diff --git a/BIN-INSTALL.md b/BIN-INSTALL.md index 361af3e64..bc689101a 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-v2.9.2.tar.gz -cd cactus-bin-v2.9.2 +tar -xzf cactus-bin-v2.9.3.tar.gz +cd cactus-bin-v2.9.3 ``` ## 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-v2.9.2 -printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\nexport LD_LIBRARY_PATH=$(pwd)/lib:\$LD_LIBRARY_PATH\n" >> venv-cactus-v2.9.2/bin/activate -source venv-cactus-v2.9.2/bin/activate +virtualenv -p python3 venv-cactus-v2.9.3 +printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\nexport LD_LIBRARY_PATH=$(pwd)/lib:\$LD_LIBRARY_PATH\n" >> venv-cactus-v2.9.3/bin/activate +source venv-cactus-v2.9.3/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 8be0b1228..549a96eaa 100644 --- a/ReleaseNotes.md +++ b/ReleaseNotes.md @@ -1,3 +1,17 @@ +# Releaes 2.9.3 2024-11-18 + +This release adds some new options to the pangenome pipeline, and hopefully improves robustness overall + +- Faster path normalization (`vg paths -n`) for pangenomes via vg upgrade to v1.61.0 +- Sanity checks added to better detect corrupted intermediate FASTA files +- Switch off abPOA's progressive mode unless input sequences have same length (otherwise sort by length) +- `--lastTrain / --scoresFile` options added to learn and/or use custom scoring models for multiple alignment using `last-train`. +- Update to latest `vcflib`. Also add `vcflib` installation command as option to `BIN-INSTALL` instructions +- Make `--maxLen` default value consistent between `cactus-align --pangenome` and `cactus-pangenome`. Previously it was 100X bigger in the former, which made it very easy to have wildly different performance between the all-at-once and step-by-step versions of the pipeline +- Fix bug where `--binariesMode singularity` could potentially attempt to write temporary files outside specified workDir +- Tighten disk usage estimate for `tile_alignments` job +- Patch `mafTools` to fix a bug where `taffy` normalization in `cactus-hal2maf` would crash if 1-character genome names were present in the input + # Release 2.9.2 2024-10-14 This release patches a couple bugs diff --git a/doc/progressive.md b/doc/progressive.md index 64673bf11..49b7733ef 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:v2.9.2 cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal +docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.9.3 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:v2.9.2 bash +docker run -v $(pwd):/data --rm -it quay.io/comparative-genomics-toolkit/cactus:v2.9.3 bash cactus /data/jobStore /data/evolverMammals.txt /data/evolverMammals.hal ``` diff --git a/setup.py b/setup.py index 08a79c54b..877b43fa8 100644 --- a/setup.py +++ b/setup.py @@ -24,7 +24,7 @@ def run(self): setup( name = "Cactus", - version = "2.9.2", + version = "2.9.3", 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 9a23df59f..5a7101f09 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 'v2.9.2' + ('-gpu' if gpu else '') + return 'v2.9.3' + ('-gpu' if gpu else '') def getDockerImage(gpu=False): """Get fully specified Docker image name."""