ def run(self): setup( name = "Cactus", - version = "2.8.3", + version = "2.8.4", author = "Benedict Paten", package_dir = {'': 'src'}, packages = find_packages(where='src'), diff --git a/src/cactus/shared/common.py b/src/cactus/shared/common.py index 92b6d790d..54d77c041 100644 --- a/src/cactus/shared/common.py +++ b/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 'v2.8.3' + ('-gpu' if gpu else '') + return 'v2.8.4' + ('-gpu' if gpu else '') def getDockerImage(gpu=False): """Get fully specified Docker image name."""