diff --git a/BIN-INSTALL.md b/BIN-INSTALL.md index 474bc8c24..8f046e057 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-v2.6.10.tar.gz -cd cactus-bin-v2.6.10 +tar -xzf cactus-bin-v2.6.11.tar.gz +cd cactus-bin-v2.6.11 ``` ## 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-v2.6.10 -printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.10/bin/activate -source venv-cactus-v2.6.10/bin/activate +virtualenv -p python3 venv-cactus-v2.6.11 +printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\n" >> venv-cactus-v2.6.11/bin/activate +source venv-cactus-v2.6.11/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 bf3868665..989db2a7b 100644 --- a/ReleaseNotes.md +++ b/ReleaseNotes.md @@ -1,3 +1,9 @@ +# Release 2.6.11 2023-10-31 + +This release fixes a bug introduced in v2.6.10 that prevents diploid samples from working with `cactus-pangenome` + +- Remove stray `assert False` from diploid mash distance that was accidentally included in previous release + # Release 2.6.10 2023-10-30 This release contains bug fixes for MAF export and the pangenome pipeline diff --git a/doc/progressive.md b/doc/progressive.md index 15c99a345..75e3f4a5e 100644 --- a/doc/progressive.md +++ b/doc/progressive.md @@ -170,12 +170,12 @@ 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:v2.6.10 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal +docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.11 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:v2.6.10 bash +docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.6.11 bash cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal ``` @@ -221,7 +221,7 @@ 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-v2.6.10/src/cactus/cactus_progressive_config.xml ./config-slurm.xml +cp cactus-bin-v2.6.11/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' ``` diff --git a/setup.py b/setup.py index 45730d100..1117ff030 100644 --- a/setup.py +++ b/setup.py @@ -24,7 +24,7 @@ def run(self): setup( name = "Cactus", - version = "2.6.10", + version = "2.6.11", 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 3275ebf63..453446e71 100644 --- a/src/cactus/shared/common.py +++ b/src/cactus/shared/common.py @@ -302,7 +302,7 @@ def getDockerTag(gpu=False): return "latest" else: # must be manually kept current with each release - return 'v2.6.10' + ('-gpu' if gpu else '') + return 'v2.6.11' + ('-gpu' if gpu else '') def getDockerImage(gpu=False): """Get fully specified Docker image name."""